Upload folder using huggingface_hub (part 2)

.gitattributes

@@ -52,3 +52,4 @@ model/Protenix-pxd/assets/constraint_metrics.png filter=lfs diff=lfs merge=lfs -
 model/Protenix-pxd/assets/mini_performance.png filter=lfs diff=lfs merge=lfs -text
 model/Protenix-pxd/assets/protenix_predictions.gif filter=lfs diff=lfs merge=lfs -text
 model/Protenix-pxd/assets/v0.5.0_metrics.png filter=lfs diff=lfs merge=lfs -text
+model/pxdesign/pxd_server/TimesNewRoman.ttf filter=lfs diff=lfs merge=lfs -text

model/Protenix-pxd/configs/configs_base.py

@@ -0,0 +1,398 @@
+# Copyright 2024 ByteDance and/or its affiliates.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# pylint: disable=C0114,C0301
+from protenix.config.extend_types import (
+    GlobalConfigValue,
+    ListValue,
+    RequiredValue,
+    ValueMaybeNone,
+)
+
+basic_configs = {
+    "project": RequiredValue(str),
+    "run_name": RequiredValue(str),
+    "base_dir": RequiredValue(str),
+    # training
+    "eval_interval": RequiredValue(int),
+    "log_interval": RequiredValue(int),
+    "checkpoint_interval": -1,
+    "eval_first": False,  # run evaluate() before training steps
+    "iters_to_accumulate": 1,
+    "finetune_params_with_substring": [
+        ""
+    ],  # params with substring will be finetuned with different learning rate: finetune_optim_configs["lr"]
+    "eval_only": False,
+    "load_checkpoint_path": "",
+    "load_ema_checkpoint_path": "",
+    "load_strict": True,
+    "load_params_only": True,
+    "skip_load_step": False,
+    "skip_load_optimizer": False,
+    "skip_load_scheduler": False,
+    "load_step_for_scheduler": False,
+    "train_confidence_only": False,
+    "use_wandb": True,
+    "wandb_id": "",
+    "seed": 42,
+    "deterministic": False,
+    "deterministic_seed": False,
+    "ema_decay": -1.0,
+    "eval_ema_only": False,  # whether wandb only tracking ema checkpoint metrics
+    "ema_mutable_param_keywords": [""],
+    "model_name": "protenix_base_default_v0.5.0",  # train model name
+}
+data_configs = {
+    # Data
+    "train_crop_size": 256,
+    "test_max_n_token": -1,
+    "train_lig_atom_rename": False,
+    "train_shuffle_mols": False,
+    "train_shuffle_sym_ids": False,
+    "test_lig_atom_rename": False,
+    "test_shuffle_mols": False,
+    "test_shuffle_sym_ids": False,
+    "esm": {
+        "enable": False,
+        "model_name": "esm2-3b",
+        "embedding_dim": 2560,
+    },
+}
+optim_configs = {
+    # Optim
+    "lr": 0.0018,
+    "lr_scheduler": "af3",
+    "warmup_steps": 10,
+    "max_steps": RequiredValue(int),
+    "min_lr_ratio": 0.1,
+    "decay_every_n_steps": 50000,
+    "grad_clip_norm": 10,
+    # Optim - Adam
+    "adam": {
+        "beta1": 0.9,
+        "beta2": 0.95,
+        "weight_decay": 1e-8,
+        "lr": GlobalConfigValue("lr"),
+        "use_adamw": False,
+    },
+    # Optim - LRScheduler
+    "af3_lr_scheduler": {
+        "warmup_steps": GlobalConfigValue("warmup_steps"),
+        "decay_every_n_steps": GlobalConfigValue("decay_every_n_steps"),
+        "decay_factor": 0.95,
+        "lr": GlobalConfigValue("lr"),
+    },
+}
+# Fine-tuned optimizer settings.
+# For models supporting structural constraints and ESM embeddings.
+finetune_optim_configs = {
+    # Optim
+    "lr": 0.0018,
+    "lr_scheduler": "cosine_annealing",
+    "warmup_steps": 1000,
+    "max_steps": 20000,
+    "min_lr_ratio": 0.1,
+    "decay_every_n_steps": 50000,
+}
+model_configs = {
+    # Model
+    "c_s": 384,
+    "c_z": 128,
+    "c_s_inputs": 449,  # c_s_inputs == c_token + 32 + 32 + 1
+    "c_atom": 128,
+    "c_atompair": 16,
+    "c_token": 384,
+    "n_blocks": 48,
+    "max_atoms_per_token": 24,  # DNA G max_atoms = 23
+    "no_bins": 64,
+    "sigma_data": 16.0,
+    "diffusion_batch_size": 48,
+    "diffusion_chunk_size": ValueMaybeNone(4),  # chunksize of diffusion_batch_size
+    "blocks_per_ckpt": ValueMaybeNone(
+        1
+    ),  # NOTE: Number of blocks in each activation checkpoint, if None, no checkpointing is performed.
+    # switch of kernels
+    "use_memory_efficient_kernel": False,  # whether to use the torch.nn.functional.scaled_dot_product_attention, Defaults to False.
+    "use_deepspeed_evo_attention": True,
+    "use_flash": False,
+    "use_lma": False,
+    "use_xformer": False,
+    "find_unused_parameters": False,
+    "dtype": "bf16",  # default training dtype: bf16
+    "loss_metrics_sparse_enable": True,  # the swicth for both sparse lddt metrics and sparse bond/smooth lddt loss
+    "skip_amp": {
+        "sample_diffusion": True,
+        "confidence_head": True,
+        "sample_diffusion_training": True,
+        "loss": True,
+    },
+    "infer_setting": {
+        "chunk_size": ValueMaybeNone(
+            64
+        ),  # should set to null for normal training and small dataset eval [for efficiency]
+        "sample_diffusion_chunk_size": ValueMaybeNone(
+            1
+        ),  # should set to null for normal training and small dataset eval [for efficiency]
+        "lddt_metrics_sparse_enable": GlobalConfigValue("loss_metrics_sparse_enable"),
+        "lddt_metrics_chunk_size": ValueMaybeNone(
+            1
+        ),  # only works if loss_metrics_sparse_enable, can set as default 1
+    },
+    "train_noise_sampler": {
+        "p_mean": -1.2,
+        "p_std": 1.5,
+        "sigma_data": 16.0,  # NOTE: in EDM, this is 1.0
+    },
+    "inference_noise_scheduler": {
+        "s_max": 160.0,
+        "s_min": 4e-4,
+        "rho": 7,
+        "sigma_data": 16.0,  # NOTE: in EDM, this is 1.0
+    },
+    "sample_diffusion": {
+        "gamma0": 0.8,
+        "gamma_min": 1.0,
+        "noise_scale_lambda": 1.003,
+        "step_scale_eta": 1.5,
+        "N_step": 200,
+        "N_sample": 5,
+        "N_step_mini_rollout": 20,
+        "N_sample_mini_rollout": 1,
+    },
+    "model": {
+        "N_model_seed": 1,  # for inference
+        "N_cycle": 4,
+        "condition_embedding_drop_rate": 0.0,
+        "confidence_embedding_drop_rate": 0.0,
+        "input_embedder": {
+            "c_atom": GlobalConfigValue("c_atom"),
+            "c_atompair": GlobalConfigValue("c_atompair"),
+            "c_token": GlobalConfigValue("c_token"),
+        },
+        "relative_position_encoding": {
+            "r_max": 32,
+            "s_max": 2,
+            "c_z": GlobalConfigValue("c_z"),
+        },
+        "template_embedder": {
+            "c": 64,
+            "c_z": GlobalConfigValue("c_z"),
+            "n_blocks": 0,
+            "dropout": 0.25,
+            "blocks_per_ckpt": GlobalConfigValue("blocks_per_ckpt"),
+        },
+        "msa_module": {
+            "c_m": 64,
+            "c_z": GlobalConfigValue("c_z"),
+            "c_s_inputs": GlobalConfigValue("c_s_inputs"),
+            "n_blocks": 4,
+            "msa_dropout": 0.15,
+            "pair_dropout": 0.25,
+            "blocks_per_ckpt": GlobalConfigValue("blocks_per_ckpt"),
+            "msa_chunk_size": ValueMaybeNone(2048),
+        },
+        # Optional constraint embedder, only used when constraint is enabled.
+        "constraint_embedder": {
+            "pocket_embedder": {
+                "enable": False,
+                "c_s_input": 3,
+                "c_z_input": 1,
+            },
+            "contact_embedder": {
+                "enable": False,
+                "c_z_input": 2,
+            },
+            "substructure_embedder": {
+                "enable": False,
+                "n_classes": 4,
+                "architecture": "transformer",
+                "hidden_dim": 128,
+                "n_layers": 1,
+            },
+            "contact_atom_embedder": {
+                "enable": False,
+                "c_z_input": 2,
+            },
+            "c_constraint_z": GlobalConfigValue("c_z"),
+            "c_constraint_s": GlobalConfigValue("c_s_inputs"),
+            "c_constraint_atom_pair": GlobalConfigValue("c_atompair"),
+            "initialize_method": "zero",  # zero, kaiming
+        },
+        "pairformer": {
+            "n_blocks": GlobalConfigValue("n_blocks"),
+            "c_z": GlobalConfigValue("c_z"),
+            "c_s": GlobalConfigValue("c_s"),
+            "n_heads": 16,
+            "dropout": 0.25,
+            "blocks_per_ckpt": GlobalConfigValue("blocks_per_ckpt"),
+        },
+        "diffusion_module": {
+            "use_fine_grained_checkpoint": True,
+            "use_efficient_implementation": GlobalConfigValue(
+                "use_memory_efficient_kernel"
+            ),
+            "sigma_data": GlobalConfigValue("sigma_data"),
+            "c_token": 768,
+            "c_atom": GlobalConfigValue("c_atom"),
+            "c_atompair": GlobalConfigValue("c_atompair"),
+            "c_z": GlobalConfigValue("c_z"),
+            "c_s": GlobalConfigValue("c_s"),
+            "c_s_inputs": GlobalConfigValue("c_s_inputs"),
+            "atom_encoder": {
+                "n_blocks": 3,
+                "n_heads": 4,
+            },
+            "transformer": {
+                "n_blocks": 24,
+                "n_heads": 16,
+            },
+            "atom_decoder": {
+                "n_blocks": 3,
+                "n_heads": 4,
+            },
+            "blocks_per_ckpt": GlobalConfigValue("blocks_per_ckpt"),
+        },
+        "confidence_head": {
+            "c_z": GlobalConfigValue("c_z"),
+            "c_s": GlobalConfigValue("c_s"),
+            "c_s_inputs": GlobalConfigValue("c_s_inputs"),
+            "n_blocks": 4,
+            "max_atoms_per_token": GlobalConfigValue("max_atoms_per_token"),
+            "pairformer_dropout": 0.0,
+            "blocks_per_ckpt": GlobalConfigValue("blocks_per_ckpt"),
+            "distance_bin_start": 3.25,
+            "distance_bin_end": 52.0,
+            "distance_bin_step": 1.25,
+            "stop_gradient": True,
+        },
+        "distogram_head": {
+            "c_z": GlobalConfigValue("c_z"),
+            "no_bins": GlobalConfigValue("no_bins"),
+        },
+    },
+}
+perm_configs = {
+    # Chain and Atom Permutation
+    "chain_permutation": {
+        "train": {
+            "mini_rollout": True,
+            "diffusion_sample": False,
+        },
+        "test": {
+            "diffusion_sample": True,
+        },
+        "permute_by_pocket": True,
+        "configs": {
+            "use_center_rmsd": False,
+            "find_gt_anchor_first": False,
+            "accept_it_as_it_is": False,
+            "enumerate_all_anchor_pairs": False,
+            "selection_metric": "aligned_rmsd",
+        },
+    },
+    "atom_permutation": {
+        "train": {
+            "mini_rollout": True,
+            "diffusion_sample": False,
+        },
+        "test": {
+            "diffusion_sample": True,
+        },
+        "permute_by_pocket": True,
+        "global_align_wo_symmetric_atom": False,
+    },
+}
+loss_configs = {
+    "loss": {
+        "diffusion_lddt_chunk_size": ValueMaybeNone(1),
+        "diffusion_bond_chunk_size": ValueMaybeNone(1),
+        "diffusion_chunk_size_outer": ValueMaybeNone(-1),
+        "diffusion_sparse_loss_enable": GlobalConfigValue("loss_metrics_sparse_enable"),
+        "diffusion_lddt_loss_dense": True,  # only set true in initial training for training speed
+        "resolution": {"min": 0.1, "max": 4.0},
+        "weight": {
+            "alpha_confidence": 1e-4,
+            "alpha_pae": 0.0,  # or 1 in finetuning stage 3
+            "alpha_except_pae": 1.0,
+            "alpha_diffusion": 4.0,
+            "alpha_distogram": 3e-2,
+            "alpha_bond": 0.0,  # or 1 in finetuning stages
+            "smooth_lddt": 1.0,  # or 0 in finetuning stages
+        },
+        "plddt": {
+            "min_bin": 0,
+            "max_bin": 1.0,
+            "no_bins": 50,
+            "normalize": True,
+            "eps": 1e-6,
+        },
+        "pde": {
+            "min_bin": 0,
+            "max_bin": 32,
+            "no_bins": 64,
+            "eps": 1e-6,
+        },
+        "resolved": {
+            "eps": 1e-6,
+        },
+        "pae": {
+            "min_bin": 0,
+            "max_bin": 32,
+            "no_bins": 64,
+            "eps": 1e-6,
+        },
+        "diffusion": {
+            "mse": {
+                "weight_mse": 1 / 3,
+                "weight_dna": 5.0,
+                "weight_rna": 5.0,
+                "weight_ligand": 10.0,
+                "eps": 1e-6,
+            },
+            "bond": {
+                "eps": 1e-6,
+            },
+            "smooth_lddt": {
+                "eps": 1e-6,
+            },
+        },
+        "distogram": {
+            "min_bin": 2.3125,
+            "max_bin": 21.6875,
+            "no_bins": 64,
+            "eps": 1e-6,
+        },
+    },
+    "metrics": {
+        "lddt": {
+            "eps": 1e-6,
+        },
+        "complex_ranker_keys": ListValue(["plddt", "gpde", "ranking_score"]),
+        "chain_ranker_keys": ListValue(["chain_ptm", "chain_plddt"]),
+        "interface_ranker_keys": ListValue(
+            ["chain_pair_iptm", "chain_pair_iptm_global", "chain_pair_plddt"]
+        ),
+        "clash": {"af3_clash_threshold": 1.1, "vdw_clash_threshold": 0.75},
+    },
+}
+
+configs = {
+    **basic_configs,
+    **data_configs,
+    **optim_configs,
+    **model_configs,
+    **perm_configs,
+    **loss_configs,
+}
+configs["finetune"] = finetune_optim_configs

model/Protenix-pxd/configs/configs_data.py

@@ -0,0 +1,251 @@
+# Copyright 2024 ByteDance and/or its affiliates.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# pylint: disable=C0114,C0301
+import os
+from copy import deepcopy
+
+from protenix.config.extend_types import GlobalConfigValue, ListValue
+
+default_test_configs = {
+    "sampler_configs": {
+        "sampler_type": "uniform",
+    },
+    "cropping_configs": {
+        "method_weights": [
+            0.0,  # ContiguousCropping
+            0.0,  # SpatialCropping
+            1.0,  # SpatialInterfaceCropping
+        ],
+        "crop_size": -1,
+    },
+    "lig_atom_rename": GlobalConfigValue("test_lig_atom_rename"),
+    "shuffle_mols": GlobalConfigValue("test_shuffle_mols"),
+    "shuffle_sym_ids": GlobalConfigValue("test_shuffle_sym_ids"),
+    "constraint": {
+        "enable": False,
+        "fix_seed": False,  # True means use use the same contact in each evaluation.
+    },
+}
+
+default_weighted_pdb_configs = {
+    "sampler_configs": {
+        "sampler_type": "weighted",
+        "beta_dict": {
+            "chain": 0.5,
+            "interface": 1,
+        },
+        "alpha_dict": {
+            "prot": 3,
+            "nuc": 3,
+            "ligand": 1,
+        },
+        "force_recompute_weight": True,
+    },
+    "cropping_configs": {
+        "method_weights": ListValue([0.2, 0.4, 0.4]),
+        "crop_size": GlobalConfigValue("train_crop_size"),
+    },
+    "sample_weight": 0.5,
+    "limits": -1,
+    "lig_atom_rename": GlobalConfigValue("train_lig_atom_rename"),
+    "shuffle_mols": GlobalConfigValue("train_shuffle_mols"),
+    "shuffle_sym_ids": GlobalConfigValue("train_shuffle_sym_ids"),
+    # If enabled, the training settings for different constraint types,
+    # providing the model a certain proportion of constraints
+    # that meet specific conditions.
+    "constraint": {
+        "enable": False,
+        "fix_seed": False,
+        "pocket": {
+            "prob": 0.0,
+            "size": 1 / 3,
+            "spec_binder_chain": False,
+            "max_distance_range": {"PP": ListValue([6, 20]), "LP": ListValue([6, 20])},
+            "group": "complex",
+            "distance_type": "center_atom",
+        },
+        "contact": {
+            "prob": 0.0,
+            "size": 1 / 3,
+            "max_distance_range": {
+                "PP": ListValue([6, 30]),
+                "PL": ListValue([4, 10]),
+            },
+            "group": "complex",
+            "distance_type": "center_atom",
+        },
+        "substructure": {
+            "prob": 0.0,
+            "size": 0.8,
+            "mol_type_pairs": {
+                "PP": 15,
+                "PL": 10,
+                "LP": 10,
+            },
+            "feature_type": "one_hot",
+            "ratios": {
+                "full": [
+                    0.0,
+                    0.5,
+                    1.0,
+                ],  # ratio options of full chain substructure constraint
+                "partial": 0.3,  # ratio of partial chain substructure constraint
+            },
+            "coord_noise_scale": 0.05,
+            "spec_asym_id": False,
+        },
+        "contact_atom": {
+            "prob": 0.0,
+            "size": 1 / 3,
+            "max_distance_range": {
+                "PP": ListValue([2, 12]),
+                "PL": ListValue([2, 8]),
+            },
+            "min_distance": -1,
+            "group": "complex",
+            "distance_type": "atom",
+            "feature_type": "continuous",
+        },
+    },
+}
+
+if "PROTENIX_DATA_ROOT_DIR" not in os.environ:
+    print(f"PROTENIX_DATA_ROOT_DIR not set, will use ../release_data/ccd_cache")
+    current_file_path = os.path.abspath(__file__)
+    current_directory = os.path.dirname(current_file_path)
+    code_directory = os.path.dirname(current_directory)
+    DATA_ROOT_DIR = os.path.join(code_directory, "release_data/ccd_cache")
+else:
+    DATA_ROOT_DIR = os.environ["PROTENIX_DATA_ROOT_DIR"]
+
+# Use CCD cache created by scripts/gen_ccd_cache.py priority. (without date in filename)
+# See: docs/prepare_data.md
+CCD_COMPONENTS_FILE_PATH = os.path.join(DATA_ROOT_DIR, "components.cif")
+CCD_COMPONENTS_RDKIT_MOL_FILE_PATH = os.path.join(
+    DATA_ROOT_DIR, "components.cif.rdkit_mol.pkl"
+)
+PDB_CLUSTER_FILE_PATH = os.path.join(DATA_ROOT_DIR, "clusters-by-entity-40.txt")
+
+if (not os.path.exists(CCD_COMPONENTS_FILE_PATH)) or (
+    not os.path.exists(CCD_COMPONENTS_RDKIT_MOL_FILE_PATH)
+):
+    CCD_COMPONENTS_FILE_PATH = os.path.join(DATA_ROOT_DIR, "components.v20240608.cif")
+    CCD_COMPONENTS_RDKIT_MOL_FILE_PATH = os.path.join(
+        DATA_ROOT_DIR, "components.v20240608.cif.rdkit_mol.pkl"
+    )
+
+data_configs = {
+    "num_dl_workers": 16,
+    "epoch_size": 10000,
+    "train_ref_pos_augment": True,
+    "test_ref_pos_augment": True,
+    "train_sets": ListValue(["weightedPDB_before2109_wopb_nometalc_0925"]),
+    "train_sampler": {
+        "train_sample_weights": ListValue([1.0]),
+        "sampler_type": "weighted",
+    },
+    "test_sets": ListValue(["recentPDB_1536_sample384_0925"]),
+    "weightedPDB_before2109_wopb_nometalc_0925": {
+        "base_info": {
+            "mmcif_dir": os.path.join(DATA_ROOT_DIR, "mmcif"),
+            "bioassembly_dict_dir": os.path.join(DATA_ROOT_DIR, "mmcif_bioassembly"),
+            "indices_fpath": os.path.join(
+                DATA_ROOT_DIR,
+                "indices/weightedPDB_indices_before_2021-09-30_wo_posebusters_resolution_below_9.csv.gz",
+            ),
+            "pdb_list": "",
+            "random_sample_if_failed": True,
+            "max_n_token": -1,  # can be used for removing data with too many tokens.
+            "use_reference_chains_only": False,
+            "exclusion": {  # do not sample the data based on ions.
+                "mol_1_type": ListValue(["ions"]),
+                "mol_2_type": ListValue(["ions"]),
+            },
+        },
+        **deepcopy(default_weighted_pdb_configs),
+    },
+    "recentPDB_1536_sample384_0925": {
+        "base_info": {
+            "mmcif_dir": os.path.join(DATA_ROOT_DIR, "mmcif"),
+            "bioassembly_dict_dir": os.path.join(
+                DATA_ROOT_DIR, "recentPDB_bioassembly"
+            ),
+            "indices_fpath": os.path.join(
+                DATA_ROOT_DIR, "indices/recentPDB_low_homology_maxtoken1536.csv"
+            ),
+            "pdb_list": os.path.join(
+                DATA_ROOT_DIR,
+                "indices/recentPDB_low_homology_maxtoken1024_sample384_pdb_id.txt",
+            ),
+            "max_n_token": GlobalConfigValue("test_max_n_token"),  # filter data
+            "sort_by_n_token": False,
+            "group_by_pdb_id": True,
+            "find_eval_chain_interface": True,
+        },
+        **deepcopy(default_test_configs),
+    },
+    "posebusters_0925": {
+        "base_info": {
+            "mmcif_dir": os.path.join(DATA_ROOT_DIR, "posebusters_mmcif"),
+            "bioassembly_dict_dir": os.path.join(
+                DATA_ROOT_DIR, "posebusters_bioassembly"
+            ),
+            "indices_fpath": os.path.join(
+                DATA_ROOT_DIR, "indices/posebusters_indices_mainchain_interface.csv"
+            ),
+            "pdb_list": "",
+            "find_pocket": True,
+            "find_all_pockets": False,
+            "max_n_token": GlobalConfigValue("test_max_n_token"),  # filter data
+        },
+        **deepcopy(default_test_configs),
+    },
+    "msa": {
+        "enable": True,
+        "enable_rna_msa": False,
+        "prot": {
+            "pairing_db": "uniref100",
+            "non_pairing_db": "mmseqs_other",
+            "pdb_mmseqs_dir": os.path.join(DATA_ROOT_DIR, "mmcif_msa"),
+            "seq_to_pdb_idx_path": os.path.join(DATA_ROOT_DIR, "seq_to_pdb_index.json"),
+            "indexing_method": "sequence",
+        },
+        "rna": {
+            "seq_to_pdb_idx_path": "",
+            "rna_msa_dir": "",
+            "indexing_method": "sequence",
+        },
+        "strategy": "random",
+        "merge_method": "dense_max",
+        "min_size": {
+            "train": 1,
+            "test": 1,
+        },
+        "max_size": {
+            "train": 16384,
+            "test": 16384,
+        },
+        "sample_cutoff": {
+            "train": 16384,
+            "test": 16384,
+        },
+    },
+    "template": {
+        "enable": False,
+    },
+    "ccd_components_file": CCD_COMPONENTS_FILE_PATH,
+    "ccd_components_rdkit_mol_file": CCD_COMPONENTS_RDKIT_MOL_FILE_PATH,
+    "pdb_cluster_file": PDB_CLUSTER_FILE_PATH,
+}

model/Protenix-pxd/configs/configs_inference.py

@@ -0,0 +1,35 @@
+# Copyright 2024 ByteDance and/or its affiliates.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# pylint: disable=C0114
+import os
+
+from protenix.config.extend_types import ListValue, RequiredValue
+
+current_file_path = os.path.abspath(__file__)
+current_directory = os.path.dirname(current_file_path)
+code_directory = os.path.dirname(current_directory)
+# The model will be download to the following dir if not exists:
+# "./release_data/checkpoint/model_v0.5.0.pt"
+inference_configs = {
+    "model_name": "protenix_base_default_v0.5.0",  # inference model selection
+    "seeds": ListValue([101]),
+    "dump_dir": "./output",
+    "need_atom_confidence": False,
+    "sorted_by_ranking_score": True,
+    "input_json_path": RequiredValue(str),
+    "load_checkpoint_dir": os.path.join(code_directory, "./release_data/checkpoint/"),
+    "num_workers": 16,
+    "use_msa": True,
+}

model/Protenix-pxd/configs/configs_model_type.py

@@ -0,0 +1,267 @@
+# Copyright 2024 ByteDance and/or its affiliates.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# model configs for inference and training,
+# such as: protenix-base, protenix-mini, protenix-tiny, protenix-constraint.
+# protenix_{model_size}_{features}_{version}
+# model_size: base, mini, tiny
+# features: default, constraint, esm, etc, if multiple split by "-"
+# version: v{x}.{y}.{z}
+
+"""
+Currently, the model_name support the following models.
+
+|           Model Name                |    ESM/MSA/Constraint    | Model Parameters(M ) |
+|-------------------------------------|--------------------------|----------------------|
+| `protenix_base_default_v0.5.0`      |      ❌ / ✅ / ❌         |         368.09       |
+| `protenix_base_constraint_v0.5.0`   |      ❌ / ✅ / ✅         |         368.30       |
+| `protenix_mini_esm_v0.5.0`          |      ✅ / ✅ / ❌         |         135.22       |
+| `protenix_mini_ism_v0.5.0`          |      ✅ / ✅ / ❌         |         135.22       |
+| `protenix_mini_default_v0.5.0`      |      ❌ / ✅ / ❌         |         134.06       |
+| `protenix_tiny_detault_v0.5.0`      |      ❌ / ✅ / ❌         |         109.50       |
+"""
+model_configs = {
+    "protenix_base_default_v0.5.0": {
+        "model": {"N_cycle": 10},
+        "sample_diffusion": {
+            "N_step": 200,
+        },  # the default setting for base model
+    },
+    "protenix_base_constraint_v0.5.0": {
+        "model": {
+            "sample_diffusion": {
+                "N_step": 200,
+            },  # the default setting for constraint model
+            "N_cycle": 10,
+            "constraint_embedder": {
+                "pocket_embedder": {
+                    "enable": True,
+                },
+                "contact_embedder": {
+                    "enable": True,
+                },
+                "substructure_embedder": {
+                    "enable": True,
+                },
+                "contact_atom_embedder": {
+                    "enable": True,
+                },
+            },
+        },
+        "data": {
+            "weightedPDB_before2109_wopb_nometalc_0925": {
+                "constraint": {
+                    "enable": True,
+                    "pocket": {
+                        "prob": 0.2,
+                        "max_distance_range": {
+                            "PP": [4, 15],
+                            "LP": [3, 10],
+                        },
+                    },
+                    "contact": {
+                        "prob": 0.1,
+                    },
+                    "substructure": {
+                        "prob": 0.5,
+                        "size": 1,
+                        "coord_noise_scale": 1,
+                    },
+                    "contact_atom": {
+                        "prob": 0.1,
+                        "max_distance_range": {
+                            "PP": [2, 12],
+                            "PL": [2, 15],
+                        },
+                        "min_distance": -1,
+                        "group": "complex",
+                        "distance_type": "atom",
+                        "feature_type": "continuous",
+                    },
+                },
+            },
+            "recentPDB_1536_sample384_0925": {
+                "constraint": {
+                    "enable": True,
+                },
+            },
+            "posebusters_0925": {
+                "constraint": {
+                    "enable": True,
+                },
+            },
+        },
+        "load_strict": False,  # If finetuning from base model, model arch has been changed,
+        # it should be False, for inference, it should be True.
+        "finetune_params_with_substring": [
+            "constraint_embedder.substructure_z_embedder",
+            "constraint_embedder.pocket_z_embedder",
+            "constraint_embedder.contact_z_embedder",
+            "constraint_embedder.contact_atom_z_embedder",
+        ],
+    },
+    "protenix_mini_default_v0.5.0": {
+        "sample_diffusion": {
+            "gamma0": 0,
+            "step_scale_eta": 1.0,
+            "N_step": 5,
+        },  # the default setting for mini model
+        "model": {
+            "N_cycle": 4,
+            "msa_module": {
+                "n_blocks": 1,
+            },
+            "pairformer": {
+                "n_blocks": 16,
+            },
+            "diffusion_module": {
+                "atom_encoder": {
+                    "n_blocks": 1,
+                },
+                "transformer": {
+                    "n_blocks": 8,
+                },
+                "atom_decoder": {
+                    "n_blocks": 1,
+                },
+            },
+        },
+        "load_strict": False,  # For inference, it should be True.
+    },
+    "protenix_mini_tmpl_v0.5.0": {
+        "sample_diffusion": {
+            "gamma0": 0,
+            "step_scale_eta": 1.0,
+            "N_step": 5,
+        },  # the default setting for mini model
+        "model": {
+            "N_cycle": 4,
+            "noisy_structure_embedder": {
+                "c_z": 128,
+            },
+            "msa_module": {
+                "n_blocks": 1,
+            },
+            "pairformer": {
+                "n_blocks": 16,
+            },
+            "diffusion_module": {
+                "atom_encoder": {
+                    "n_blocks": 1,
+                },
+                "transformer": {
+                    "n_blocks": 8,
+                },
+                "atom_decoder": {
+                    "n_blocks": 1,
+                },
+            },
+        },
+        "load_strict": False,  # For inference, it should be True.
+    },
+    "protenix_tiny_default_v0.5.0": {
+        "sample_diffusion": {
+            "gamma0": 0,
+            "step_scale_eta": 1.0,
+            "N_step": 5,
+        },  # the default setting for tiny model
+        "model": {
+            "N_cycle": 4,
+            "msa_module": {
+                "n_blocks": 1,
+            },
+            "pairformer": {
+                "n_blocks": 8,
+            },
+            "diffusion_module": {
+                "atom_encoder": {
+                    "n_blocks": 1,
+                },
+                "transformer": {
+                    "n_blocks": 8,
+                },
+                "atom_decoder": {
+                    "n_blocks": 1,
+                },
+            },
+        },
+        "load_strict": False,  # For inference, it should be True.
+    },
+    "protenix_mini_esm_v0.5.0": {
+        "sample_diffusion": {
+            "gamma0": 0,
+            "step_scale_eta": 1.0,
+            "N_step": 5,
+        },  # the default setting for mini model
+        "model": {
+            "N_cycle": 4,
+            "msa_module": {
+                "n_blocks": 1,
+            },
+            "pairformer": {
+                "n_blocks": 16,
+            },
+            "diffusion_module": {
+                "atom_encoder": {
+                    "n_blocks": 1,
+                },
+                "transformer": {
+                    "n_blocks": 8,
+                },
+                "atom_decoder": {
+                    "n_blocks": 1,
+                },
+            },
+        },
+        "esm": {
+            "enable": True,
+            "model_name": "esm2-3b",
+        },
+        "load_strict": False,  # For inference, it should be True.
+        "use_msa": False,  # For efficiency, this model does not use MSA by default.
+    },
+    "protenix_mini_ism_v0.5.0": {
+        "sample_diffusion": {
+            "gamma0": 0,
+            "step_scale_eta": 1.0,
+            "N_step": 5,
+        },  # the default setting for mini model
+        "model": {
+            "N_cycle": 4,
+            "msa_module": {
+                "n_blocks": 1,
+            },
+            "pairformer": {
+                "n_blocks": 16,
+            },
+            "diffusion_module": {
+                "atom_encoder": {
+                    "n_blocks": 1,
+                },
+                "transformer": {
+                    "n_blocks": 8,
+                },
+                "atom_decoder": {
+                    "n_blocks": 1,
+                },
+            },
+        },
+        "esm": {
+            "enable": True,
+            "model_name": "esm2-3b-ism",
+        },
+        "load_strict": False,  # For inference, it should be True.
+        "use_msa": False,  # For efficiency, this model does not use MSA by default.
+    },
+}

model/Protenix-pxd/docs/colabfold_compatible_msa.md

@@ -0,0 +1,33 @@
+### Using Local Colabfold_search to Generate Protenix-Compatible MSA
+
+Colabfold provides an easy-to-use and efficient MSA search pipeline that's ideal for generating MSAs during inference. Unfortunately, this pipeline cannot fully match Protenix's MSA search process designed for training, as the current `colabfold_search` omits species information in the MSA, preventing correct pairing by Protenix's data pipeline. To address this issue, we provide the `scripts/colabfold_msa.py` script, which post-processes `colabfold_search` results by adding pseudo taxonomy IDs to paired MSAs to match Protenix's data pipeline.
+
+Here's an example:
+```bash
+python3 scripts/colabfold_msa.py examples/dimer.fasta <path/to/colabfold_db> dimer_colabfold_msa --db1 uniref30_2103_db --db3 colabfold_envdb_202108_db --mmseqs_path <path/to/mmseqs> 
+```
+
+#### Configuring Colabfold_search
+Installation of colabfold and mmseqs2 is required.
+
+colabfold can be installed with: `pip install colabfold[alphafold]`. 
+
+Build MMseqs2 from source:
+
+```bash
+wget https://github.com/soedinglab/MMseqs2/archive/refs/tags/16-747c6.tar.gz
+tar xzf 16-747c6.tar.gz 
+cd MMseqs2-16-747c6/
+mkdir build && cd build
+cmake -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=. ..
+make -j8
+make install
+```
+
+Download ColabFold database:
+```bash
+git clone https://github.com/sokrypton/ColabFold.git
+cd ColabFold
+# Configure database:
+MMSEQS_NO_INDEX=1 ./setup_databases.sh <path/to/colabfold_db>
+```

model/Protenix-pxd/docs/docker_installation.md

@@ -0,0 +1,30 @@
+### Run with Docker
+
+1. Install Docker (with GPU Support)
+
+    Ensure that Docker is installed and configured with GPU support. Follow these steps:
+    *  Install [Docker](https://www.docker.com/) if not already installed.
+    *  Install the [NVIDIA Container Toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html) to enable GPU support.
+    *  Verify the setup with:
+        ```bash
+        docker run --rm --gpus all nvidia/cuda:12.1.0-base-ubuntu22.04 nvidia-smi
+        ```
+        
+2. Pull the Docker image, which was built based on this [Dockerfile](../Dockerfile)
+    ```bash
+    docker pull ai4s-cn-beijing.cr.volces.com/infra/protenix:v0.0.3
+    ```
+
+3. Clone this repository and `cd` into it
+    ```bash
+    git clone https://github.com/bytedance/protenix.git 
+    cd ./protenix
+    pip install -e .
+    ```
+
+4. Run Docker with an interactive shell
+    ```bash
+    docker run --gpus all -it -v $(pwd):/workspace -v /dev/shm:/dev/shm ai4s-cn-beijing.cr.volces.com/infra/protenix:v0.0.3 /bin/bash
+    ```
+  
+  After running above commands, you’ll be inside the container’s environment and can execute commands as you would on a normal Linux terminal.

model/Protenix-pxd/docs/infer_json_format.md

@@ -0,0 +1,329 @@
+### Format of the input JSON file
+The JSON file format closely resembles that used by the AlphaFold Server, with a few key differences:
+
+1. There are no restrictions on the types of ligands, ions, and modifications, whereas the AlphaFold Server currently supports only a limited set of specific CCD codes.
+2. Users can specify bonds between entities, such as covalent bonds between ligands and polymers.
+3. It supports inputting ligands in the form of SMILES strings or molecular structure files.
+4. Ligands composed of multiple CCD codes can be treated as a single entity. This feature is useful for representing glycans, for example, "NAG-NAG".
+5. The "glycans" field is no longer supported. Glycans can be fully represented by inputting multiple ligands with defined bonding or by providing their SMILES strings.
+
+Here is an overview of the JSON file format:
+```json
+[ 
+  {
+    "name": "Test Fold Job Number One",
+    "sequences": [...],
+    "covalent_bonds": [...]
+  }
+]
+```
+The JSON file consists of a list of dictionaries, where each dictionary represents a set of sequences you want to model. 
+Even if you are modeling only one set of sequences, the top-level structure should still be a list.
+
+Each dictionary contains the following three keys:
+* `name`: A string representing the name of the inference job.
+* `sequences`: A list of dictionaries that describe the entities (e.g., proteins, DNA, RNA, small molecules, and ions) involved in the inference.
+* `covalent_bonds`: An optional list of dictionaries that define the covalent bonds between atoms from different entities.
+
+Details of `sequences` and `covalent_bonds` are provided below.
+
+#### sequences
+There are 5 kinds of supported sequences:
+*   `proteinChain` – used for proteins
+*   `dnaSequence` – used for DNA (single strand)
+*   `rnaSequence` – used for RNA (single strand)
+*   `ligand` – used for ligands
+*   `ion` – used for ions
+
+##### proteinChain
+```json
+{
+  "proteinChain": {
+    "sequence": "PREACHINGS", 
+    "count": 1,
+    "modifications": [
+      {
+        "ptmType": "CCD_HY3", 
+        "ptmPosition": 1,
+      },
+      {
+        "ptmType": "CCD_P1L",
+        "ptmPosition": 5
+      }
+    ],
+    "msa":{
+      "precomputed_msa_dir": "./precomputed_msa",
+      "pairing_db": "uniref100",
+    },
+  },
+}
+```
+* `sequence`: A string representating a protein sequence, which can only contain the 20 standard amino acid type and X (UNK) for unknown residues.
+* `count`: The number of copies of this protein chain (integer).
+* `modifications`: An optional list of dictionaries that describe post-translational modifications.
+
+  * `ptmType`: A string containing CCD code of the modification. 
+  * `ptmPosition`: The position of the modified amino acid (integer).
+* `msa`: A dictionary containing options for Multiple Sequence Alignment (MSA). **If you want to search MSAs using our inference pipeline, you should not set this field or set it to an empty dictionary**:
+  * `precomputed_msa_dir`: The path to a directory containing precomputed MSAs. This directory should contain two specific files: "pairing.a3m" for MSAs used for pairing, and "non_pairing.a3m" for non-pairing MSAs.
+  * `pairing_db`: The name of the genomic database used for pairing MSAs. The default is "uniref100" and you should not change it. In fact, The MSA search against the UniRef30, a clustered version of the UniRef100.
+
+##### dnaSequence
+```json
+{
+  "dnaSequence": {
+      "sequence": "GATTACA",
+      "modifications": [
+          {
+              "modificationType": "CCD_6OG",
+              "basePosition": 1
+          },
+          {
+              "modificationType": "CCD_6MA",
+              "basePosition": 2
+          }
+      ],
+      "count": 1
+  }
+},
+{
+    "dnaSequence": {
+        "sequence": "TGTAATC",
+        "count": 1
+    }
+}
+```
+Please note that the `dnaSequence` type refers to a single stranded DNA sequence. If you
+wish to model double-stranded DNA, please add a second `dnaSequence` entry representing
+the sequence of the reverse complement strand.
+
+* `sequence`: A string containing a DNA sequence; only letters A, T, G, C and N (unknown ribonucleotide) are allowed.
+* `count`: The number of copies of this DNA chain (integer).
+* `modifications`: An optional list of dictionaries describing of
+the DNA chemical modifications:
+  * `modificationType`: A string containing CCD code of modification.
+  * `basePosition`: A position of the modified nucleotide (integer).
+
+##### rnaSequence
+```json
+{
+  "rnaSequence": {
+      "sequence": "GUAC",
+      "modifications": [
+          {
+              "modificationType": "CCD_2MG",
+              "basePosition": 1
+          },
+          {
+              "modificationType": "CCD_5MC",
+              "basePosition": 4
+          }
+      ],
+      "count": 1
+  }
+}
+```
+* `sequence`: A string representing the RNA sequence (single-stranded); only letters A, U, G, C and N (unknown nucleotides) are allowed.
+* `count`: The number of copies of this RNA chain (integer).
+* `modifications`: An optional list of dictionaries describing RNA chemical modifications:
+  * `modificationType`: A string containing
+    CCD code  of modification.
+  * `basePosition`: The position of the modified nucleotide (integer).
+
+##### ligand
+```json
+{
+    "ligand": {
+        "ligand": "CCD_ATP",
+        "count": 1
+    }
+},
+{
+    "ligand": {
+        "ligand": "FILE_your_file_path/atp.sdf",
+        "count": 1
+    }
+},
+{
+    "ligand": {
+        "ligand": "Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)[C@@H](O)[C@H]1O",
+        "count": 1
+    }
+}
+```
+* `ligand`: A string representing the ligand. `ligand` can be one of the following three:
+  * A string containing the CCD code of the ligand, prefixed with "CCD_". For glycans or similar structures, this can be a concatenation of multiple CCD codes, for example, "CCD_NAG_BMA_BGC".
+  * A molecular SMILES string representing the ligand.
+  * A path to a molecular structure file, prefixed with "FILE_", where the supported file formats are PDB, SDF, MOL, and MOL2. The file must include the 3D conformation of the molecule.
+
+* `count` is the number of copies of this ligand (integer).
+
+##### ion
+```json
+{
+    "ion": {
+        "ion": "MG",
+        "count": 2
+    }
+},
+{
+    "ion": {
+        "ion": "NA",
+        "count": 3
+    }
+}
+```
+* `ion`: A string containing the CCD code for the ion. Note that, unlike ligands, the ion code **does not** start with "CCD_".
+* `count`: The number of copies of this ion (integer).
+
+#### covalent_bonds
+```json
+"covalent_bonds": [
+            {
+                "entity1": "2",
+                "copy1": 1,
+                "position1": "2",
+                "atom1": "N6",
+                "entity2": "3",
+                "copy2": 1,
+                "position2": "1",
+                "atom2": "C1"
+            }
+]
+```
+
+The `covalent_bonds` section specifies covalent bonds between a polymer and a ligand, or between two ligands.
+To define a covalent bond, two atoms involved in the bond must be identified. The following fields are used:
+
+* `entity1`, `entity2`: The entity numbers for the two atoms involved in the bond. 
+The entity number corresponds to the order in which the entity appears in the `sequences` list, starting from 1.
+* `copy1`, `copy2`: The copy index (starting from 1) of the `left_entity` and `right_entity`, respectively. These fields are optional, but if specified, both `left_copy` and `right_copy` must be filled simultaneously or left empty at the same time. If neither field is provided, a bond will be created between all pairs of copies of the two entities. For example, if both entity1 and entity2 have two copies, a bond will be formed between entity1.copy1 and entity2.copy1, as well as between entity1.copy2 and entity2.copy2. In this case, the number of copies for both entities must be equal.
+* `position1`, `position2` - The position of the residue (or ligand part) within the entity. 
+The position value starts at 1 and can vary based on the type of entity:
+  * For **polymers** (e.g., proteins, DNA, RNA), the position corresponds to the location of the residue in the sequence.
+  * For **ligands** composed of multiple CCD codes, the position refers to the serial number of the CCD code.
+  * For **single CCD code ligands**, or ligands defined by **SMILES** or **FILE**, the position is always set to 1.
+    
+* `atom1`, `atom2` - The atom names (or atom indices) of the atoms to be bonded.
+  * If the entity is a polymer or described by a CCD code, the atom names are consistent with those defined in the CCD.
+  * If the entity is a ligand defined by SMILES or a FILE, atoms can be specified by their atom index. The atom index corresponds to the position of the atom in the file or in the SMILES string, starting from 0.
+
+Deprecation Notice: The previous fields such as old `left_entity`, `right_entity`, and other fields starting with `left`/`right` have been updated to use `1` and `2` to denote the two atoms forming a bond. The current code still supports the old field names, but they may be deprecated in the future, leaving only the new field names. An alternative approach is to write the element name of the specified atom in the SMILES/file, along with its sequential number for that element, e.g., "C2" indicates it is the second carbon.
+
+Here is a revised user guide compatible with **Version 2** of the `constraint` format for the Complex Structure Predictor:
+
+---
+
+### constraint
+The `constraint` section specifies additional structural information to enable inter-chain guidance for Protenix. Currently, Protenix support two kind of constraint: `contact` and `pocket` constraint. 
+The `contact` constraint allows you to specify residue/atom-residue/atom level priors. The `pocket` constraint is used to guide the binding interface between a chain of interest (e.g. a ligand or an antibody) and specific residues in another chain (e.g. epitopes).
+
+> 💡 *This is a **soft constraint**: the model is encouraged, but not strictly required, to satisfy it.*
+
+#### contact constraint
+
+The `contact` field consists of a list of dictionaries, each describing one contact. The residues and atoms involved in the contact are now represented as compact lists, making the format more concise and flexible.
+
+##### Example:
+
+```json
+"contact": [
+    {
+        "residue1": ["1", 1, 169],
+        "atom2": ["2", 1, 1, "C5"],
+        "max_distance": 6,
+        "min_distance": 0
+    }, // token-contact
+    {
+        "atom1": ["1", 1, 169, "CA"],
+        "residue2": ["2", 1, 1],
+        "max_distance": 6,
+        "min_distance": 0
+    }, // token-contact
+    {
+        "residue1": ["1", 1, 169],
+        "residue2": ["2", 1, 1 ],
+        "max_distance": 6,
+        "min_distance": 0
+    }, // token-contact
+    {
+        "atom1": ["1", 1, 169, "CA"],
+        "atom2": ["2", 1, 1, "C5"],
+        "max_distance": 6,
+        "min_distance": 3
+    }, // atom-contact
+    ...
+]
+```
+
+Each contact dictionary includes the following keys:
+* `residue1` or `residue2` (list):
+  Specifies a **residue** in the format:`[entity_number, copy_index, position]`
+
+* `atom1` or `atom2` (list):
+  Specifies an **atom** (commonly from a ligand or another residue) in the format:`[entity_number, copy_index, position, atom_name]`
+
+* `max_distance` (float):
+  The **expected maximum distance** (in Ångströms) between the specified residues or atoms.
+* `min_distance` (float):
+  The **expected minimum distance** (in Ångströms) between the specified residues or atoms. For token-contact, you do not need to specify this field. It is 0 by default.
+
+#### pocket constraint
+
+The `pocket` constraint is defined as a dictionary with three keys: `"binder_chain"`, `"contact_residues"`, and `"max_distance"` to allow chain-residue binding specification.
+
+##### Example
+
+```json
+"pocket": {
+  "binder_chain": ["2", 1], 
+  "contact_residues": [
+    ["1", 1, 126],
+    ...
+  ], 
+  "max_distance": 6
+}
+```
+
+* `binder_chain` (list):
+  Specifies the **binder chain** in the format:  `[entity_number, copy_index]`
+
+* `contact_residues` (list of lists):
+  A list of residue  that are expected to be in spatial proximity (i.e., in or near the binding pocket). Each residue is specified as:
+  `[entity_number, copy_index, position]`
+
+* `max_distance` (float):
+  The **maximum allowed distance** (in Ångströms) between the binder and the specified contact residues.
+
+
+### Format of the model output
+The outputs will be saved in the directory provided via the `--dump_dir` flag in the inference script. The outputs include the predicted structures in CIF format and the confidence in JSON files. The `--dump_dir` will have the following structure:
+
+```bash
+├── <name>/  # specified in the input JSON file
+│   ├── <seed>/  # specified via the `--seeds` flag in the inference script
+│   │   ├── <name>_<seed>_sample_0.cif
+│   │   ├── <name>_<seed>_summary_confidence_sample_0.json
+│   │   └──... # the number of samples in each seed is specified via `--sample_diffusion.N_sample ` flag in the inference script
+│   └──...
+└── ...
+```
+
+The contents of each output file are as follows:
+- `<name>_<seed>_sample_*.cif` - A CIF format text file containing the predicted structure
+- `<name>_<seed>_summary_confidence_sample_*.json` - A JSON format text file containing various confidence scores for assessing the reliability of predictions. Here’s a description of each score:
+
+    - `plddt` - Predicted Local Distance Difference Test (pLDDT) score. Higher values indicate greater confidence.
+    - `gpde` - Globl Predicted Distance Error (PDE) score. Lower values indicate greater confidence.
+    - `ptm` - Predicted TM-score (pTM). Values closer to 1 indicate greater confidence.
+    - `iptm` - Interface Predicted TM-score, used to estimate the accuracy of interfaces between chains. Values closer to 1 indicate greater confidence.
+    - `chain_ptm` - pTM score calculated for individual chains with the shape of [N_chains], indicating the reliability of specific chain structure.
+    - `chain_pair_iptm`: Pairwise interface pTM scores between chain pairs with the shape of [N_chains, N_chains], indicating the reliability of specific chain-chain interactions.
+    - `chain_iptm` - Average ipTM scores for each chain with the shape of [N_chains].
+    - `chain_pair_iptm_global` - Averge `chain_iptm` between chain pairs with the shape of [N_chains, N_chains]. For interface containing a small molecule, ion, or bonded ligand chain (named `C*`), this value is equal to the `chain_iptm` value of `C*`. 
+    - `chain_plddt` - pLDDT scores calculated for individual chains with the shape of [N_chains].
+    - `chain_pair_plddt` - Pairwise pLDDT scores for chain pairs with the shape of [N_chains, N_chains].
+    - `has_clash` - Boolean flag indicating if there are steric clashes in the predicted structure.
+    - `disorder` - Predicted regions of intrinsic disorder within the protein, highlighting residues that may be flexible or unstructured.
+    - `ranking_score` - Predicted confidence score for ranking complexes. Higher values indicate greater confidence.
+    - `num_recycles`: Number of recycling steps used during inference.

model/Protenix-pxd/docs/kernels.md

@@ -0,0 +1,24 @@
+### Setting up kernels
+
+- **Custom CUDA layernorm kernels** modified from [FastFold](https://github.com/hpcaitech/FastFold) and [Oneflow](https://github.com/Oneflow-Inc/oneflow) accelerate about 30%-50% during different training stages. To use this feature, run the following command:
+  ```bash
+  export LAYERNORM_TYPE=fast_layernorm
+  ```
+  If the environment variable `LAYERNORM_TYPE` is set to `fast_layernorm`, the model will employ the layernorm we have developed; otherwise, the naive PyTorch layernorm will be adopted. The kernels will be compiled when `fast_layernorm` is called for the first time.
+- **[DeepSpeed DS4Sci_EvoformerAttention kernel](https://www.deepspeed.ai/tutorials/ds4sci_evoformerattention/)** is a memory-efficient attention kernel developed as part of a collaboration between OpenFold and the DeepSpeed4Science initiative. To use this feature, run the following command:
+  ```bash
+  export USE_DEEPSPEED_EVO_ATTENTION=true
+  ```
+  DS4Sci_EvoformerAttention is implemented based on [CUTLASS](https://github.com/NVIDIA/cutlass). If you use this feature, You need to clone the CUTLASS repository and specify the path to it in the environment variable CUTLASS_PATH. The [Dockerfile](Dockerfile) has already include this setting:
+  ```bash
+  RUN git clone -b v3.5.1 https://github.com/NVIDIA/cutlass.git  /opt/cutlass
+  ENV CUTLASS_PATH=/opt/cutlass
+  ```
+  If you set up `Protenix` by `pip`, you can set environment variable `CUTLASS_PATH` as follows:
+
+  ```bash
+  git clone -b v3.5.1 https://github.com/NVIDIA/cutlass.git  /path/to/cutlass
+  export CUTLASS_PATH=/path/to/cutlass
+  ```
+
+  The kernels will be compiled when DS4Sci_EvoformerAttention is called for the first time.

model/Protenix-pxd/docs/model_train_inference_cost.md

@@ -0,0 +1,51 @@
+### Training 
+Some settings follow those in the [AlphaFold 3](https://www.nature.com/articles/s41586-024-07487-w) paper, The table below shows the training settings for different fine-tuning stages:
+
+  | Arguments  | Initial training | Fine tuning 1   |  Fine tuning 2  | Fine tuning 3 |
+  |-----------------------------------------|--------|---------|-------|-----|
+  | `train_crop_size`                       | 384    | 640    | 768    | 768 |
+  | `diffusion_batch_size`                  | 48     | 32     | 32     | 32  |
+  | `loss.weight.alpha_pae`                 | 0      | 0      | 0      | 1.0 |
+  | `loss.weight.alpha_bond`                | 0      | 1.0    | 1.0    | 0   | 
+  | `loss.weight.smooth_lddt`               | 1.0    | 0      | 0      | 0   | 
+  | `loss.weight.alpha_confidence`          | 1e-4   | 1e-4   | 1e-4   | 1e-4|
+  | `loss.weight.alpha_diffusion`           | 4.0    | 4.0    | 4.0    | 0   |
+  | `loss.weight.alpha_distogram`           | 0.03   | 0.03   | 0.03   | 0   |
+  | `train_confidence_only`                 | False  | False  | False  | True|
+  | full BF16-mixed speed(A100, s/step)     | ~12    | ~30    | ~44    | ~13 |
+  | full BF16-mixed peak memory (G)         | ~34    | ~35    | ~48    | ~24 |
+  
+  We recommend carrying out the training on A100-80G or H20/H100 GPUs. If utilizing full BF16-Mixed precision training, the initial training stage can also be performed on A800-40G GPUs. GPUs with smaller memory, such as A30, you'll need to reduce the model size, such as decreasing `model.pairformer.nblocks` and `diffusion_batch_size`.
+
+### Inference
+
+The model will be infered in BF16 Mixed precision, by **default**, the `SampleDiffusion`,`ConfidenceHead` part will still be infered in FP32 precision.
+
+Below are reference examples of cuda memory usage (G).
+
+| Ntoken | Natom | Memory(G) | Inference time(s) |
+|--------|-------|-------|------------------|
+| 500    | 5000  | 5.2   | 72   |
+| 1000   | 10000 | 11.5  | 229  |
+| 2000   | 20000 | 42.8  | 933  |
+| 3000   | 30000 | 73.9  | 2295 |
+| 3500   | 35000 | 69.5  | 3329 |
+| 4000   | 40000 | 67.5  | 4483 |
+
+The script in [runner/inference.py](../runner/inference.py) will automatically change the default precision to compute `SampleDiffusion`,`ConfidenceHead` to avoid OOM as follows:
+```python
+def update_inference_configs(configs: Any, N_token: int):
+    # Setting the default inference configs for different N_token and N_atom
+    # when N_token is larger than 3000, the default config might OOM even on a
+    # A100 80G GPUS,
+    if N_token > 3840:
+        configs.skip_amp.confidence_head = False
+        configs.skip_amp.sample_diffusion = False
+    elif N_token > 2560:
+        configs.skip_amp.confidence_head = False
+        configs.skip_amp.sample_diffusion = True
+    else:
+        configs.skip_amp.confidence_head = True
+        configs.skip_amp.sample_diffusion = True
+    return configs
+```

model/Protenix-pxd/docs/msa_pipeline.md

@@ -0,0 +1,101 @@
+## MSA data pipeline
+If you download our released wwPDB dataset as in [training.md](./training.md), the mmcif_msa [450G] dir has the following directory structure.
+  ```bash
+  ├── seq_to_pdb_index.json [45M] # sequence to integers mapping file
+  ├── mmcif_msa [450G] # msa files
+    ├── 0
+      ├── uniref100_hits.a3m
+      ├── mmseqs_other_hits.a3m
+    ├── 1
+      ├── uniref100_hits.a3m
+      ├── mmseqs_other_hits.a3m
+    ├── 2
+      ├── uniref100_hits.a3m
+      ├── mmseqs_other_hits.a3m
+    ...
+    ├── 157201
+      ├── uniref100_hits.a3m
+      ├── mmseqs_other_hits.a3m
+
+  ```
+
+Each integer in the first-level directory under mmcif_msa (for example, 0, 1, 2, and 157201) represents a unique protein sequence. The key of `seq_to_pdb_index.json` is the unique protein sequence, and the value is the integer corresponding to the first-level subdirectory of mmcif_msa mentioned above.
+
+This document is used to provide the steps to convert the MSA obtained from colabfold into the Protenix training format.
+
+### Steps to get your own MSA data for training
+
+#### Step1: get input protein sequence 
+Run the following command:
+
+```python
+python3 scripts/msa/step1-get_prot_seq.py
+```
+you will get outputs in `scripts/msa/data/pdb_seqs` dir. The result dir is as follows,
+
+```bash
+  ├── pdb_index_to_seq.json # mapping integers to sequences
+  ├── seq_to_pdb_index.json # mapping sequences to integers identifiers when saving MSA, This file is required in training for finding local MSA path from sequence
+  ├── pdb_seq.fasta # Input of MSA
+  ├── pdb_seq.csv # Intermediate Files
+  ├── seq_to_pdb_id_entity_id.json # Intermediate Files
+```
+
+#### Step2: run msa search
+We give detailed environment configuration and search commands in 
+
+```python
+scripts/msa/step2-get_msa.ipynb
+```
+
+The searched MSA is in `scripts/msa/data/mmcif_msa_initial`, The result dir is as follows,
+```bash
+  ├── 0.a3m
+  ├── 1.a3m
+  ├── 2.a3m
+  ├── 3.a3m
+  ├── pdb70_220313_db.m8
+  ├── uniref_tax.m8 # record Taxonomy ID which is used by MSA Pairing
+```
+#### Steps3: MSA Post-Processing
+
+The overall solution is to search the MSA containing taxonomy information only once for the unique sequence, and pair it according to the species information of each MSA. 
+
+For MSA Post-Processing, Taxonomy ID from UniRef30 DB is added to MSAs and MSAs is split into `uniref100_hits.a3m` and `mmseqs_other_hits.a3m`, which correspond to `pairing.a3m` and `non_pairing.a3m` in inference stage respectively.
+
+You can run:
+```python
+python3 scripts/msa/step3-uniref_add_taxid.py
+
+python3 scripts/msa/step4-split_msa_to_uniref_and_others.py
+```
+
+The final pairing and non_pairing MSAs in `scripts/msa/data/mmcif_msa` is as follows:
+
+
+```
+>query
+GPTHRFVQKVEEMVQNHMTYSLQDVGGDANWQLVVEEGEMKVYRREVEENGIVLDPLKATHAVKGVTGHEVCNYFWNVDVRNDWETTIENFHVVETLADNAIIIYQTHKRVWPASQRDVLYLSVIRKIPALTENDPETWIVCNFSVDHDSAPLNNRCVRAKINVAMICQTLVSPPEGNQEISRDNILCKITYVANVNPGGWAPASVLRAVAKREYPKFLKRFTSYVQEKTAGKPILF
+>UniRef100_A0A0S7JZT1_188132/	246	0.897	6.614E-70	2	236	237	97	331	332
+--THRFADKVEEMVQNHMTYSLQDVGGDANWQLVIEEGEMKVYRREVEENGIVLDPLKATHAVKGVTGHEVCHYFWDTDVRNDWETTIDNFNVVETLSDNAIIVYQTHKRVWPASQRDILFLSAIRKILAKNENDPDTWLVCNFSVDHDKAPPTNRCVRAKINVAMICQTLVSPPEGDKEISRDNILCKITYVANVNPGGWAPASVLRAVAKREYPKFLKRFTSYVQEKTAGNPILF
+>UniRef100_A0A4W6GBN4_8187/	246	0.893	9.059E-70	2	236	237	373	607	608
+--THRFANKVEEMVQNHMTYSLQDVGGDANWQLVIEEGEMKVYRREVEENGIVLDPLKATHSVKGVTGHEVCHYFWDTDVRMDWETTIENFNVVEKLSENAIIVYQTHKRVWPASQRDVLYLSAIRKIMATNENDPDTWLVCNFSVDHNNAPPTNRCVRAKINVAMICQTLVSPPEGDKEISRDNILCKITYVANVNPGGWAPASVLRAVAKREYPKFLKRFTSYVQEKTAGKPILF
+```
+
+```
+>query
+MAEVIRSSAFWRSFPIFEEFDSETLCELSGIASYRKWSAGTVIFQRGDQGDYMIVVVSGRIKLSLFTPQGRELMLRQHEAGALFGEMALLDGQPRSADATAVTAAEGYVIGKKDFLALITQRPKTAEAVIRFLCAQLRDTTDRLETIALYDLNARVARFFLATLRQIHGSEMPQSANLRLTLSQTDIASILGASRPKVNRAILSLEESGAIKRADGIICCNVGRLLSIADPEEDLEHHHHHHHH
+>MGYP001165762451	218	0.325	1.019E-59	5	230	244	3	228	230
+-----DKVEFLKGVPLFSELPEAHLQSLGELLIERSYRRGATIFFEGDPGDALYIVRSGIVKISRVAEDGREKTLAFLGKGEPFGEMALIDGGPRSAIAQALEATSLYALHRADFLAALTENPALSLGVIKVLSARLQQANAQLMDLVFRDVRGRVAQALLDLARR-HGVPLTNGRMISVKLTHQEIANLVGTARETVSRTFAELQDSGIIRIeGRNIVLLDAAQLEGYAAG-------------
+>A0A160T8V6	218	0.285	1.019E-59	0	227	244	0	229	237
+MPTTRDsnAVQALQVVPFFANLPEDHVAALAKALVPRRFSPGQVIFHLGDPGGLLYLISRGKIKISHTTSDGQEVVLAILGPGDFFGEMALIDDAPRSATAITLEPSETWTLHREEFIQYLTDNPEFALHVLKTLARHIRRLNTQLADIFFLDLPGRLARTLLNLADQ-YGRRAADGTIIDLSLTQTDLAEMTGATRVSINKALGRFRRAGWIQvTGRQVTVLDRAALEAL----------------
+>AP58_3_1055460.scaffolds.fasta_scaffold1119545_2	216	0.304	3.581E-59	10	225	244	5	221	226
+----------LSRVPLFAELPPERIHELAQSVRRRTYHRGETIFHKGDPGNGLYIIAAGQVKIVLPSEMGEEAMLAVLEGGEFFGELALFDGLPRSATVVAVQNAEVLVLHRDDFMSFVGRNPEVVSALFAALSRRLRDADEMIEDAIFLDVPGRLAKRLLDLAEKHGRAEEKGGVAIDLKLTQQDLAAMVGATRESVNKHLGWMRDHGLIQLDRqRIVILKPDDLR------------------
+```
+### Format of MSA 
+In `uniref100_hits.a3m`(training stage) or `pairing.a3m`(inference stage), the header must starts with the following format, which we use for pairing:
+```
+>UniRef100_{hitname}_{taxonomyid}/
+```
+
+we also provide a pipeline of local Colabfold_search to Generate Protenix-Compatible MSAs in [colabfold_compatible_msa.md](./colabfold_compatible_msa.md).

model/Protenix-pxd/docs/prepare_training_data.md

@@ -0,0 +1,119 @@
+# Start with CIF files and prepare your own training data.
+
+## Data Preparation
+
+1. **Prepare CIF Files**: Place the CIF files you want to convert into training data in a folder. Alternatively, you can use a `txt` file to record the paths to these CIF files, with each line corresponding to the path of a specific CIF file.
+
+2. **Prepare Protein Clustering File (Optional)**: The protein clustering file contains category information for each `[PDB ID]_[Entity ID]`. In the Protenix training data, we cluster protein sequences using a 40% sequence identity threshold.
+
+   You can download the official clustering results file provided by RCSB PDB using the following command, and use it directly:
+   ```bash
+   wget https://cdn.rcsb.org/resources/sequence/clusters/clusters-by-entity-40.txt
+   ```
+
+    If you prefer to perform your own clustering of protein sequences, ensure the final results are formatted as a text file like this:
+    Each line represents a cluster, containing `[PDB ID]_[Entity ID]` entries separated by spaces.
+
+3. **Update the CCD (Chemical Component Dictionary) Cache File (If needed)**: We provide a pre-processed file, with a cutoff date of 2024-06-08, that records the reference conformers for each CCD Code. If the training data you're preparing is more recent than this date, there may be issues with some CCD Codes might be missing. For example, the CCD Code "WTB," appearing in the PDB ID: 8P3K released on 2024-11-20, is not defined in the previously provided CCD file. In such cases, you need to run the following script to download and update the CCD CIF files:
+
+    ```bash
+    python3 scripts/gen_ccd_cache.py -c [ccd_cache_dir] -n [num_cpu]
+    ```
+
+    After running the script, three files will be generated in the specified "ccd_cache_dir":
+    
+    - `components.cif` (CCD CIF file downloaded from RCSB)
+    - `components.cif.rdkit_mol.pkl` (pre-processed dictionary, where the key is the CCD Code and the value is an RDKit Mol object with 3D structure)
+    - `components.txt` (a list containing all the CCD Codes)
+
+    When running Protenix, it first uses 
+    ```bash
+    `release_data/ccd_cache/components.cif`
+    `release_data/ccd_cache/components.cif.rdkit_mol.pkl`
+    ```
+    if unavailable, it switches to 
+    ```bash
+    `release_data/ccd_cache/components.v20240608.cif`
+    `release_data/ccd_cache/components.v20240608.cif.rdkit_mol.pkl`
+    ```
+    Notes:
+    - The `-c` parameter is optional. If not specified, files will be saved in the "release_data/ccd_cache" folder within the Protenix code directory by default.
+    - You can add the `-d` parameter when running the script to skip the CIF file download step, in which case the script will directly process the "components.cif" file located in the "ccd_cache_dir".
+
+## Data Preprocessing
+Execute the script to preprocess the data:
+```bash
+python3 scripts/prepare_training_data.py -i [input_path] -o [output_csv] -b [output_dir] -c [cluster_txt] -n [num_cpu]
+```
+
+The preprocessed structures will be saved as `.pkl.gz` files. Additionally, a `CSV` file will be generated to catalog the chains and interfaces within these structures, which will facilitate sampling during the training process.
+
+You can view the explanation of the parameters by using the `--help` command.
+```
+python3 scripts/prepare_training_data.py --help
+```
+
+Note that there is an optional parameter `-d` in the script. When this parameter is not used, the script processes CIF files downloaded from RCSB PDB by applying the full set of WeightedPDB training data filters. These filters include:
+
+- Removing water molecules
+- Removing hydrogen atoms
+- Deleting polymer chains composed entirely of unknown residues
+- Eliminating chains where the Cα distance between adjacent numbered residues exceeds 10 angstroms
+- Removing elements labeled as "X"
+- Deleting chains where no residues have been resolved
+- When the number of chains exceeds 20, selecting one central atom from those capable of forming interfaces and retaining the 20 nearest chains to it. If a ligand is covalently bonded to a polymer, it is considered as one chain together. Additionally, if the number of chains is greater than 20 but the total number of tokens in these chains is less than 5120, more chains will be retained until the 5120 token limit is reached.
+- Removing chains with one-third of their heavy atoms colliding
+
+For CIF files generated through model inference where these filtering steps aren't desired, you can run the script with the `-d` parameter, which disables all these filters. The CIF structure will not be expanded to Assembly 1 in this case.
+
+
+## Output Format
+### Bioassembly Dict
+In the folder specified by the `-b` parameter of the data preprocessing script, a corresponding `[pdb_id].pkl.gz` file is generated for each successfully processed CIF file. This file contains a dictionary saved with `pickle.dump`, with the following contents:
+```
+| Key                        | Value Type    | Description                                                                   |
+|----------------------------|---------------|-------------------------------------------------------------------------------|
+| pdb_id                     | str           | PDB Code                                                                      |
+| assembly_id                | str           | Assembly ID                                                                   |
+| sequences                  | dict[str, str]| Key is polymer's label_entity_id, value is canonical_sequence                 |
+| release_date               | str           | PDB's Release Date                                                            |
+| num_assembly_polymer_chains| int           | Number of assembly polymer chains (pdbx_struct_assembly.oligomeric_count)     |
+| num_prot_chains            | int           | Number of protein chains in AtomArray                                         |
+| entity_poly_type           | dict[str, str]| Key is polymer's label_entity_id, value is corresponding to entity_poly.type  |
+| resolution                 | float         | Resolution; if no resolution, value is -1                                     |
+| num_tokens                 | int           | Number of tokens                                                              |
+| atom_array                 | AtomArray     | AtomArray from structure processing                                           |
+| token_array                | TokenArray    | TokenArray generated based on AtomArray                                       |
+| msa_features               | None          | (Placeholder)                                                                 |
+| template_features          | None          | (Placeholder)                                                                 |
+```
+
+### Indices CSV
+After the script successfully completes, a CSV file will be generated in the directory specified by `-o`. 
+Each row contains information about a pre-processed chain or interface, and the content of each column is described as follows: 
+```
+| Column Name    | Value Type | Meaning                                                                | Required |
+|----------------|------------|------------------------------------------------------------------------|----------|
+| type           | str        | "chain" or "interface"                                                 | Y        |
+| pdb_id         | str        | PDB Code (entry.id)                                                    | Y        |
+| cluster_id     | str        | Cluster_id of the chain/interface                                      | Y        |
+| assembly_id    | str        | Assembly id                                                            | N        |
+| release_date   | str        | Release date                                                           | N        |
+| resolution     | float      | Resolution; if no resolution, value is -1                              | N        |
+| num_tokens     | int        | Number of tokens in AtomArray of Bioassembly Dict                      | N        |
+| num_prot_chains| int        | Number of protein chains in AtomArray of Bioassembly Dict              | N        |
+| eval_type      | str        | Classification used for evaluation                                     | N        |
+| entity_1_id    | str        | Chain 1's label_entity_id                                              | Y        |
+| chain_1_id     | str        | Chain 1's chain ID                                                     | Y        |
+| mol_1_type     | str        | Chain 1's corresponding mol_type ("protein", "nuc", "ligand", "ions")  | Y        |
+| sub_mol_1_type | str        | Sub-classification of Chain 1's entity corresponding to mol_type       | N        |
+| cluster_1_id   | str        | Chain 1's cluster ID                                                   | Y        |
+| entity_2_id    | str        | Chain 2's label_entity_id                                              | Y        |
+| chain_2_id     | str        | Chain 2's chain ID                                                     | Y        |
+| mol_2_type     | str        | Chain 2's corresponding mol_type ("protein", "nuc", "ligand", "ions")  | Y        |
+| sub_mol_2_type | str        | Sub-classification of Chain 2's entity corresponding to mol_type       | N        |
+| cluster_2_id   | str        | Chain 2's cluster_id                                                   | Y        |
+```
+Notes: 
+- In the table, columns marked with 'Y' under 'Required' indicate that these columns are essential for training. If you are creating your own CSV for training purposes, these columns must be included. Columns marked with 'N' are optional and can be excluded. 
+- For rows where the "type" is "chain", the values in columns related to Chain 2 should all be filled with empty strings.

model/Protenix-pxd/docs/training.md

@@ -0,0 +1,88 @@
+### Preparing the datasets
+To download the [wwPDB dataset](https://www.wwpdb.org/) and preprocessed training data, you need at least 1T disk space.
+
+Use the following command to download the preprocessed wwpdb training databases:
+
+```bash
+wget -P /af3-dev/release_data/ https://af3-dev.tos-cn-beijing.volces.com/release_data.tar.gz
+tar -xzvf /af3-dev/release_data/release_data.tar.gz -C /af3-dev/release_data/
+rm /af3-dev/release_data/release_data.tar.gz
+```
+
+
+The data should be placed in the `/af3-dev/release_data/` directory. You can also download it to a different directory, but remember to modify the `DATA_ROOT_DIR` in [configs/configs_data.py](../configs/configs_data.py) correspondingly. Alternatively, you can set an environment variable "PROTENIX_DATA_ROOT_DIR" to specify the path. Data hierarchy after extraction is as follows:
+
+  ```bash
+  ├── components.v20240608.cif [408M] # ccd source file
+  ├── components.v20240608.cif.rdkit_mol.pkl [121M] # rdkit Mol object generated by ccd source file
+  ├── indices [33M] # chain or interface entries
+  ├── mmcif [283G]  # raw mmcif data
+  ├── mmcif_bioassembly [36G] # preprocessed wwPDB structural data
+  ├── mmcif_msa [450G] # msa files
+  ├── posebusters_bioassembly [42M] # preprocessed posebusters structural data
+  ├── posebusters_mmcif [361M] # raw mmcif data
+  ├── recentPDB_bioassembly [1.5G] # preprocessed recentPDB structural data
+  └── seq_to_pdb_index.json [45M] # sequence to pdb id mapping file
+  ```
+
+Data processing scripts have also been released. you can refer to [prepare_training_data.md](./prepare_training_data.md) for generating `{dataset}_bioassembly` and `indices`. And you can refer to [msa_pipeline.md](./msa_pipeline.md) for pipelines to get `mmcif_msa` and `seq_to_pdb_index.json`.
+
+### Training demo
+After the installation and data preparations, you can run the following command to train the model from scratch:
+
+  ```bash
+  bash train_demo.sh 
+  ```
+Key arguments in this scripts are explained as follows:
+* `dtype`: data type used in training. Valid options include `"bf16"` and `"fp32"`. 
+  * `--dtype fp32`: the model will be trained in full FP32 precision.
+  * `--dtype bf16`: the model will be trained in BF16 Mixed precision, by default, the `SampleDiffusion`,`ConfidenceHead`, `Mini-rollout` and `Loss` part will still be training in FP32 precision. if you want to train and infer the model in full BF16 Mixed precision, pass the following arguments to the [train_demo.sh](../train_demo.sh):
+    ```bash
+    --skip_amp.sample_diffusion_training false \
+    --skip_amp.confidence_head false \
+    --skip_amp.sample_diffusion false \
+    --skip_amp.loss false \
+    ```
+* `ema_decay`: the decay rate of the EMA, default is 0.999.
+* `sample_diffusion.N_step`: during evalutaion, the number of steps for the diffusion process is reduced to 20 to improve efficiency.
+
+* `data.train_sets/data.test_sets`: the datasets used for training and evaluation. If there are multiple datasets, separate them with commas.
+* Some settings follow those in the [AlphaFold 3](https://www.nature.com/articles/s41586-024-07487-w) paper, The table in [model_performance.md](../docs/model_performance.md) shows the training settings and memory usages for different training stages.
+* In this version, we do not use the template and RNA MSA feature for training. As the default settings in [configs/configs_base.py](../configs/configs_base.py) and [configs/configs_data.py](../configs/configs_data.py):
+  ```bash
+  --model.template_embedder.n_blocks 0 \
+  --data.msa.enable_rna_msa false \
+  ```
+  This will be considered in our future work.
+
+* The model also supports distributed training with PyTorch’s [`torchrun`](https://pytorch.org/docs/stable/elastic/run.html). For example, if you’re running distributed training on a single node with 4 GPUs, you can use:
+  ```bash
+  torchrun --nproc_per_node=4 runner/train.py
+  ```
+  You can also pass other arguments with `--<ARGS_KEY> <ARGS_VALUE>` as you want.
+
+
+If you want to speed up training, see [<u> setting up kernels documentation </u>](./kernels.md).
+
+### Finetune demo
+
+If you want to fine-tune the model on a specific subset, such as an antibody dataset, you only need to provide a PDB list file and load the pretrained weights as [finetune_demo.sh](../finetune_demo.sh) shows:
+    
+```bash
+# wget -P /af3-dev/release_model/ https://af3-dev.tos-cn-beijing.volces.com/release_model/model_v0.5.0.pt
+checkpoint_path="/af3-dev/release_model/model_v0.5.0.pt"
+...
+
+--load_checkpoint_path ${checkpoint_path} \
+--load_checkpoint_ema_path ${checkpoint_path} \
+--data.weightedPDB_before2109_wopb_nometalc_0925.base_info.pdb_list examples/subset.txt \
+```
+
+, where the `subset.txt` is a file containing the PDB IDs like:
+```bash
+6hvq
+5mqc
+5zin
+3ew0
+5akv
+```

model/Protenix-pxd/examples/7wux/msa/1/pairing.a3m

@@ -0,0 +1,544 @@
+>query
+MASWSHPQFEKGGTHVAETSAPTRSEPDTRVLTLPGTASAPEFRLIDIDGLLNNRATTDVRDLGSGRLNAWGNSFPAAELPAPGSLITVAGIPFTWANAHARGDNIRCEGQVVDIPPGQYDWIYLLAASERRSEDTIWAHYDDGHADPLRVGISDFLDGTPAFGELSAFRTSRMHYPHHVQEGLPTTMWLTRVGMPRHGVARSLRLPRSVAMHVFALTLRTAAAVRLAEGATT
+>UniRef100_UPI000B1A43EC_1463901/	204	0.926	4.008E-55	15	232	233	0	217	218
+---------------MAETSVRTEGRPDTRVLRLPGAASAPEFRLIDIDGLLNNRATTDVRDLGSGRLNAWGNSFPAAELPAPGSLIEVAGIPFTWANAHATGDNVRCEGQVVDIPPGRYDWIYLLAASERRSEDTIWAHYDDGHADPLRVGISDFLDGTPAFGELSAFRTSRMHYPHHVQEGLPTTMWLTRVGMPRHGVAHSLRLPRSVAMHVFALTLRTTADVRLAQGATT
+>UniRef100_UPI001BE85A7B_2819193/	186	0.830	5.494E-49	19	230	233	4	215	218
+-------------------SVLTAAKPGPRVHRLPGTASAPEFCLIGIDDLLNNRATTSVSDLDSGRLNAWGNSFPAEELPTPGALIEVAGIPFTWANAHAKGDNVRCEGQVIDIPPGQYDWIYLLAASERRSEDTIWAHYEDGHADPLRVGVSDFLDGTPAFGELTAFRTSRMHYPHHVQERLPTTMWLTRVGMPRRGIAQSLRLPRLVAMHVFALTLVTGIDVRRAQGA--
+>UniRef100_UPI0006899DE6_66377/	178	0.726	2.919E-46	15	230	233	3	218	221
+---------------ISSNTIRTHTPSDRLLDRLHGKASAPEFCLISIDDLLNNRATTSTEDLDSGRLNAWGNSFPAEELPAPGARIEIAGIPFAWARSHAEGDNVRCEGQVIEIPPGQYDWIYLLAASERRSENTLWAHYADGTADPLRLGVSDFLDGTPAFGELPAFSTERMHYPHHVQQGLPTTMWLSRVGMPRRGRATALRLPRCVALHVFALTLLTGIDVRLADGA--
+>UniRef100_UPI0012DD7F77_35754/	178	0.705	2.919E-46	15	231	233	3	219	237
+---------------VSDRPVLVPGAYDRLVQRLPGTTAQPDFCLIGIDDLLNNRATTGTGDLDAGRLNAWGNSFPSRELPEPGAVIEIAGIPFVWPDANPDGDNVRSEGQVIDIPPGRYDWIYLLAASERRSEDTLWVHYDDGHADPLRVGVSDFLDGTPAFGELPAFRTARMHYPHHVQERLPTTMWLARVGMPRRGRAQALRLPRLVALHVFAITLVTGIDVRLADGAD-
+>UniRef100_A0A510HIW1_49319/	171	0.295	8.250E-44	29	219	233	889	1080	1084
+-----------------------------RVVEARCAAEDRGFCAADLRHSLNSDGVSTDANPGDGDFDGLGFSYPAEELPVPG-PFESGGVLYWFTETsDGAPNNIEARGQTVPLVPERYAAAHILGAAHHGAVETaATVTYADGSTERLQLSLSDWAQETPQFGEEVAVRTTHRHQEGAGDVGPPVAIFAFSLELDPSREVRFLTLPAEVRLHLFAITLR-------------
+>UniRef100_A0A5N0E9G2_2545717/	168	0.765	1.013E-42	27	222	233	11	206	217
+---------------------------DRLVRRLPAGPARPEFCLIDLDDLLNNRATTGTADLDQGRLNAWGNSFPAEELPQPGTQIDVAGIPFVWANAHAHGDNVRCEGQLIDLPPGQYDWIYLLAASERRSEDTLWAYYDDGHADPLPVGISDFLDGTPAFGELSAFRTTRMHYPHHVQHGLPTTVWLTRVGLPRRGNAHAIRFPRLVAMHIFALTLLTGS----------
+>UniRef100_Q1ASW4_266117/	167	0.295	2.592E-42	29	219	233	69	260	264
+-----------------------------RVVEARCAAEDRGFCAAGLGHSLNSDGVSTDANPNDGDFDGLGFSYPAEELPAPG-PFESGGVLYWYPETsDGAPNNIEARGQTVPLVPGRYAAAHILGAAHHGAVETaATVTYADGSTGRLQLRLSDWAREAPQFGEEVAVRTTHRHQEGAGDVGPPVAIFAVRLELDPSREARFLTLPEEARLHLFAITLR-------------
+>UniRef100_A0A4R7V1K6_502181/	167	0.406	2.592E-42	28	217	233	100	290	300
+----------------------------TLVPW-PSDDTSGNAVPVDLSAHLNCVGIEPKERPGRGAFNIWHNTFPIEELPRPGSITVVGGVSFRFPAADGtRPDNLRCRGQRIELPSSRVDWLHLLAAAERRTEDVVTVHYADGTTRPQWLRVSDFWPETPSrFGELPAFRTSAMLYPNHVDSRMPPVIWHQRVPVAVRDGVVAVTLPDNPAVHVFAMT---------------
+>UniRef100_UPI000B27D092_285514/	166	0.425	3.546E-42	31	224	233	1	195	204
+-------------------------------TAIPGpPTEESPYDPVDLTPCFNNTGISPASDTGRGSFNVWGNSFPAESLPSGRAPVTVDGVPFRFPPVGRGNDNVRCAGQFVPVETGRFDWLHLLAAAERRTEDTMAMHFEDGTVDPEWIRVSDFWAAPARFGETKAFETPVMHYPHHVQQGVSALLWAQRVPVTRRADLKGFRLPRNVALHIFAATLQQTAVV--------
+>UniRef100_A0A920BQ67_571911/	166	0.423	6.637E-42	42	223	233	3	185	190
+------------------------------------------PLAVDLDPYADNTGITTADRKDAGGFNIWGNTYPADQLPAAG-PVRVDDIPFRFPPaAPGRPDNVRCAGQLIEVPAGRYDWIQLLAAAERRTEDPLWLHYADGGVDPEWLRVSDfWPETAAHFGETAAYRCTHLHYPRHVDRKFGPSIWRQRVPVPRDAALRAVRLPDNPAIHIFAMTLVPAAG---------
+>UniRef100_UPI000AF72EB5_718014/	165	0.748	1.242E-41	29	231	233	17	219	221
+-----------------------------PVRSVRATTSSPEFLLVGIDDLLNNRAITGAADLGDGRLNAWGNSFPAEELPAPGMLVEVAGIPFQWANAHTEGDNVRCEGQIIDIPPARYDWIYLLAASERRSEDTLWAYYDDGYADPLRVGVSDFLDGTPVFGELPGFRTTRMHYPHHVQHGLPTTMWLSRVGMPRHGRALALRLPRSVALHVFAVTLLTGIDVRRADGTT-
+>UniRef100_A0A939I1U9_2815937/	164	0.273	1.699E-41	6	220	233	502	723	724
+------PQGAPGTTVTAVTATASYRAQSTAVDTVSGEQTITQVVPYPsLEAAFNNVGATSESDTTPGNFDGGGDSYSTQALaragATPGAAISANGLGFTWPSADaGRADNVSAAGQEITF-GGQGQTLGFLGAEAGSVSGTVTVTYTDGTTSTGQLGFPNWcCTPTDAFGAKTAFTMDHRNTPTGPANfGISYGVFTNTVPLTPGKTIRSVRLPDAPAIHVFALTVQP------------
+>UniRef100_UPI001F407CE4_1463833/	163	0.462	4.348E-41	28	227	233	5	205	217
+----------------------------TPPGTATPPASAPRYRVVELAAHRNNRAATRVHTTGAGGFNVWRNSFPVEHLPPGGSEVEVGGVPFRFPPVGEGDDNVRCDGQFVEVPAGRYDWIHLLAAAERRTEDTVELHYADGSVDSEWLRVSDFWSAPAWFGELPALRTPVMHYPYHVQPGLSAHLWAQRVPVPRRTALAGLRLPRNIAVHLFAATVqEPPGAAGLP-----
+>UniRef100_UPI000E241227_68246/	163	0.451	5.947E-41	45	228	233	12	196	197
+---------------------------------------------LDLTAFANNTGITTEDRLSDGAFNIWGNTFPAEELPA-GGEITVDGIPFRFPaPAAGAPDNVRCAGQLLELPAGRYDWIHVLAAAERRTEDFVQLHYTDGSVDPEWLRISDfWPQTGARFGESAAFSCTRLHYPRHVQRSMGPTIWRQRVPVTRQRELTALTLPDNPAIHVFAMTLAPTTPPEAAE----
+>UniRef100_A0A944KLD5_2819145/	163	0.258	5.947E-41	46	222	233	506	691	697
+----------------------------------------------DLAPYFDNTGISDDANQATANLDGYGFSYSAEALAAsgltPGATVTSDGVQYGWSGAAGQADNVVAAGQVLAVPAitGATELGVMGSATNGPSSGTMTITYTDGTTQQATLGFTDWTAGSPSLGNGVAASTQYRNSTGGSSQGLGTHLYTTTIALQAGKTVASVTLPtraDQGLLHVFALGTDKGA----------
+>UniRef100_A0A1C6VGZ9_683228/	161	0.443	2.082E-40	35	229	233	7	200	206
+-----------------------------------GAGAGTRQRHVDLTDHVDNLGIVVPRWPHGGGFNIWGNAFPADELPPAGGVCTVDGVSFSFP-LAGNRDNIRCRGQVVALPPGHYDWLYVLAAAERRTEDTVRLHYTDGSTAEQWLRISDfWPDTAPRFGDVLAFRCSRMLYPRHPQPSMAPAIWQQRIPVSRPGEVHAVRLPDNPAMHVFALTAVT-DAELPAEG---
+>UniRef100_UPI0021D8E261_2853165/	161	0.440	2.082E-40	28	227	233	5	206	218
+----------------------------TPPGTATPPAGAPRYRVVELAAHRNNRAASRMHTTGAGGFNVWRNSFPVEHLPPGGSEVEVGGVPFSFPPVGEGYDNVRCDGQFVEVPAGRYDWIHLLAAAERRAEDTVELHYADGSVDTEWLRVSDFWSAPAWFGELPAYRTPVMHYPYHVQPGIGAHLWAQRVPVPRRTALAGLRLPRNIAVHVFAATVQepPPGTAGLP-----
+>UniRef100_A0A246RSA7_1185415/	161	0.500	2.847E-40	44	223	233	12	191	196
+--------------------------------------------PVDISRHRNNIAISSATATKAGHFNVWGNSFAAEHLPAGGSLVHVAGVPFRFPPVCAGPDNVRCEGQFVPVTESRYDWIHVLAAAERRCEDTVELHFGDGSVDAEPLRISDFWAAPAWFGELLAFRSPVMHYPHHVQQGVPAVMWAQRVPVTRRADLVGIRLPRNVAMHIFAVTLEHAEA---------
+>UniRef100_UPI0018912F4F_2705253/	160	0.262	3.894E-40	47	219	233	1054	1238	1525
+-----------------------------------------------LPAAFNNDAITNDSNRGGADLDGAGASYSAQALAAvgvtPGAPLVHDGLTFTWPDRQvGQSDNVVAAGQTIDV-SGSGSTLGLLGTSTWGPStGSGTITYTDGSTQPYTIGFGDWANGTPPTGADVAIRAPYGNQP-GNQTGWAATVDYYPITLDPAKTVQSITLPSGsaqphggiPALHIFAMSIK-------------
+>UniRef100_A0A2A3HR12_1938860/	160	0.480	7.284E-40	37	217	233	8	188	212
+-------------------------------------ASAPRYRVVELADHRNNRAATRVHTTAAGGFNVWRNSFPAEHLPPGGSQVEVGGVPFSFPPVGEGDDNVRCDGQFIAVPAGRYDWVHLLAAAERRTEDTVELHYADGSVDTEWLRVSDFWAAPAWFGELPAYRTPVMHYPYHVQPGVSAHLWAQRVPVPRRTELAGLRLPRNIAVHVFAAT---------------
+>UniRef100_A0A838IYH6_2026798/	159	0.292	9.962E-40	29	221	233	647	843	845
+-----------------------------PRLALPEAFASDGFVALDLERAFNNDAFSSPSQPLKGNFDsrsgVLGATYPAERAPASLERIELGGVPFLFPPTDADANNVAFHGQRLEVPPGHYDELHLLGVSEQGNyQDTVRLVYEDGSVDEIPLGLSDWCQ-TPRYGEAIAFAFEQRRGAGGAIERITCRILVQLLPVRADSSLLRVDLPDRETMHLFALTLRHA-----------
+>UniRef100_UPI001C21EFA6_2849653/	159	0.434	1.362E-39	41	220	233	11	191	199
+-----------------------------------------EPVPVPLTEHFDNVGFTQPDQLSSGAFNIWGNTFPADELP-PGPEVRLDGVPFLIPAAPvGSPDNLRCAGQLVAVPPGRYDWVRLLCAAERRTEDRVWLHYTDGTIDPEWLRVSDfWPETAPRFGESLAFRFSRMHYPRHVDRRMKPAIWSQRLPITRAAELAAVRLPDNPAIHLFAMTLVP------------
+>UniRef100_A0A3M9MI77_2294115/	158	0.270	1.863E-39	44	217	233	562	741	744
+--------------------------------------------YANLAAAYNNVGVTAGADPTPGNFDGSGNSFNAELLAgqglTPGANVTANGFSFTWPNvAPGVADNAEAAGQLIKLT-GTGSTLAFLGSGVGDQSDTVTVHYTDGSTSTGTVGFPNWSFSDPtEFGAKLAFSTMGRNTPTGLADTAYAYrIFTNTIPLDTGKTVQSVQLPNNSALHLFAWT---------------
+>UniRef100_A0A5N8W5X6_1803180/	158	0.272	2.548E-39	44	219	233	760	936	940
+--------------------------------------------PVDLTAHFDSDGISTHENTQDGDFDGTGRTYPAEELPAAG-PLTFEGVRYTFPSyADGALDNVTAKGQTIPVPPGRYAKVRVLGACSYGAlKTTLTATYTDGSTQEVELAMSDWAGTAPASGSEV-VRCTHRHGRSG-PDTLQVALFQTAVTVDQARELRSLTLPDTtkPALHLFALSVE-------------
+>UniRef100_UPI0018923E89_280293/	158	0.283	2.548E-39	47	219	233	1056	1240	1527
+-----------------------------------------------LPAAFNNDAITNDSNRGGADLDGAGASFSAQALtsvgVTPGAPLVHDGLTFTWPNRQvGQSDNVVAAGQTIDVT-GSGSTLGLLGTSTWGAStGSGTITYTDGSTQPYTIGFGDWANGTPPTGGDVAIRAPYGNQP-GNQTGWAATIDYFPVTLDPSKTVQSITLPSGsaqphggiPAMHVFAMSIK-------------
+>UniRef100_A0A9E3EXL3_2740538/	158	0.256	3.485E-39	48	216	233	351	533	733
+------------------------------------------------STAYNNVGISDDSNSSTANFDGGGYSYSAEALQAagltPGQQITANGITFTWPGVPaGVNDNYQANGQTIPITPvsGATTLAFLGSATNGPSSGTVTITYTDNSTQSFSLGFSDWTlnagNSPPSFGNSVIATTSYRNHSGAGPDNVDTNILYAGVTLQTGKTLQSVTLPSTTNqgkIHVFAI----------------
+>UniRef100_UPI000AB2585B_688067/	156	0.466	8.913E-39	44	223	233	6	185	188
+--------------------------------------------PVDIAGHRNNTGISAATETKAGAFNVWGNSFAAEYLPEGDSLVHVAGVPFRFPPVCEGPDNIRCAGQFVRVPEGRYDWVHVLAAAERRCEDLVEMNYGDGSVDQEPLRVSDFWAAPAWFGEVKAFETPVMHYPHHVQQRVPAVMWAQRVPVTRRADLAGLRLPRNVAVHVFAMTLQRTEA---------
+>UniRef100_A0A542DYC5_402171/	156	0.261	8.913E-39	46	228	233	869	1066	1093
+----------------------------------------------DIWPYYTNAGITDDAHTGAASFDGGGWSYSAQALAAagvtPGSTVTADGVHYTWPDVPvATPDNIEESGQTIPLKvPAGASTIGLLGSASNagssGAGGTVTVHYTDGTSSTFDAFFSDWTlgggGGTPVPGDTTAVTTAYRN-SSGGRDPVKTYVFSVSAPLDAGKTVASITLPqaQGGDAHVFAIGFDTTGASSQAP----
+>UniRef100_UPI001AEB6A42_1365924/	156	0.290	1.219E-38	7	220	233	695	914	917
+-------DLERGGevlVHGPSPDLGIGPVPIsTPAPRwgLPALPDGGQTVIVDLAAALNNDAITSEFHMGDGDFDGAGNTYPAAQLPQTGQT-TDDGIPFEFVNgSEGTPNNVIPAAQTITLPPGNYMTLHLLAASDNGNtNRSMTITYADGTSQ-VPLQITDW-RTSPAFGETEALRTSQMHARTG-PQPVRLSIFHQKIPLDPAKQLVSITLPgaATPRPHLFAITLEK------------
+>UniRef100_UPI0023608C19_1392640/	156	0.216	1.219E-38	47	219	233	883	1071	1072
+-----------------------------------------------LLALFNNTGISSDDDPSSANYDGVGYSYSEQALAtagvKPGGTVSAGGMEFVWPNVPaGEPDNIAADGQTINLSdvPAGASELAFLGSAtNGPSQGEVKITYTDGSTQTATLGFSDWTlnagSSSPSFGNVVAAKMPYRNSTSGNRDQVTTYVFASRpIPLEQGKQPKSVTLPssvDQGTLHVFAVSVK-------------
+>UniRef100_C7PY52_479433/	156	0.272	1.219E-38	47	219	233	1074	1258	1548
+-----------------------------------------------LPAAFNNDAITNDSNRGGADLDGAGASFSAQALAsvgvTPGAPLVHDGLTFTWPDRQvGQSDNVVAAGQTIDI-SGSGSTLGLLGTSTWGaSSGSGTIAYTDGSTQPYTIAFGDWANGTPPTGGDVAIRAPYGNQP-GNQTGWAATIDYFPITLDATKTVQSITLPPgsaqphggTPAMHIFAMSIK-------------
+>UniRef100_UPI0021F5AFBA_1550616/	156	0.480	1.667E-38	36	218	233	7	189	195
+------------------------------------PAGIGLYDTVDISGHRNNTAISAATETGAGAFNVWRNSFAAEYLPAGGSLVHVDGVPFEFPPVCEGPDNIRCAGQFIRVPEGRYDWIHVLAASERRSEDTVELNFADGSVDAEALRVSDFWAAPPWFGEVRAFESLVMHYPHHVQRGIPAVMWAQRVPVTRRAGLTGILLPRNVAVHVFALTL--------------
+>UniRef100_UPI0004C58EA0_1883/	156	0.436	1.667E-38	36	221	233	2	188	196
+------------------------------------TSTTTTPVPLDLTALADNVGVTRPDRLSEGAFNIWGNTFPAEELP-PAGTVEVHGIPFRWPaTGDGSPDNVRCRGQLVTVPEGRYDWIHVLAAAERRTEDPLLLHFADGSVDPEWLRVSDFWPETASrFGERPAFSCTRLHYPRHIQHAMGPTVWRQRVPVTREERLRAFRLPDNPAMHLFAITLAPA-----------
+>UniRef100_UPI001BCF2EC7_1581705/	156	0.483	1.667E-38	44	223	233	15	194	199
+--------------------------------------------PVDISGHRNNTAISAATQTGAGAFNVWGNSFAAEYLPAGESLVHVAGVPFRFPPVCDGPDNVRCAGQFVTVPAGRYDWLHVLAAAERRCEDTVELNFGDGSVDAEPLRVSDFWAAPAWFGEIKAFESPVMHYPHHVQRGVPAVMWAQRVPVTRRAGLAGLRLPRNVAVHVFAVTLQRAEA---------
+>UniRef100_A0A2S9PQ64_2100817/	156	0.422	1.667E-38	33	232	233	0	197	206
+---------------------------------MPSTASTT-TRILDLSAVFDNIGASRAAATSTGAFNVWRNSFSAEHLPEPGTTVTVDEVPFLVPPfGTGGPDNVRCAGQLLEVQPDRYDWLYLLAAAERRVEDEVALHFADGTVDFEALRLSDFWAAPAVFGESEAFRTPAMHYPQHVQFGVPAGLFCQRVPVTRRAPLAGVRLPRNTAVHVFAATLLRAAAA--AGGPRT
+>UniRef100_A0A367FP16_509200/	155	0.478	2.279E-38	44	224	233	5	186	192
+--------------------------------------------PVDLTGHWNNRGISAAAGTGSGGFNVWRNSFPAEYLPPPGAQVEVEGVPFRFGGPDPAGDNIRCAGQYVELPEGRYDWIHLLTAAERRTEDTVALHFAGGEVDFEPLRVSDfWARAHAAFGEAKAFETPVMHYPHHVQPRVEALMWSQRVPVTRRAPLRGLRLPRNVAIHLFAMTLQTAGEP--------
+>UniRef100_A0A1W5T2H2_1977088/	155	0.458	2.279E-38	44	224	233	15	195	197
+--------------------------------------------PVDISGHRNNTAVSAATETKAAAFNVWGNSFAAEYLPAGGTLVHIAGVPFRFPPVCDGPDNIRCAGQFLDLPEGRYDWIHVLAAAERRCEDTAELHFDDGSVDPEPLRVSDFWSAPAWFGEVKAYESPVMHYPHHVQRNVSAVMWAQRVPVTRRAGLTGVRLPRNDALHLFAVTLQRAEAA--------
+>UniRef100_A0A372M322_2293568/	155	0.392	2.279E-38	22	220	233	12	215	222
+----------------------TSELTHTPADFAPPGSPPADFTPVGLQQHFNGKGVSAPrRWPTTGGFNVWGNTFPAEGLPTGGGDAEVACIPFRFPvddSAAGAPDNLRCRGQSVDVPPGEYQWIHVLAAAERRTEDEAVLHYADGSTRREWLRISDFWPETDqRFGELLAFRTRYLMYPRHSQHNMVPSIWLQRVPVTAPGTVTAVELPDNPAIHIFAITLET------------
+>UniRef100_UPI00131A6ADB_1840409/	155	0.241	2.279E-38	49	218	233	893	1078	1080
+-------------------------------------------------SVVNNTGISPDAKPAAANFDGVGWSYSADALAAagakPGGTVTVDGLSYTWPNFPvGEPDNVVAQGQTVALPgaAAGAGKLALLGAAANGkASGTLTITYTDGSTTRADIGFSDWTlgggSDQPSFGNRIAVSTPYRNSTGGQPQQIRTNVFAtVPIALDPGKRVRGITLPaqvQGGSLHVFAVAL--------------
+>UniRef100_UPI001C84E3F6_763782/	155	0.494	3.117E-38	44	218	233	2	177	189
+--------------------------------------------PVDLAAHWNNRAISAADDRGSGGFNVWRNSFPAEYLPPPGARVEVAGVPFRFGGPSAAGDNVRCAGQYVELPEGRYDWIHLLTAAERRTEDTVALHFSDGEVDFESLRVSDfWAQAHAAFGETKAFETPVMHYPHHTQPRVEALMWSQRVPVTRRAPLTGLRLPRNIAVHVFALTL--------------
+>UniRef100_UPI000B2085DA_46164/	155	0.422	3.117E-38	43	227	233	5	190	191
+-------------------------------------------VPVDLAPFFDNVGITPAGDLSSGAFNIWGNTFPAEELP-ERSPTTLGGVPFRFPDrGPGGADNLRCGGGLIPLPEGRYDWLYLLAAAERRTEDPVHLHYADGTVDPEWLRVSDfWPETQAWFGEREAIRCRSLHYPRHVQRPMGPALWRERIPVPREMPLAALRLPDNPAVHVFAVTLLPAGEVAPA-----
+>UniRef100_A0A7K0CJB4_2585196/	155	0.419	3.117E-38	43	221	233	7	186	196
+-------------------------------------------VPVDLAPYADNTGITSARATAAGAFNLWGNTFPAGELPPPGTAV-VDGLPFRFPLAPaGEPDNVRCAGQLLPLPPGRYDWIQLLAAAERRTEDQALLHYADGAVDPEWLRVSDfWPQTRSRFGAAPAYECRVLHYPRHVDDKFGPVVWRHRVPVPRESDLAAVRLPDNPAIHVFAMTLVPA-----------
+>UniRef100_UPI0018922BF9_280293/	154	0.446	5.828E-38	44	218	233	2	178	189
+--------------------------------------------PVDISPHFDNRGITGRGELSQGGFNIWDNTYPAEELPTPGGVVEVGSAPFLFPAlSPDGGDNLRCVGQFIQLPVGRYDWLYLLAASERRSEDTVYLHYADGSVDPEWLRVSDfWAETPPHFGEEAGLRCTVLHYPRHVQPFMGPAIWRTRVPVPRETPLSAVRLPDNPAIHIFALSL--------------
+>UniRef100_A0A6H9Z8I5_359158/	154	0.263	5.828E-38	20	220	233	743	944	947
+--------------------APVRVTTKAPPWGLPPLPPAGQAVPVELAGHFDNDGITSEFFMGDGDFDGTGATYPAAALPQTG-RVTADGVEFLFVNGiEGSANNVTAAGQTIPVPAGRYARLHVLGASDNGNAGtTVTAVYADGGTAAVPLRLTDW-KSNPAYGESAAVRAPQFHTRTGAKD-IAVTIFHQKADLDPARELTALRLPNltRPRPHLFSLTLEK------------
+>UniRef100_UPI00104757B6_1213861/	153	0.475	1.090E-37	37	221	233	4	188	190
+-------------------------------------TTANTFRPVEITEHWNNRSMSTVDDKGDGRFNVWRNSFPAEHLPRPGERVTVGGVPFDFPPATSAGDNARCAGQFVTLPPGHFDWIRLLASAERRVEDTVALHFADGQVDFEAIRVSDFWAAPACFGETLAYRTPVMHYPHHVQPRVEAMLWSQRVPVTRDATLTGLRLPNNRALHIFALTLQES-----------
+>UniRef100_UPI001C690D85_2749435/	153	0.444	1.490E-37	45	222	233	0	178	185
+---------------------------------------------MDLTALADNVGVTRPDRLSEGAFNIWGNTFPADELP-PAGPVEVHGIPFRWPaTGDGSPDNVRCRGQLVTVPEGHYDWIHVLGAAERRTEDPLLLHFTDGSVDPEWLRVSDFWPETASrFGERPAFSCTRLHYPRHIQQAMGPTIWRQRVPVTREEPLRAFRLPDNPAIHLFAITLAPAA----------
+>UniRef100_UPI0021556BFD_2675858/	153	0.471	1.490E-37	45	218	233	16	189	195
+---------------------------------------------VDISGHRNNTAISASTETKAGAFNVWGNSFAAEYLPAGESIVHVDGVPFEFPPVCDGPDNVRCAGQFIRVPEGRYDWIHVLAASERRSEETVELTFADGSVDPEPLRVSDFWAAPAWFGEVKAFESLVMHYPHHVQRGVPAVMWAQRVPVTRRAGLTGILLPRNVAVHVFAVTL--------------
+>UniRef100_UPI002254C514_2975865/	153	0.436	2.037E-37	42	227	233	2	189	191
+------------------------------------------STVIDISEACNNLGIGKSGAGEDYGFNIWRNTFPAEDLPAPGSTVAVDGVDFEFPPrETGKGDNIRCRGQLVALPGGHYEWIYLLGAAERRTEDEVELHYADGAARTEWLRMSDFWPETDSwFGEPEAFRATGLRYPRHTQAGHRPVIWQQRIPVTVPGALTALRLPDNPAMHVFALTAVTDPGVRHA-----
+>UniRef100_UPI0020A32361_334858/	153	0.456	2.037E-37	41	220	233	1	182	191
+-----------------------------------------KNTVVDISALCDNRGIQPPGTEGDYGFNIWSNTFPAEELPEPGSLVPVAGVPFEFPaRPAPGGDNIRCRGQLVPVPPGDYDWLYLLGAAERRTEDQVLLHYRDGTVRAEWLRMSDfWPQTEARFGEPLAFRTSAMRYPRHTHPAHAPSIWQQRVPVTVPGEITAVRLPDNPAMHVFALTLGT------------
+>UniRef100_A0A8F5GM97_2750812/	153	0.412	2.037E-37	45	224	233	8	188	192
+---------------------------------------------VDLAPFFDNVGITPSGDPSAGAFNIWGNTFPAGELP-EGPRAMLGGVPFRFPDrGPGGADNLRCAGGLIPLPEGRYDWLYLLAAAERRTEDPVHLHYADGTVDPEWLRVSDfWPETEPWFGEREGIRCESLHYPRHVQRPMGPALWRERIPVPRETPLAALRLPDNPAVHVFAITLLPAEEV--------
+>UniRef100_A0A4R2JNF3_1213861/	153	0.455	2.037E-37	43	218	233	11	188	194
+-------------------------------------------TPVDLGGHFDNRGITRGGELDQGGFNIWDNTFPAEDLPEPGGTVRIGDVPFLFPAPDPAGrDNLRCSGQVIELPTGRYDWLYLLAASERRSEDVITLHHADGSVDPQWLRVSDFWAETPAhFGEQASVRCRSLHYPRHIQRNMAPVIWRTRVPVPRETDLAAIGLPDNVAIHIFALTL--------------
+>UniRef100_UPI001E5DF7EA_2714955/	153	0.267	2.037E-37	2	221	233	797	1034	1035
+--SWLPESlFLNGGTVTVEVGATANTAWGsgaadlpvdrvpsapTPVPNLPAAcVVQGDYCLQSLAGQYDVDGVTTDDDMSQGVFGTNGWSWPAELLPAPG-VGTAAGRPYLFPDTTGtAGNFLSARGQTVYLTPGRYSALHAVTASHNGSfRGDVTVTYSDGTTSKASLLSTDWAAASPAYGEETALDVPTRHRNTGIHDGLRVRMWHVPLAVDSTRTAVSITLPSLPNLKVYALSARTA-----------
+>UniRef100_A0A1I3MHH7_115433/	153	0.280	2.037E-37	52	216	233	897	1073	1077
+----------------------------------------------------NNAGISPDSKPAAANFDGVGFSYSADALAAagakAGSTVTVGGLSYTWPNYPaGSPDNVQAQGQTI-IASGSGRLAFLGAASNGSASGTLTISYTDGSSSTAQLGFSDWTLGaggqQPAFGNQVAFTTPYRNSTGGTPQQINTYVFAsAPITLPAGKTVRSVTLPSNvsgGQLHVFAI----------------
+>UniRef100_A0A7K2PPX2_2690297/	152	0.474	2.786E-37	44	218	233	15	189	195
+--------------------------------------------PVDISGHRNNVAVSAAAETKAGAFNVWGNSFSAEHLPAGESLVNVDGVPFEFPPLCEGPDNIRCAGQFIRVPEGRYDWIHVLAASERRCEDTVELIFADGSVDAEALRVSDFWAAPAWFGEVKAFESLVMHYPHHVQRGIPAVMWAQRVPVTRRAGLTGIVLPRNVAIHVFAVTL--------------
+>UniRef100_A0A248YPR0_2024580/	152	0.491	2.786E-37	44	222	233	12	190	195
+--------------------------------------------PVDISGHRNNTAISSATATKAGHFNVWGNSFAAEHLPAGGSLVHVAGVPFRFPPVCAGPDNIRCEGQFIAVTQGRYDWVHVLAAAERRCEDTVELSFSDGPVDAESLRVSDFWAAPAWFGELLAFRSPVMHYPHHVQRGVPALMWAQRVPVTRRADLVGIRLPRNVAMHIFAVTLQHGA----------
+>UniRef100_UPI0010FB6E0B_1905/	152	0.434	2.786E-37	43	222	233	7	187	203
+-------------------------------------------VPVDLTAHADNTGITPADALDAGAFNLWGNTFPAEELP-PGGPVEVDGIPFLFPrHAPGAPDNIRCAGQLIELPAGRYDWIQVLAAAERRTEDQVLLHYGDGSVDPEWLRVSDFWPETASrLGGTAAYTCGRLHYPRHVERKFGPTLWRHRVPVPREAELTAVRLPDNPAVHLFALTLVPAP----------
+>UniRef100_UPI0022EA6403_1229659/	152	0.444	3.809E-37	41	218	233	1	180	191
+-----------------------------------------KNTVVDISALCDNRGIQPPGTEGEYGFNVWSNTFPAEELPEPGGLVPVAGVPFEFPaRPAPGGDNIRCRGQLVEVPPGEYDWLHLLGAAERRTEDQVLLHYRDGTVREEWLRMSDfWPQTDARFGEPLAFRTSAMRYPRHTHRSHAPSIWQQRVPVTVPGEITAVRLPDNPAMHVFALTL--------------
+>UniRef100_A0A1B4ZDD3_1213862/	152	0.413	3.809E-37	45	228	233	26	210	211
+---------------------------------------------LDLTAFADNVGVTSPDRLSEGAFNIWGNTFPADELPK-GGPVDIHGIPFRFPAvGTGQPDNVRCAGQFIDVPVGRYDWIHVLAAAERRTEDFVRLHYTDGAVDPEWLRVSDFWPETASrFGESAAVSCTRLHYPRHIQRSMGPTLWRQRVAVPREQDLSAIRLPDNPAIHIFAMTLAPATQPETTQ----
+>UniRef100_A0A5N8VJT9_1609272/	151	0.468	5.207E-37	42	218	233	7	183	189
+------------------------------------------YEPVDISGHRNNTAISAATETGAGAFNVWRNSFAAEYLPAGGSLVHVEGVPFEFPPVCDGPDNVRCGGQFIRVPEGRYDWIHVLAASERRCEDTVELSFADGSVDTEPLRVSDFWAAPAWFGEVKAFESLVMHYPHHVQRGVPAVMWAQRVPVTRRAGLTGILLPRNVAVHVFAVTL--------------
+>UniRef100_A0A229REX4_76020/	151	0.406	5.207E-37	45	224	233	8	189	192
+---------------------------------------------LSLLEHVNNTGLSTVGDLAAAGFNIWGNSFPAADLPSPGATSVVGGVPFRFPeRAPDGRDNVRCRGQRIDVPEGRWDWVHVLGAAERRTEDPLLLRYADGTVRPQWLRMSDfWPETEPRFGELLAYRCATMHYPRHVQRTTAPAIWAQRVPLSVPDGVVALELPDNPALHLFAITLQAGERV--------
+>UniRef100_A0A7K2T631_2690338/	151	0.423	5.207E-37	36	222	233	1	188	195
+------------------------------------TTSTTAPVPLDLTALADNVGVTRPDRLSDGAFNIWGNTFPADELP-PAGPVEVHGVPFRWPaTGGGAPDNVRCRGQLVPVPEGRYDWIHVLAAAERRTEDPLLLHFADGGVDPEWLRVSDfWPETSSRFGERPAFSCTRLHYPRHVQHAMGPTVWHQRVPVTREERLRAFRLPDNPAIHLFAITLAPSA----------
+>UniRef100_UPI0020D28210_193462/	151	0.423	5.207E-37	42	221	233	6	189	195
+------------------------------------------STVVDISEVCDNRGITKSGAEESDGFNIWRNTFPAEDLPAPGSSVEVTGVAFEFPaRATGRGDNIRCRGQLLPLPGVRADWLYLLGAAERRTEDEVELHYADGAVRTAWLRMSDfWPETAAWFGEPEAFRGSGLRYPRHTQDGHRPAIWQQRVPVTVPGELTALRLPENPAMHVFALTavLEPG-----------
+>UniRef100_A0A2N8NVN7_66423/	151	0.424	5.207E-37	33	221	233	3	194	202
+---------------------------------LPARADrrQTEAVPVNLAGLADNTGITRADALSEGAFNIWGNTFPADELPT-GGPVVVDGVPFLFPEaAPGRPDNVRCAGQLIEVPTGRYDWIQLLAAAERRTEDQVLLHYADGSVDPEWLRVPDFWPETGSrVGGSPAFTCTRMHYPRHVERKMGPVIWRHRVPVPRESDLGAVRLPDNPAVHLFAMTLLPA-----------
+>UniRef100_A0A9E3EXL3_2740538/	151	0.250	5.207E-37	51	216	233	551	729	733
+---------------------------------------------------YNNAGISDDSNTTSANFDGGGYSYSAQSLQAagitPGGSVTTKGVTFTWPNvASGVADNYQTNGQTIPVTPvsGATTLAFLGSATNGPSSGTATITYTNGSTQSFSLGFSDWTlnanTASASFGNAIAATLSYRNGANG-RDNVNTYVFYADITLQAGKTLKSVTLPsttNQGRLHVFAI----------------
+>UniRef100_A0A840IWR6_1181879/	151	0.287	5.207E-37	52	218	233	903	1081	1083
+----------------------------------------------------DNAGISPDSDPSAGNFDGGGWSYSADALaeagAKPGGTVTSDGIDFTWPSYPaGDPDNVVAAGQTVNVTGSG--KLALLGSSSNGnAEGTLTVTYTDGSTSTATVGLSDWTlgggDAEPAYGNKSVLSTSYRNSSGGDPQEISTVVFATTpITLDAGKTVASVTLPDDvdgGAMHVFALGL--------------
+>UniRef100_A0A941IQY1_1508375/	151	0.262	5.207E-37	47	219	233	1034	1218	1510
+-----------------------------------------------LTAAFNNSAITSDGNRGCANLDGAGASYSQQALAsvgvTPGTALVHDGLTFTWPSGGAcDADNVVAAGQTIDV-SGSGSTLGFLGTSAWGAiSGTGTVTYTDGTTQPFTIGFGDWANGTPPTGDDIAIRAPYGNQP-GNQTSWQTTIEYAPVQLDPSKTVQSITLPPGnpqpsggiPSMHIFAMSIK-------------
+>UniRef100_C7QK71_479433/	151	0.480	7.120E-37	44	218	233	15	189	195
+--------------------------------------------PVDISGHHNNKAISAATETKAGAFNVWGNSFAAEYLPAGGSIVEVDGVPFRFPQAGDGPDNIRTAGQFITVPEGRYDWIHLLAASERRTEDCMDLSFADGSVDAEKVRVSDFWGAPAWFGEVKAFESLTMHYPHHVQRGVPAMMWAQRVPVTRRAVLSGILLPRNVALHIFAVTL--------------
+>UniRef100_C7PW55_479433/	151	0.248	7.120E-37	47	220	233	547	726	727
+-----------------------------------------------LAGAFNNTAITDETNTAPGNFDGDGDSYSAQSLatagATPGATISAGGTTFTWPSaAAGTNDNVAGSGVMVNL-AGQGSKLGFLGSEAGFSTDTVTVAYTDGTSSTGSLGFPNWCCSSPtGYGATPAIVTDHRNTPSGPANFGTAYdVFYNSIAIDATKTVKTVTVPSDPAIHVFAMTVQP------------
+>UniRef100_A0A1V2PT88_1933779/	151	0.315	7.120E-37	33	231	233	723	921	924
+---------------------------------LPPLPNQGTTVTVDLAAVLNNDAFTNEFHMGDGDFDGAGNTYPAAQLPQTGQA-NDDGIPFEFVNGNeGAPNNIVPQAQTIQLPPGKYTTVHLLAASDNGNTDrTVTINYADG-AANAPLRITDW-RTAPAFGETEALRTNQMHTRTGPSPTR-LAIFHQKITLDPVRDLVSITLPaaATPRPHIFAITLQKKSSAAPAEGGD-
+>UniRef100_UPI00207D370E_2944808/	151	0.279	7.120E-37	15	221	233	764	967	972
+---------------IAPVTVTTPAAPWGLPPLPPG----GDMVTVDLEPFYTNDGITNEFYLGDGDFDGTGRTYPSGALPQNG-SLSNDGVPFRFTNGhEGTRNNVTAAGQTLELPEGNYRKLHLLGASDNGNTDaTATLHYTDGGTAPVRLALTDWLSP-AAFGESEPLRTNQIHTRTGPVDRRAT-VFHQVLAADPTRRLRAITLPASakPRSHVFAVTLEKA-----------
+>UniRef100_A0A1C5JFJ4_47864/	151	0.457	9.734E-37	44	218	233	15	189	195
+--------------------------------------------PVDISGHRNNTAVSAATETKAGEFNVWGNSFAAEYLPKGRSTVHVDGVPFLFPPVCEGPDNIRCAGQFIEVPEGRYDWVHVLAASERRCEDTVDLNFADGSVDAEALRVSDFWAAPAWFGEVKAFQSLVMHYPHHVQRGVPAVMWAQRVPVTRRADLTGILLPRNVAVHVFAVTL--------------
+>UniRef100_UPI00143C2064_1431344/	151	0.465	9.734E-37	45	218	233	16	189	195
+---------------------------------------------VDISGHRNNVAISAATRTRDGAFNVWRNSYAAEYLPTGGSTVRVGGVPFTFPPVCDGPDNVRCEGQFIPVRRARYDWIHLLAASERRCEDTVGLDFADGTADAEPLRVSDFWAAPAWFGEIKAFESPAMHYPHHVQRGVPAVMWAQRVAVTRRADLTGILLPRNVAVHVFAVTL--------------
+>UniRef100_A0A660RIY0_28240/	151	0.242	9.734E-37	41	221	233	380	568	581
+-----------------------------------------DFTILDISSFFNNDGIASFKHPRYGNFDnhsgIYGATYPLEELQnymNENGRLEVDDIPFVLKGLEGhMKNNTALQGEKIYLPEGRYSYIYFLGSSEHGSfRAPVTFEYSDGSRQTDDSGFSDWCQG-PQLGEKIACKMPYRYDSNGSRQSITCYLFMQTLKLAPKKELITILLPRKNTMHIFAITLRKS-----------
+>UniRef100_UPI001CB7FD65_1930280/	150	0.457	1.331E-36	44	218	233	15	189	195
+--------------------------------------------PVDISGHRNNTAISAATETRAGKFNVWGNSFAAEYLPEGKSLVHVDGVPFEFPPVCEGPDNVRCAGQFIRVPEGRYDWVHVLAASERRCEDTVELNFADGSVDAEPLRISDFWAAPAWFGEVKAFESLVMHYPHHVQRGVAAVMWAQRVPVTRRAGLTGILLPRNVAVHVFAVTL--------------
+>UniRef100_UPI0006902850_348818/	150	0.243	1.331E-36	47	220	233	552	731	732
+-----------------------------------------------LAHAFDDVGVSDESDTAPGNFDGDGDSYSAQALAAagvtPGATLSANGYTFTWPSaAAGAPDNVAGGSPTIEL-SGSGSRLAFLGAEAGFTSDTVTVHYTDGSSSTGTLGFPNWCCGaTDSYGAKTAFTTDHRNTPTGpANYGVSYRLYTNAIPLTAGKQVASVTLPSSSAIHVFAMAVQP------------
+>UniRef100_A0A832K4Y2_2282144/	150	0.279	1.331E-36	41	218	233	25	200	1038
+-----------------------------------------DFLLLDLTSYFNNNGAATEENPSEGNFDYGGFSYAFELLPKPG-KVSVKEIPFIFPQTSQEGNNIACHSQVIKIQPDRYRAILLLGSSTNGDYEaCLWVQFSDGSRSCLKTGLTDWCRDS-VFGEIPAFSFPYRIGPEG-RQEIQNYIWLQVLRIKEEKFLSAIILPENKNIHIFAITL--------------
+>UniRef100_UPI000B17B6CC_28444/	150	0.474	1.819E-36	44	218	233	6	180	193
+--------------------------------------------PVDISGHLNNTGISAATDTKSGAFNVWGNSFAAEYLPGGGDLVHVAGVPFRFPPVGDGPDNIRCAGQFLTVPEGRYDWVHVLAAAERRCEDVVETHYADGSVDAEPLRVSDFWAAPAWFGEVKAFESLVMHYPHHVQRGVSAVMWAQRVPVTRRADLTGLRLPRNAAVHLFAVTL--------------
+>UniRef100_A0A7W3TA43_1472722/	150	0.477	1.819E-36	45	218	233	15	188	194
+---------------------------------------------VDISGHRNNTAVSAATETKAGEFNVWRNSFAAEYLPAGGSLVHVDGVPFRFPPLCEGPDNVRCAGQFIRVPEGHYDWIHVLAASERRSEDTVQLNFADGSVDAEALRVSDFWAAPAWFGEIKAFESLVMHYPHHVQRGIPAVMWAQRIPVTRRTGLTGILLPRNVAVHVFALTL--------------
+>UniRef100_UPI0006C193CE_1415555/	149	0.390	2.487E-36	43	227	233	5	191	193
+-------------------------------------------TVVNLSAHFNNRGIQPPDTPGDYGFNIWRNTFPAEELPEPGSLVDLVGAVFEFPaRASAAGDNVRCRGQLVELPGGRWDWIGLVGAAERRTEDEVELHYADGTVRREWLRMSDfWPQTAAYFGEPRAFVTGGMRYPRHTHPHHAPSIWQQRVPVRVPAPLAAVRLPDNPAMHVFAMTVTADEESRLA-----
+>UniRef100_A0A977Y500_2809700/	149	0.418	2.487E-36	42	218	233	11	187	200
+------------------------------------------YHAVDLAPYSNNVGISAAGHTSRGAFNVWGNSFPAEHLPESGAPVSVGGVPFRFPRVGVGDDNVRCDGQFIAVEAGRFDWLHLLTASERRAEDVVEMHFANGSVDPEWLRVSDFWAAPAWFGEATAFATPVMHYPHHVQRGVSAMLWSQRVPVTRRADLSGFRLPRNAAVHVFAATL--------------
+>UniRef100_UPI00189254C3_280293/	149	0.243	2.487E-36	47	220	233	554	733	734
+-----------------------------------------------LASAFNNIAISDETNPGPGNFDGDNDSYSAQALAAagatPGASIKAGGTTFTWPsSATGTNDNVAGSGVLVNVT-GQGSKLGFLGAEAGFATDTVTVTYTDGSSGSGSLGFPNWCCSSPtAYGATPTIVTTHRNTPSGPANfGIDYDVFYNSIAIDATKTVKTVSVPNDPAIHIFAMTVQP------------
+>UniRef100_UPI001E52087D_2714956/	149	0.259	2.487E-36	2	217	233	772	1005	1010
+--SWLPESlFLNGGTVTVEVgskantgwgtkaaDLPVDRMPTapAPVPNLPtACVVQGSNCLQSLAGQYDIDGVTTDDNMGQGVFGTNGWSWPAELLPAPG-VGTAAGRPYLFPDTTGtAGNFLSARGQTIHLTPGRYSALDAVTASHNGNyRGDVTVTYSDGTTSKASLMSTDWAAAAPAYGEETAIDVPTRHRNTGIHDGLRVRMWHVALAVDSTRTAVSITLPNLPNMKVYALT---------------
+>UniRef100_A0A557ZXY0_715473/	149	0.264	2.487E-36	52	216	233	868	1044	1048
+----------------------------------------------------NNAGISPDAKPAAANFDGVGFSYSSDALAAagakAGSTVTVNGLSYSWPNYPaGSPDNVIAQGQTVNV-SGSGQLAFLGAAANGNASGTVTVTYTDGTTSTANLGFSDWTLGagaaQPAFGNQVAFRTPYRNSVGGDSQQINTYVFAsAPIALAAGKTVKSVTLPSSvsgGQLHVFAI----------------
+>UniRef100_A0A0N0T605_1519492/	149	0.437	3.401E-36	44	218	233	2	175	180
+--------------------------------------------PIPLAPHLNNTGLTGADGLDGGGFNIWGNTFPAGELPPSGSTTVVHDVPFLFPAA--GADNVRCRGQRVEVPPGRWDWVHVLGAAERRTEDLLEVHYSDGSVRGQWLRMSDfWPQTEPRFGELLAFRCRHMHYPRHVQRTMSPSIWAQRVPVTVPSDVVALVLPDNPALHVFALTL--------------
+>UniRef100_A0A918SWL6_67368/	149	0.385	3.401E-36	43	227	233	5	191	193
+-------------------------------------------TVVNLSAHFNNRGIQPPDTSGEYGFNIWRNTFPAEELPEPGSLVELEGTVFAFPaRDTGAGDNVRCRGQLVELPAGRWDWIGLVGAAERRTEDEVELHHADGTVRREWLRMSDfWPQTAPYFGEPLAFSTSGMRYPRHTHRHHAPSLWQQRVPVRVPAPLAAVRLPDNPAMHVFAMTVTADEESRLA-----
+>UniRef100_UPI0012EAE0B8_2654677/	149	0.413	3.401E-36	42	225	233	6	191	195
+------------------------------------------STVVDISEACDNRGIAKSGADESYGFNIWRNTFPAESLPAPGSSVAVAGVTFEFPaRESGRGDNIRCRGQLLPLPAVRPDWLYLLGAAERRTEDEVELHYADGAVRTAWLRMSDfWPETAAWFGEPEAFRTSGLRYPRHTHDGHRPAIWQQRIPVTVAGELTALRLPDNPAMHVFALTAVREPGVR-------
+>UniRef100_A0A428Z1R9_2030/	149	0.327	3.401E-36	45	220	233	733	908	910
+---------------------------------------------VDLAAALNNDGFTNEFQMNDGDFDGAGNTYPAAQLPQTG-HAEDDGIPFEFVNGNeGAPNNIIPAGQTIQLPPGKYPTMHLLAASDNGNTNTkLTVTYADGTAQ-VPLQITDW-RASPAFGETEALRTRQMHTRTGPAETR-LSIFHQKVPLDPARELLSITLPaaAKPRPHIFAITLQK------------
+>UniRef100_UPI0019405FD2_566021/	149	0.472	4.649E-36	41	221	233	2	182	190
+-----------------------------------------EQVPIELAAHLNNAGITPASDTGRGRFNVWRNSLPGEELPL-GRPFTAGGVRFAFPAAgPGRPDNVRCEGQLVTVPPGRYDWCCLLAAGERRVEDEVALHFADGSVDFEPVRVSDFWAASAVFGEEEAVATSVMHYPQHVQPGVTAHIWCQRVPVTRRAELRRLRLPHNVALHVFAATLCPS-----------
+>UniRef100_UPI001AEB6BB5_882444/	149	0.457	4.649E-36	44	218	233	12	187	194
+--------------------------------------------PVDLSAYFNNTGATAKSDLARGRLNVWQNSFPAEELPDAG-IFVATSVPFEFPAiGPGRHDNIRCAGQRVELPAGRWDWIYLLACSERRSEDVLQLHYTDGTVDAEWLRVSDfWPASPPHFGEVEAIRCEQMHFPRHIQPRVGPRIWQQRVPVPRQHDLAALRLPDNIAIHVFAMTL--------------
+>UniRef100_UPI001C40B55E_200378/	148	0.497	6.356E-36	43	217	233	6	182	190
+-------------------------------------------VPIDLGPLFNNIGATVETDLGRGGLNVWKNSLPAADLPAAGSLFRYTDVPFRFPEvGSGLPDNVRCEGQRVDLPPGRYDWIYLLACSERRSEDVVHLHYASGEADDEWLRVSDFWAAAPShFGEVEAVPCSRIHFPRHVQRGIAPRIWQQRLPVPRQQPLAYLRLPDNIAIHVFAMT---------------
+>UniRef100_A0A7K2ZJK9_2690253/	148	0.464	6.356E-36	44	224	233	15	195	197
+--------------------------------------------PVDISGHRNNTAISAATETKAGAFNVWGNSFAAEYLPAGESLVHVDGIPFRFPPVCEGPDNVRCAGQFFGVPEGRYDWLHLLAASERRCEDTVELHFADGTLDAEPLRISDFWSAPAWFGEVKAFESLVMHYPHHVQRSVSAVMWAQRVPVTRRAVLTGVRLPRNVAVHVFAATVQRTEGA--------
+>UniRef100_UPI001BA8A0F4_2802641/	148	0.274	6.356E-36	36	220	233	30	212	765
+------------------------------------ASDAPNPVPVPLDGLFDNDGI-DTATTHDGNFDGSGYTFPAEGLPS--GQVTVDGVPFTFPSATGK-NNIVAMGQQIPLPQGRYvTALFLTACSYGATGGTATIHYADGSTSEAQLGGADWYSG---SGQLVA---PFRYTPGGRTDQSPVSISTSQVWIDPNRDAVAITLPTTspavegkSSLHIFALSLQP------------
+>UniRef100_UPI001F2867CD_211113/	148	0.322	6.356E-36	45	220	233	733	908	910
+---------------------------------------------VDLAAVLNNDGLTNEFQMNDGDFDGAGNTYPAAQLPQTG-YVEDDGIPFEFVNGNeGAANNIVPIGQTIPLPPGKYPTMHLLAASDNGNtTTTLTVTYTDGAAQ-VPLQITDWRTP-PAYGETEALRTRQMHTRNGTAETRLT-IFHQKLQLDPARDLVSITLPaaTKPRPHIFAITLQK------------
+>UniRef100_A0A563EK61_2591470/	148	0.295	6.356E-36	5	223	233	739	949	950
+-----HPDFTIAPVKITE-PARAWGLPALP----PGGVAA----PVDITGLFDNDGLSNEFTSRDGDFDGAGNTYPAAQVPQTGG-VTDDGIPFEFTNGDEaSKNNVIAAGQTIAMPAGRYAKLHLLAAADTGNVDaPGVATYVDGTTAPIRFAVTAWRSG-PQFGESEPITTTLMHTPSGPQQA-KVAIFHQVIGLDPARDLASITLPKlaGPRLHVFGITLEKAKA---------
+>UniRef100_A0A7V2UGE7_2026780/	148	0.264	6.356E-36	41	219	233	33	223	1084
+-----------------------------------------GQVPLNLEGLFDNDAIADAQRRADGNFdcpdhaaDIPGSVFPAENLPATGSKFSFDGIHFLFPSKErGDLNNVACEGQRIDVPPARYKALHIIGTSENGSfRDSLQLAYKEG-PAEAELTLRDWCQ-KPAAGDRVAFEAPCRYTwspqkRGMIREEIQPRIWRQTIPLDPAKTLEALTLPYNRRMHVFAATLE-------------
+>UniRef100_A0A919S905_113560/	148	0.440	8.688E-36	45	227	233	5	188	190
+---------------------------------------------IDLSGFFTNRGLQPPGTTGDYGFNIWSNTFPAEELPPAGTVADVAGVPFSFPPDAATGDNIRCRGQVIPLPEGDWDWIYLIGAAERRTEDRVELRYRDGSVRPAWLRMSDFWPETPmRFGEPLAFRTRSMRYPRHTHRNHAPALWQQRIGVAQPEDLAAVRLPDNPAMHVFALTLVADEEARCA-----
+>UniRef100_UPI0019447DF0_113566/	148	0.445	8.688E-36	45	227	233	5	188	190
+---------------------------------------------IDLSGFFTNRGLQPPGTTGDYGFNIWSNTFPAEELPPAGTVADVAGVPFSFPPDAATGDNIRCRGQVIALPAGDWDWIYLIGAAERRTEDQVELRYRDGSVRPAWLRMSDFWPETPvRFGEPLAFRTRSMRYPRHTHQNHAPALWQQRIGIAEPGNLSAVRLPDNPAMHVFALTLVADEEARCA-----
+>UniRef100_UPI001FEC609C_2508722/	148	0.477	8.688E-36	44	223	233	15	194	197
+--------------------------------------------PVDISGHRNNTAVSAATDTKAGRFNVWGNSFAAEYLPAGGSLVHVAGVPFRFPPVCDGPDNVRCEGQFLEVPEGRYDWVHVLAASERRCEDTVGMHFADGAVDAEPLRVSDFWAAPAWFGEVRAFESLVMHYPHHVQRNVSALMWAQRVPVTRRAGLTGVRLPRNIAVHVFAVTLQRTEA---------
+>UniRef100_A0A6G7PB94_2714844/	148	0.482	8.688E-36	45	218	233	19	192	198
+---------------------------------------------IDISDLRNNAAISSAVETGAGAFNVWRNSFAAEYLPAGGSLVHVDGVPFEFPPVCEGPDNIRCAGQFIKVPRDRYDWIHVLAASERRSEDTVELTFADGSVDAEPLRVSDFWAAPAWFGEVKAFESLAMHYPHHVQRGVPAVMWAQRVAVTRRADLTGILLPRNVAVHIFAVTL--------------
+>UniRef100_A0A4R0HF04_1124743/	148	0.394	8.688E-36	25	218	233	35	228	237
+-------------------------MPDQMPDQMPATSVQARCRAVNLAPHRNNVGSTPATDTRGGAFNIWGNSFPAEELPAPGQ-FVVDQVAYDFPPTGrGTADNVRAAGQFIEVPSGRYDWLYVLGAAERRVEDELAFHFADGSVDFEQLRLSDFWAAPGWFGETQVRATRSMHYPFHVQAGVPAMLWSQRVPVTRRAALAAVRLPRNPAVHLFAATL--------------
+>UniRef100_A0A3E0IAZ0_1045776/	148	0.284	8.688E-36	36	220	233	31	213	766
+------------------------------------ASDAPNPVPVPLDGLFDNDGI-DTATTHDGNFDGSGYTFPAEGLPS--GPITVDGVPFTFPAATGK-NNIVAMGQQIPLPKGRYvTALFLTACSYGATGGTATVHYADGTTSQAQLGGADWYSG---SGQLVA---PFRYTPGGGTDQSPVSISTSQVWLDPARDAVAITLPTTnpavegkSSLHVFALSLQP------------
+>UniRef100_UPI000DE266A4_2249762/	148	0.264	8.688E-36	33	221	233	747	936	938
+---------------------------------LPPIQPPGETTPVDLSAHFDNDGVSTHENMADGDFDGTGRTYPAEELPPAGPYL-HQGVSFLIPSfADGAHNNLTARGQVIAVPPGRYARLRLVGACAYGSLDTkLIATYADGSTAELPFVMSDW-AGQPAAGGSEVTRCTHRHGKAG-PDALKVALFEVPIALDPARELRSITMPVRvkPQLHVFALSVEKS-----------
+>UniRef100_A0A7L6B3W5_2749844/	147	0.422	1.188E-35	45	217	233	14	188	196
+---------------------------------------------VDLSACFNNTAATTPETTGAGGLNVWRNSFPIEELPDATEVFRPGAVPFRFPRTgPGRLDNVVCAGQRIDLRPARYDWIYLLACAERRIEDVVHLHYRDGSVDEEWLRVSDfWPASPPRFGELEAVRCDRIHFPRHVQPGIGPRIWQQRLPVPRQEELVYLRLPDNIAVHIFAMT---------------
+>UniRef100_A0A2M7SAS6_1974543/	147	0.279	1.188E-35	35	220	233	24	215	216
+-----------------------------------GAGGGAGCVPVDISKLCNNDGIAPDDDATGGDFDAGGASYTAKAWPKVGKTgVTVNGVPFLVAGADKKVNNIACEGEAVQVPAGSYKAILMLASATNVPEGSmedaLTLVYKDGTKSAVNFKLTDWC-VEPKEGEKKAYSFTYRmsTGTEGGHHEIPCYLFLQTVKIDGKKELASIRLPEQKDIHIFAITLQK------------
+>UniRef100_A0A938MG41_2026780/	147	0.286	1.188E-35	43	218	233	67	249	254
+-------------------------------------------TLLDLAAAFNSDGISTEENAKDGNMDApgkpNGASYPKDELPAAHSLLTLKGkpvMTFLFPDGqDGKLNNIACSGQTVHVPAASYVELWVLGAATYGAQtSDLELRYEDGS-ETEPLELSDWC-ETPGFGERQAVVAKHRHGWKGEEEDIPCGLWAQRVPLDAKRKLVALVLPQNAKMHIFALSL--------------
+>UniRef100_A0A938S8T3_2026780/	147	0.286	1.188E-35	43	218	233	743	925	930
+-------------------------------------------TLLDLAAAFNSDGISTEENAKDGNMDApgkpNGASYPKDELPAAHSLLTLKGkpvMTFLFPDGqDGKLNNIACSGQTVHVPAASYVELWVLGAATYGAQtSDLELRYEDGS-ETEPLELSDWC-ETPGFGERQAVVAKHRHGWKGEEEDIPCGLWAQRVPLDAKRKLVALVLPQNAKMHIFALSL--------------
+>UniRef100_A0A5N0UUJ1_2596893/	147	0.258	1.188E-35	52	216	233	884	1060	1065
+----------------------------------------------------NNAGISPDAQPGVANFDGVGFSYSSDALAAagatPGGTVTVDGLSYTWPNYPaGDPDNVLAQGQTVNV-SGSGRLAFLGAAANGNASGTVTITYTDGSTSTAQLGFSDWTLGAGaqqlAYGNVKAVTTSYRNSTGGDTQQIGTYVFAsAPITLDSGKQVASVTLPSSvsgGQLHVFAI----------------
+>UniRef100_A0A2H5B2X5_2018025/	147	0.488	1.624E-35	45	218	233	15	188	194
+---------------------------------------------IDISGHRNNTAVSAATDTGAGAFNVWRNSFAAEYLPAGGSLVEVDGVPFDFPPVCQGPDNVRCAGQYLEVPRDRYDWIHLLAASERRCEDTVELTFADGSVDAEPLRVSDFWAAPAWFGEVKAFESLTMHYPQHVQRGVPAVMWSQRVAVTRRVDLTGLLLPRNVAVHVFAVTL--------------
+>UniRef100_A0A5C4LYC7_2547244/	147	0.269	1.624E-35	52	216	233	867	1043	1050
+----------------------------------------------------NNAGISPDAKPAAANFDGVGYSYSADALAAagakAGSTVTVNGFSYTWPAYPaGSPDNVIAQGQTVNV-SGSGQLAFLGAGSNGNASGTVTITYTDGSTTAASLGFSDWTLGgggaQPAFGNQKAFTTSYRNSVGGDPQQINTYVFASTpITLSAGKTVQSVTLPSSvsgGQLHVFAI----------------
+>UniRef100_A0A0K3B8B7_703222/	147	0.259	1.624E-35	47	216	233	898	1082	1086
+-----------------------------------------------LRSAYNNVGISPDNAMASANFDNVGFSYSANALAngglKPGGTVTVDGLAHTWPITDiGEPDNVVAGGQTVNVQaQSGASKLALLGSAANGtASGQLTITYTDGSTQQAQVGFSDWTLGgggqQPSFGNRIAATSSYRNSVNGSSQGLNTYVFATEpVGLDPSKQVKSVTLPPTvsgGTLHVFAL----------------
+>UniRef100_A0A8J3I4R3_2778364/	147	0.284	1.624E-35	51	216	233	1027	1201	1205
+---------------------------------------------------YNNVGTSDDSAPSFGNFDAQGNSYSAQALQQvgliPSQNVTVNGVTFIWPNmAPGYFNNYQAAGQTIGVTPidGATTLAFLGSASNKGSSGTATITYTDGSTQTFTLGFTDWVTSTLSYGNSIAATMSYHNASTGKQTG-NTYIFYTSVTLQAGKTIQSVTLPatfTGGQPHVFAI----------------
+>UniRef100_UPI00143BFCD2_2720606/	147	0.482	2.219E-35	45	218	233	4	177	183
+---------------------------------------------IDISGHRNNTAVSAATETTAGEFNVWRNSFAAEYLPAGGSLVHVDDVPFRFPPVCEGPDNIRCSGQFIRVPEGRYDWIHVLAASERRTEDTVELSFADGSVDAEALRVSDFWAAPAWFGETKAFESLVMHYPHHVQRGIPAVMWAQRVPVTRRTGLTGILLPRNVAVHVFALTL--------------
+>UniRef100_UPI00058392A0_703222/	147	0.312	2.219E-35	33	220	233	726	913	917
+---------------------------------LPKLPDQGSTVPVDLVAALNNDAFTNEFHMGDGDFDGAGNTYPAAQLPQTGQA-SDDGIPFEFVNGNeGAPNNIVPAGQQIALPPGQYTTLHLLAASDNGNtNAKLTVTYTDGTAQ-VPLQVTDW-RAAPAYGETEALRTSQMHTRTG-PQPVRLSIFHQKIPLEEARHLVSIALPaaATPRPHIFAVTLQK------------
+>UniRef100_A0A9E9FHN1_2979468/	146	0.434	3.034E-35	39	221	233	1	183	192
+---------------------------------------AADFQCIDLSAWYNNVGLTRPDNTSAGAFNVWRNSLPAPELPC-GQRVTVEGVPFLLPPADGnRYDNVRCDGQVAPVPRGAYDWVYLLTTAERRVEDEMSLHFADGAVDFEPLRVSDFWVAPAVFGETAAFTTTVMHYPRHIQRNVPATVWSQRVPVTRRGRLRAVRFPDNLAVHILAMTLCEA-----------
+>UniRef100_UPI001E6135CD_1617086/	146	0.480	3.034E-35	44	218	233	18	192	200
+--------------------------------------------PVDISGHRNNTAISAATETKAGAFNVWGNSFAAEYLPAGGSLVHVDGVPFEFPPVCDGPDNIRAAGQFIGVTPGRYDWIHVLAASERRCEDTIELSFADGSVDAEPLRISDFWAAPAWFGEVKAFESLVMHYPHHVQRGVPAMMWAQRVPVTRRAELTGILMPRNVALHVFAVTL--------------
+>UniRef100_A0A9E3BI44_2740538/	146	0.268	3.034E-35	31	217	233	734	926	930
+-------------------------------PSFPPAATGGNS--------FNNEGTSNDSNTAVGNFDGGGNSYSNNALSaagfASGSTVMVNGISFQWPTvAAGSDDNWQVAGQGIPVNgrSGATTLAFLGAATSGPSSGTIMVTYTDGSTQTFTLAFSDWTlnggRSTILSGDSIAVQMSYRNTPTGQQTNHPTYVFLTSVTLAAGKTVKSINLPssvSQGTMHVFAIS---------------
+>UniRef100_A0A941IQY1_1508375/	146	0.278	3.034E-35	33	215	233	1314	1504	1510
+---------------------------------LSGAATQVPYS--SLAAGFNNVSITDDSDHSptgfDGGLDGGGNSFSAEALAAagltPGTDFTFDGVVFTWPNsAAGTPDNIEADGRAFDVTGTGSTLGFLGAAANGASSGTVTVTYTDGTTQQFTIGFGDWASTTPYAGGQVAVTSAYGNTSSGTS-PWKASVFYDSVTLPAGKTVQSVSLPTAGSapLHVFA-----------------
+>UniRef100_UPI0018E54A72_714197/	146	0.443	4.147E-35	45	218	233	1	176	190
+---------------------------------------------VDLSRYCNNRGIQPPGSSGEYGFNIWGNTFPAEELPEPGTRVGVCGVPFEFPvGAAPSGDNVRCRGQLVEVPPGDYDWVYLLGAAERRTEDHLGLVYADGTELAEHLRMSDFWPETGSrFGEPLAFRTTALRYPRHTHTPHEPSIWQQRSPVSVRGRLRALRLPDNPAMHVFAVTL--------------
+>UniRef100_A0A1R0KG38_76021/	146	0.390	4.147E-35	40	224	233	3	189	192
+----------------------------------------AGMRSLSLLEHVNNTGLSAVDDLAAAGFNIWGNSFPAADLPAPGATSVVGGVSFRFPeRAPDGRDNVRCRGQRIAVPEGRWDWVHVLGAAERRTEDPLLLRYADGAVRAQWLRMSDfWPETEPRFGELLAYRCAAMHYPRHVQRTTAPAIWAHRVPLTVPDGVVALELPDNPALHLFAITLQAGERV--------
+>UniRef100_A0A1K1S937_546364/	146	0.289	4.147E-35	40	227	233	46	234	781
+----------------------------------------PPPVPVALDTWFTNDGIDSASATG-GDFDGSGYTFPAEQLPV-GRTATVGGVPFRLGSaAAGAKNNIAATGQTIDLPKGRYFVAYFLVAASYGtAGGTATVHYADGSTSTGSLSGPDWYTGTG------ALVSPFRYAPGGVVDGNPVSLATGQVWIDPAREAVALTLPTTANpapnvasLHVFALTLQPVAVGRAA-----
+>UniRef100_UPI001AE5AA53_130796/	146	0.301	4.147E-35	39	220	233	768	950	953
+---------------------------------------GGDTVRVDLEPHHTNDAITNEFYLGDGDFDGTGRTYPSGQLPQNGA-LTNDGIPFTFTNGhEGTRNNVLAAGQTIPLPEGAYTRLHVLGASDNGNTDaQATLHYTDGTAATVRLALTDWL-TSAAFGESEAVRTNQIHDRTGPR-PRRASVFHQVLPVDPARRLRALTLPttTRPRAHVFALTLEK------------
+>UniRef100_A0A7I8EN04_2717365/	146	0.263	4.147E-35	43	227	233	43	230	968
+-------------------------------------------TPVSLSSLFNNKGVG--GAPGQANFDGSGYAYPANQLPGAGQQ-TLNGIPYLFPNYsAGANDNVVALGQTVSLSPGeqqQYQQISLLaAASYGPSGGTLTIHYTDGSSSSVSLTVSDWYTPTAG-----LVSTTYRYTPTGTEQ-HAVHIYALSALVDATRTVASLILPNtaqpaagQASLHIFALTLLPSTQVPVP-----
+>UniRef100_UPI002020D29A_211113/	146	0.240	4.147E-35	19	214	233	835	1059	1065
+-------------------SVAVRVEPGTPeatyqvVVQFTGPQGVLQSAPLqilvaqpgSLRSVYNNVGISPDNAMASANFDNVGFSYSANALfnagLKPGGTVTVDGLTHTWPvTAVGEPDNVIAGGQTVNVPaAAGATKLAFLGSAANGtASGTLTITYTDGSTQQAQVGFSDWTLGgggqQPSFGNRKAVTSSYRNSVNGSSQGLNTYVFATEpVALDPSKQVKGVTLPSSvsgGTLHVF------------------
+>UniRef100_A0A495L449_2183912/	145	0.437	5.669E-35	42	217	233	17	192	209
+------------------------------------------WAPVDLRAHVDNRGISPADESAAGAFNIWGNSFPSEHLPRAGSRVEVEGVPFEFPVSSDNGDNVQCAGQLVSVPVERYDWIYVLAAAERRAEDEAALHFTDGWVDFEPLRVSDFWAAPSVFGEVSAYRTPVMHYPHHVQPGVQAALWCQRLPVVRRAALTSIRLPRNNAVHVFAMT---------------
+>UniRef100_UPI001C636FC7_1291556/	145	0.410	7.748E-35	55	220	233	1	167	172
+-------------------------------------------------------GIEFTRRPGDGAFNIWRNTFPAEDLPR-GEIVDVGGVPFCFPAADGRhPDNLRCRGQRIELPVGRVDWLCFLAAAERRTEDTLSVHYADGATRAQWLRVSDfWPETPPRFGDVLAFRTPYLLYQRHAQSGMAPAIWRQRVPVTIPGDVAAVTLPENPAMHIFALTLLT------------
+>UniRef100_UPI00099B8A4C_89050/	145	0.275	7.748E-35	32	224	233	836	1038	1167
+--------------------------------WASGASAAPPSYA--GSPTYTDVGVSDDASPAAADFDGVGNSYSAQALAAagasPGAKITAGGTTFTWPtPAAGQPDNYEANGQSVAVSGSG--SIAFLGAANHGPStGTATVHFTDGTTQSVQLTFSDWTLGggkaTPAAGDTTALTTSYRNKTGASSEQVATYVFAtAPVALPSGKTADSVRLPSDtsaGGLHVFAIGFGGAAAA--------
+>UniRef100_A0A6H9XE76_1873/	145	0.427	1.059E-34	33	218	233	0	185	195
+---------------------------------MPTSATIAAHV-LDLASHFNNVGASRAEDTSAGRFNVWGNSFAAEHLPSAGSQVVVDGVPFQLPPlGTGTPDNVRCDGQFVRVAPGRYDWLYLLASAERRVEDEMALHFAHGAVDFEPLRVSDFWAAPATFGETRAFESPLMHYPHHVQFGVPAAMWCQRVPVVRRADLTAVRLPHNIAVHVFAATL--------------
+>UniRef100_K0JYB8_1179773/	145	0.428	1.059E-34	37	224	233	6	193	196
+-------------------------------------TGHDVFCSVDIAGHRNNVGITSVGGTGVGGLNVWRNSLPAEQMPC-GEVVVLDGVPFEFPTAgSGEPDNVRGDGQLLELPAGYYDWVHLLACGERRVEDELALYFTDGSIDFEHVRVSDFWAAEPVFGETSALRSTVMHYPQHVQPRVPGIIWAQRVPVPRRAELKAVRLPRNVALHVFALTAQRATGA--------
+>UniRef100_A0A8J3IWF3_2778369/	145	0.229	1.059E-34	47	217	233	916	1098	1101
+-----------------------------------------------LLSYYNNIGISNDSSANTADFDGDGYSYSAQQLTsagfTPGATVTVSGIAYTWPNVqPGVYDNIEVNGQTIQTPnaPANAAHLSFLGSATNGDtQGTVTITYTDGSTQTAQLGFSDWTLGagaePVAYNNVVAAKTSYRN----PNDKVTTYVFASeSIALSSGKTVASITLPNPMNMgalHIFTFT---------------
+>UniRef100_A0A1V2RDC8_1857892/	144	0.434	1.448E-34	39	221	233	1	183	192
+---------------------------------------AAGFTCVDLSAWYNNVGLTRPDNTSAGAFNVWRNSLPAHELPC-GQRVTVEGVPFVLPQADGdRCDNVRCDGQVAPVPCGAYDWVYLLTTAERRVEDEMALHFADGAVDFEPLRVSDFWVAPAVFGETAAFTTTVMHYPHHIQRNVPATVWSQRVPVTRRGRLRAVRFPDNLAVHILAMTLCGA-----------
+>UniRef100_A0A918GZH9_1951/	144	0.457	1.448E-34	44	218	233	15	189	195
+--------------------------------------------PVDISDHRNNTAISAATETRAGAFNVWRNSFAAEYLPAGQSLVHVDGVPFEFPPVCDGPDNVRCAGQFIRVPVGRYDWIHVLAASERRCEDTVELNFADSSVDAESLRISDFWAAPAWFGEVRAFESLVMHYPHHVQRGIPAVMWAQRVPVTRRADLTGILLPRNVAVHVFAVTL--------------
+>UniRef100_A0A918U5A5_68238/	144	0.295	1.448E-34	44	219	233	48	225	603
+--------------------------------------------PVPLDRLFDNRAVSDDARPGAADFDGSGASLSAQDLAAagwtPGRSLTVQGARLTWPrPAAGRPDNVRADGQTVRV-RGRGDALAFLAAGTGGEdlTGTGTVRYADGSRSAYRLDVGDWRTGPLA---TKAVALPHVNTP-GGRLAERARLYVVTVPLARGREVASVHLPREPDLHVFALSVR-------------
+>UniRef100_A0A4R2IR67_1213861/	144	0.266	1.448E-34	36	225	233	31	220	766
+------------------------------------TAAAPTPVTVSLTQYFDNNGIDSASAR-DGNFDGSGYTYPAEALPTGG--ITVDGVPFTFPSaAKGVKNNIVAMGQTLDIPRGKYHAGHFLVAgSYGMASGTATVHYADGGTTTASLAGPDWYNSSGP------ISASYRYAPNNGTDQHPVAIAAAQIWLDAGREAVSVTLPVtqpaqagQTSLHVFAMTVQAAAKGR-------
+>UniRef100_UPI001FE67354_2698649/	144	0.245	1.448E-34	47	214	233	887	1069	1075
+-----------------------------------------------LRAAYNNVGISPDNAMSVANFDNVGFSYSANALSnaglKPGGTVTVDGLPHTWPLTEvGEPDNVIASGQTVNVQaAAGATKLAFLGSAANGtASGTLTITYTDGSTQQAQIGFSDWTLGgggqQPSFGNRIAVTSSYRNSVNGSSQGLNTYVFATEpIALDPSKQVRSVTLPSSvsgGTLHVF------------------
+>UniRef100_UPI002092D67B_79912/	144	0.259	1.979E-34	47	215	233	906	1090	1096
+-----------------------------------------------IEWYQNNAGISDDGKAGTANFDGGGWSYSAQALAAaglkPGQPVAWKGFTFTWPNrTPGQLDNVQANGQVVDLPaaPKGASQLAFLGAAGNGDaSSTVKITYTDGSTATAKLELSDWALGadayPPKFGNEIVAKTPYRNTSDGGTQKLNIYVFAATpIALDASKQVQSVTLntPSSgGSLHVFA-----------------
+>UniRef100_A0A9E9MNL7_2944128/	144	0.265	1.979E-34	47	222	233	934	1125	1423
+-----------------------------------------------LLAAFDNRGISDDTAVAAGNFDGGGRSYSAQALAAagltAGQPVTAGGISYGWPlPAPGYPDNAIAAGQAITLdaPSGTAQVGVLGAASNGPSQGIATLTYADGSTDRYWLGLSDWTlnggSAHPSYGNLVAARTTYRNCAgcSGGRDSVDTDIFATSLPADPAKTLTSLTLPsgtTRGQLHVFAIGTSTSA----------
+>UniRef100_A0A6B2VD27_2706027/	143	0.471	2.704E-34	42	219	233	6	183	195
+------------------------------------------FLPVRLDKHWNNRAVSAVGETGTGRFNVWRNSFPAEHLPAPGGELVVGDVPYRFPQTTADGDNIRCAGQYLPLPEGRYDWIHLLASGERRVESELALHFADGEVDFEAVRVSDFWAAPARFGEREAARTPVMHYPHHVQQGVAAVLWSQRVPVTRIATLHGVRLPRHIALHVLALTLE-------------
+>UniRef100_A0A3R9DPL9_2267691/	143	0.289	2.704E-34	40	227	233	48	236	783
+----------------------------------------PPPVPVTLDAWFTNDGIDSASATG-GDFDGSGYTFPAEHLPA-GQTTTVGGVPFKLGSaAAGAKNNIAATGQRVDLPKGRYFVAYFLVAGSYGtAGGTATVHYADGTTSTGSLSGPDWYTGTG------ALVSPFRYAPGGVVDNNPVSLATGQVWVDPAREAVAVTLPTTANpapnvasLHVFALTLQPVAVGRSA-----
+>UniRef100_UPI0021528536_2945988/	143	0.284	2.704E-34	26	227	233	40	236	783
+--------------------------PDTPIVPPP------PPVPVALDTWFSNDGIDSASATG-GDFDGSGYTFPAEHLPA-GRTTNVSGVPFTLGSaAAGAKNNIAATGQTIDLPKGRYFVAYFLVAASYGtTGGTATVHYADGSTSTGSLSGPDWYTGTG------ALVSPFRYAPGGVVDNNPVSLATGQVWVDPARDAVALTLPTTANpapnvasLHVFALTLQPVAVGRSA-----
+>UniRef100_UPI00210A4B97_68230/	143	0.387	3.696E-34	43	223	233	17	198	199
+-------------------------------------------HPVAIEDFLDSVGVEPNSRSGLGAFNIWGNAFPAEALPC-GTLTELDRVPFRFPPADGvRPDHLRCRGQRIPLPAGRADWIHVLGAAERRTEDDVLLEYADGSARRQWLRLSDfWPQTGPRFGERLAFRTGSMLYPRHEQLTMSPSIWHQRIPVAVSDGLRAIVLPHNPAMHLFALTLVEAAA---------
+>UniRef100_UPI001FB83ACA_1213861/	143	0.250	3.696E-34	23	217	233	831	1054	1057
+-----------------------RAEPDTPeatyqvAVTFSGPGGSLGSATLqilvappgSLRASFNNIGISPDNAMSVANFDNVGFSYSANALAnvgvKPGAAITVDGLAHTWPiTGLGEPDNVVAAGQTIVVTaPAGATKLALLGSAANGSaSGTLTVTYTDGTTQQAAVGFSDWTLGgggqTPSFGNRIAAASQYRNSVNGNTQGITTYVFAtAPIGLDATKQIRSVTLPgsvSGGSLHVFALT---------------
+>UniRef100_A0A399GYA9_2259644/	143	0.377	5.051E-34	38	223	233	12	198	199
+--------------------------------------TVGAAHPVAIEDYLDSVGVEPNSRSGRGAFNIWGNAFPAEELPC-GNLTELDRVPFRFPAADGkRPDHLRCRGQRIPLPAVRADWIHVLGAAERRTEDSVLVEYADGTVRRQWLRLSDfWPQTGPRFGERLAFRTTAMLYPRHEQNTMSPSIWHQRVPLAVADGLSALVLPHNPAMHLFALTLVTEAA---------
+>UniRef100_UPI0015643D0C_2698649/	143	0.455	5.051E-34	39	217	233	18	196	206
+---------------------------------------GSRFHLVDLDLHRDNVGVTSSSATGYGAFNVWGNSLPAEELP-SGRAIQVEDVPFTFPaTGGGRPDNVRCAGQHITVEPGQYDWLYLLTAAERRVEDEIAFHYADGAVDFEPLRVSDFWAAPAVFGETSAFTTLTMHYPYHVQANVSAMVWCQRVPLVRGAALAAMRLPRNPAVHIFAAT---------------
+>UniRef100_UPI00234B0C2D_2944250/	142	0.465	6.903E-34	45	218	233	0	173	179
+---------------------------------------------MDISGHRNNAAVSAATETKAGEFNVWGNSFSADYLPAGKSLVHVDGVPFEFPPVCEGPDNVRCAGQFIRVPEGRYDWIHVLAASERRCEDTVELSFADGFVDAEALRVSDFWAAPAWFGEVKAFESLVMHYPHHVQRGIPAVMWAQRVPVTRRAGLTGILLPRNVAIHLFAVTL--------------
+>UniRef100_UPI000A54E855_1710355/	142	0.464	6.903E-34	45	222	233	3	182	196
+---------------------------------------------IDLSPLLDNVGTSTTADTSAGRFNVWGNSFAAEDLPAPGSVVMVDAVPFTIPPvGTGAPDNVRCAGQYLALPGGPatADWIHVLAAGERRVEDEIALHFADGSVDFEPVRVSDFWAAPPAFGETRAFAT-LMNYPIHTQFGVPASVWSQRVPVTRRAPVVGLGLPRNLALHIFAVTLQPVA----------
+>UniRef100_UPI001CFA9BF6_146923/	142	0.387	6.903E-34	43	223	233	17	198	199
+-------------------------------------------HPVAIEDFLDSVGVEPHSRTGRGAFNIWGNAFPAEELPC-GTLIEHDRVPFRFPPADGEwPDHLRCRGQRIPLPAARADWIHVLGAAERRTEDSVLLEYADGSVRRQWLRLSDfWPQTGPRFGERLAFRTSAMLYPRHEQRTMSPSVWHQRVPVAVPDGLRALVLPHNPAMHLFALTLVEEQA---------
+>UniRef100_UPI0022AC71CD_47760/	142	0.284	6.903E-34	31	219	233	18	209	585
+-------------------------------VTVPAAAApGAEDRPLPLERLFDNTAVSDDTRPGEADFDGSGGSLSAQDLTAagwtPGRSLTVQGARLTWPrRVPGRPDNVRADGQSVRV-RGHGDALAFLVAGTGGGdeSGTGTVRYRDGSRSSYRLTASDWRGGPLA---TKAVALPHVNTP-GGQLTEKARLYVVTVPLVRGRSVDSVELPHNSDLHVFALSVR-------------
+>UniRef100_UPI0007C6D0A7_105422/	142	0.283	6.903E-34	47	216	233	1003	1180	1184
+-----------------------------------------------LAAAFDNVGVTDDSATAAGNLDGSGSSYSAQALAAagvtPGTALSHGGVSFSWPGaASGRPDNVVAQGQPIDLT-GSGTTLGFLAAGTSGAGaGTGEIVYTDGSTQSYTVTVPDWYATPPA-GSDVAIATAYRNRAGNVQQVHATNVYYTGVPLTAGKTVAMVVLpaptPASGALHVFAL----------------
+>UniRef100_A0A5J4L056_2607529/	142	0.254	9.435E-34	31	217	233	145	346	349
+-------------------------------VKLPISAlTVVVAKPGNLLGLFNNAGISND-GQGNADFDGDGYSYSAQQLAAsgykPGATVTVNGTQYLWPNvAPATFDNVQVAGQTIQTPdakAGATHLTFLGSATNGPSSGNVTITYTDGSTQTAQLGFSDWTlgagNSQPSYGNVVAVKTSYRNAGSG-QDQVGTYVFAsAPIALNASKQVASITFPssvDQGALHIFALT---------------
+>UniRef100_A0A5P9PZG3_2653857/	142	0.291	9.435E-34	34	221	233	769	953	954
+----------------------------------PGGAS----VPVDLTAFLTNDAITSEFYLGDGDFDGAGNTYPAAQLPQTG-KVVDDGIEFVFVNGhEGTPNNVVPGGGPIALPEGAYGVLHLLGASDNGNtNSTMTITYTDGSTAELPLKLTDW-RASAAFGESEAITTSQLHAKDGPK-PVKLAIFHQAIELDPARSPKSLTLPATakPRPHLFAITLEKG-----------
+>UniRef100_A0A7K2QB93_2690325/	141	0.385	1.289E-33	43	227	233	5	191	193
+-------------------------------------------TVVNLSAHFNNRGIQPPETSGDYGFNIWRNTFPAEELPEPGSLVDLVGAVFEFPaRESAAGDNVRCRGQLVELPVGSWDWIGLVGAAERRTEDEVELHYADGTVGREWLRMSDfWPQTGAYFGEPRAFATGSMRYPRHTHLHHAPSIWQQRVPVRVPAPLAAVRLPDNPAMHVFAMTVTADEESRLA-----
+>UniRef100_UPI001E589C24_1915/	141	0.271	1.289E-33	36	225	233	45	234	785
+------------------------------------WVSVPDPVPVPLDALFDNDGIDTATARG-GDFDGSGYTFPGEELPA--GRIDVDGISFLFPsSAAGAGNNVVALGQRVDLPKGRYmSALFLTAGSYGDASGTATVHYADGSSTTAALGGADWYAAGGP------LSAAYRYGPDGTKDEHSVGIGVSEVWTDPRREAVALTLPKTnpvevgkTSLHVFALSLQPAAQGR-------
+>UniRef100_UPI00167AA00B_33897/	141	0.259	1.289E-33	33	220	233	770	960	961
+---------------------------------LPEPAQSGTVTRIDLTGFFDNDGITTEMYYGDGDFDGSGRTYPMAQLPQTGET-TDNGIAFLFTNgSEGTTNNVVVAGQEITVPRGAYAKLHVLGAGDTAAvTVPAVVRYADGTSETARLTLTNWLASGPENGETEAVTTSQIHTPTGPV-ATKAAVFHQVIELDASRQLTTITLtaPDgTARAHVFALSLEQ------------
+>UniRef100_A0A1H5IBI8_1855349/	141	0.259	1.289E-33	47	216	233	906	1086	1090
+-----------------------------------------------LLAAYSNTGISDDSgDHDEADFDGGGWSYSRQALAAagltPGTEATVDGLAYTWPNAPaGRPDNATATAQTIELPTPAATLSFLGSATNGNQSAPATVTYTDGTTGTLDLSFTDWTigggGGTVQYGNTIVARTAYRNVSGADKDPVATYVFATRpFTAPAGKTVRSVRLPENSDLHVFAL----------------
+>UniRef100_UPI001FFEE4A7_2620835/	141	0.276	1.762E-33	15	220	233	754	956	962
+---------------IAPVKVTTPAPPWGLPPLPPG----GDMVTVDLEPFYTNDGITNEFYLGDGDFDGTGRTYPSGALPQNG-SLTNDGVPFRFTNGhEGTRNNIIAAGQTVELPEGNYRRLHILGASDNGNTDsTVTLHYTDGTATPVKFALTDWL-ASAAFGESEALRTNQIHTRTG-PAPLRAAVFHQVLAADSTRRLRAITLSANakPRSHVFAVTVEK------------
+>UniRef100_A0A919K8V0_1050105/	140	0.292	3.291E-33	33	224	233	4	198	752
+---------------------------------VPGGARAAiftDPVPVPLDDLFDNNGIGVAA--GDANLDGSGHGFPAAGMPT--GSVTVDGVPYRIAatSAAGQNDNVVALGQSVAVPAGQYVAGFLLAASAYGSaGGTVTVHYADGTTSSAEVSAPDWFS-----GDAGAVTAPYRYGPGGT-DQHAVALYAVQVWMDPARTAQSITLPSTaapaegvSSLHVFAFSLQPAVAV--------
+>UniRef100_UPI001A8F7A74_2814588/	140	0.287	3.291E-33	34	220	233	762	945	946
+----------------------------------PGGAS----VPVDLTAFLGNDAITSEFYLGDGDFDGAGNTYPAAQLPQTG-KVVDDGIEFTFVNGhEGTPNNVVPGGGPIALPSGAFRALHLLGASDNGNTNTkMTITYTDGSTAELPLRLTDWRN-SAAFGESEAITTSQLHAKDGPK-PVKLAIFHQTIELDPARSPKALTLPaaTRPRPHLFAITLEK------------
+>UniRef100_A0A7C3IRJ5_2026780/	140	0.248	3.291E-33	41	219	233	54	244	1084
+-----------------------------------------GQVPLKLEALFDNDAIADAQRRSDGNFdcpdhaaDIPGSVFPAENLPATGSKFSFDNVSFLFPSKErGDFNNVSCNGQRIEVPPGRYKALHVVGTSENGSfRDRLSLAYKEG-PAEADLALKDWCQ-KPTEGDRVAFEAPCRYTWSSekrtmVREEVQPRLWLQRIALDPQKTLEAIALPYNRRMHVFAATLE-------------
+>UniRef100_UPI0019308D5B_2282478/	140	0.250	4.497E-33	52	217	233	916	1093	1096
+----------------------------------------------------NNVAVTDDANTNLGDFDGGRASLSAQALAsvgvRPGGAVDFSGLRFAWPDaAPGTPDNVVASGQVLKLAGSGGRLGFLVSSTWGPASGTGIVRYTDGTRQPFALSSPDWY-GAPKPGGVAAVVVPYQNRPNNQRQNTPATIYFAEVALQAGKQVRSVELpnvsaaarPNTPALHVFAVT---------------
+>UniRef100_A0A401ZWU8_2014871/	140	0.252	4.497E-33	31	217	233	752	959	1369
+-------------------------------VTLPATAGPGtmhifavSTKYVPQAAVYNNIGTSDDSAPATGIFDGT-NSYSAQALAAvnitPGATVSYNGVNFIWPNvMVGTPNNYAAKGQMIPVnPVPNATTLAVLGSStDGNSTGTAVITYTDGTTQSFPLGLSDWTLGggysTPAYGNKVVATTAYRNTPSGQQSTDKPTILYADVTLNyPGKTVQSLTLPatmTGGQLHVFAVS---------------
+>UniRef100_A0A5S5C606_582686/	140	0.276	4.497E-33	42	228	233	2516	2703	2715
+------------------------------------------YAVVPLEAYMNDQGFGSLA-SGRANLTGMGtYFLPDDAITVEG--FRVDDRPFGIADlIDGQNDNISCHGQIIRLPQGRYDEIALLGCSEWGNYiEPCTAVYKDGTKEVFRLRFTDWT-GTPRFGEQIAWEGRiaERNEIRTFVIDQPGRIFMQTYALDGRKEAATLQLPYSPGMHIFAITLRQSQAALLPD----
+>UniRef100_UPI0021AB612D_2867961/	139	0.422	6.145E-33	52	223	233	1	175	183
+----------------------------------------------------DNTGITRPDDLGAGAFNVWSNTFPAQHLPpaDPDGTVDVGGVPFRFPAQLTGPDNLRCAGQRLDAPKGRYDWIYLLAAGERRTEDVLHLHFADGTTDPEWLRVPDfWPQTPPHFGFTTGITFPVMHYPRHIQRDMSPSVWRVRVPVPREAELTGIHLPDNPAIHVFALTLCGPAA---------
+>UniRef100_UPI001C9D367C_1827978/	139	0.403	6.145E-33	43	227	233	5	195	197
+-------------------------------------------TVIDLSAHYDNRGIQPPDEPGEFGFNIWRNTFPAEELPEPGSLVEVAGTAFVFPPrPTAGGDNIRCRGQLVELPdgaaGGRYDWIGLVGAAERRTEDEVELHYRDGSVSRAWLRMSDfWPQTAAYFDEPLAFRTASMRYPRHTHRHHAPALWQQRIAVVRPEPLAAVRLPDNPAMHVFAMTAVVDEESRLA-----
+>UniRef100_UPI00099FEB85_1841249/	139	0.280	6.145E-33	33	222	233	765	957	958
+---------------------------------LPELPQTGQGTQVDLVGVFDNDAITTEMYYGDGDFDGTGRTYPMVQLPQTGQT-EDDGITFAFTNgSEGSNNNVIAAGQKIDVPAGGYANLHVLGAGDSGNVTiPAVATYADGSTAKADIRLTAWLSG-PAYGETEAVRTSQIHARSGPV-GTKAAIFHQKVALDPAKELSSITLtaPASGtaRAHVFALTLEKKS----------
+>UniRef100_A0A401ZJF4_1936993/	139	0.245	6.145E-33	46	216	233	922	1106	1110
+----------------------------------------------DLLGLFNNAGISND-GQGNADFDGDGYSYSEQQLTaagyAPGATVTVNGIQYSWPNVPaAAYDNVQVAGQTIQTPDAKagATQLTFLGSATNGPSvGNITITYTDGSTQTAQLGFSDWTLGagtsQPSYGNVVAVKTPYRNAGAGT-DNVGTYIFAsAPIALNTSKQVASITFPsslNQGALHVFAL----------------
+>UniRef100_UPI00048B7B40_311244/	139	0.270	8.397E-33	41	220	233	1	180	183
+-----------------------------------------DYYKINLNSYYNNNAFTYEESSSKGDLTSFGSSYPAEYLPNEHE-ITVNGIPFIFPTKENKFNNIELENQSIIVPDDSYSTIYILGSSENGSYkEYMELRQNNDLKSRNIFALTDWISNYPMFMEQVAFECGYVHTKDSSIHSLKPKIWIQTLHLDPATEFNTIRLPDNPCIHIFSLTLQK------------
+>UniRef100_A0A229H6X1_1945643/	139	0.271	8.397E-33	31	220	233	762	950	953
+-------------------------------PALPETGAA---TPVDLAGHFDNDAITTEMYYGDGDFDGTGRTYPMAQLPQTGQT-EDDGITFSFTNgSEGSNNNVIAAGQKISVPAGGYARLHVLGSGDTADvTVPAELGYADGSTAKVDVKLTAWLSG-PKYGETEAVRTSQIHTRTG-PLGTKAAIFHQKVALDPAKELATVTLgaPSgTARAHVFALTLEK------------
+>UniRef100_A0A4D4LI39_68280/	139	0.269	8.397E-33	33	220	233	763	952	955
+---------------------------------LPELPQAGAVTQVDLTGHFDNDAITTEMYYGDGDFDGTGRTYPMAQLPQTGQT-EDDGITFAFTNgSEGSNNNVIAAGQKVTVTAGGYTKLHVLGAGDTGNvSVPAEATYADGSTGKLTIQLTAWMSG-PAYGETEAVRTSQIHTRTG-PLGTKAAIFHQVVELDPGKELSAITLgaPSgTARAHIFALSLEK------------
+>UniRef100_UPI0016620FE8_1896314/	139	0.259	8.397E-33	48	217	233	961	1136	1139
+------------------------------------------------AAAYNNKGISADSDPGTGTLDPAGYSFSATQLAAvgytPGATVTAGGLPYTWPDTrPGQPDNVAAAGQVIRV-QGRGARLGLLGTGiSSTHAGTVTVTYTDGTSTDLAVVLPDWYSNAASGNSQLAVTTANWNRPPGDTLGdHAVSLYTTGGALDPAKTVATVTLPNDSGFHVFALS---------------
+>UniRef100_A0A919QKH3_1070424/	139	0.459	1.147E-32	38	221	233	10	193	209
+--------------------------------------TAEGHHLLDLAGHRNNVGATAPDHLGAGAFNIWGNSFPAGELP-SGRPVLVDGVPFDLPvCGAAAPDNVRADGQFIEVAPARYDWLYVLAAAERRVEDEIAFHFTDGSVDFEPLRLSDFWAAPAVFGESAAVVTEVMHYPLHVQADVPAMLWCQRVPVTRRAVLRAARLPRNPAVHVFAATLREA-----------
+>UniRef100_A0A5J4KKR6_2607529/	139	0.250	1.147E-32	32	217	233	166	359	362
+--------------------------------TLP-KTTGGQMHIFDFSyrvGPFNNIGGTIDEDLQQiQNFDGQHNGYSYDALSAaglPKGSVTINGVNFNWrSAADGNADNYQASGQVVPVtPVAQAKTLAFLGASTGGaASGTATITYTDGSQQTFTLGLTDWCAPTVAYNNRVAAAATYRRTPHG-NQTIKTSVYYTDVALQSGKTIKSVTLPTNGQIHIFDIS---------------
+>UniRef100_E2PX58_1901/	139	0.288	1.147E-32	33	221	233	751	941	944
+---------------------------------LPPLGPTGGVTPVDLAAHFDNDAITTEMFFGDGDFDGTGRTYPMAQLPQTGRT-TDDQITFSFANgSEGSKNNVVAAGQRVAVEPGSYARLHVLGSGDTGNvTVPAVLSYADGTAATVPVRLTGWLSG-PAYGETEAVRTSQIHTRGGPV-GTKSAIFHQRVPVDPGRRLVSVTLGRpsgTARAHVFALSLEAA-----------
+>UniRef100_UPI001C0E2853_2842201/	139	0.268	1.147E-32	6	220	233	745	952	955
+------PDFR-----IAPVQVTTPAEPWG-LPELPQAGAVTQ---VDLTGHFDNDGITTEMYYGDGDFDGTGRTYPMAQLPQTGQT-EDDGITFAFTNgSEGSDNNVIAAGQKVAVPAGGYTKLHVLGAGDTGNvSVPAVATYADGSTGPLTIQLTGWMSG-PAYGETEAVRTSQIHTRTG-PLGTKAAIFHQVVEVDPAKELSAITLtaPTgTARAHVFALSLEK------------
+>UniRef100_D2PSN6_479435/	138	0.394	1.568E-32	12	218	233	11	216	225
+------------MVAVRPYSGPVTVGPDS-VTEPPPESPHVGCRPVDLAPHRNNVGSTPASGTRNGAFNIWGNSFPAEELPPPG-LCAVDQVVYDFPPTePGTADNVRAAGQFVEVPAGRYDWLYVLGAAERRVEDELAFHFADGAVDFEQLRLSDFWAAPAWFGETQVRATRSMHYPFHVQAGVPAMLWSQRVPVTRRSVLSAVRLPRNPAVHLFAATL--------------
+>UniRef100_A0A1H6EW60_1144553/	138	0.264	1.568E-32	52	215	233	201	378	384
+----------------------------------------------------NNAGVGDDTEPGQADFDNGGWSYSAQALAAgarPGGTVTWKDHTFTWPNrKPGEWDNVQAAGQTVDLTaPAGAGTLALLGAGASGDIETgVTITYTDGSTQETKVGFSDWALArdayPPRFGNEIVLRTPYRLDGGGGRQDINVYVFAVTpIRLDPAKQVKSLTLarPAGAAtAHIFA-----------------
+>UniRef100_UPI00143AD3F7_2720023/	138	0.262	1.568E-32	52	215	233	905	1083	1089
+----------------------------------------------------NNAGIGDDDEAGLANFDGVGWSYSAQALAAagarPGGTVTWKGYDFTWPDrEPGEWDNVQASGQTVDLaAPAGAKTLALLGAGASGDiQTDVTITYTDGSTQQVKVGFSDWALArdayPPRFGNEIVLRTPYRLDGGGGRQDINVYVFAVTpIELDASKQVKSLTLakPTGAAtAHVFA-----------------
+>UniRef100_A0A2T5BN31_2135609/	138	0.460	2.142E-32	45	219	233	17	190	194
+---------------------------------------------VDLTPYRNNIALTTDKTLHRGMLNVWGNSLPAEVLPHDG--LTVGGIPFRgVPGGGAEPDNVRCAGQYLELPRTTADWLHLLATSERRCEETAFVHYASGAADPEWVRVSDFLPARAHFGEVLAARSDALHYPHHRQENLGGRLWAVRIPVTRREPVCGLRLPDNPALHVFALSLE-------------
+>UniRef100_UPI001915634B_2778368/	137	0.250	5.464E-32	31	216	233	907	1107	1111
+-------------------------------VKLPISAlTVVVAKPGNLLGLFNNAGISND-GQGNADFDGDGYSYSAQQLNAagytPGATVTVNGIQYTWPNVAvATFDNVQVAGQTIQTPDakvGATHLTFLGSATNGPSSGNVTITYTDGSTQTAQLGFSDWTlgagNSQPSYGNVVAVKTPYRN-AGPGRDQVATYVFAsAPISLNASKQVASITFPasvDQGALHVFAL----------------
+>UniRef100_A0A8J3HZW2_2778364/	137	0.241	5.464E-32	51	222	233	775	958	1149
+---------------------------------------------------YNNVATSDDGSPAGGSFDGI-NSYSSQATQSlgliPGASVNVYSTTFIWPAVnPSYKNNYVAQGQVLPIkPVNNAGTLAFLGsSSYGPSSGTLTVAYTDGSTETFTLGFSDWTlaggKASPSFNNLVAMSMPYRNTPHG-KQNINTYIFYSEIPLAVDKTVQSITLPsdvKNGQLHVFAISTRTGS----------
+>UniRef100_UPI001EF7C8F6_2807632/	136	0.486	1.393E-31	38	218	233	15	194	208
+--------------------------------------GSPLFRTVDLTGHLNNKAVTTESRKGEGRLNVWRNTIPAQHFSAAGSRVEVDGIPYLLAP-ESAYDNVRCAGQYVTVPEGRYDWIRILATGERRAETEIAVHFADGHIDFEALRVSDFWHAPPRFGESVAYRTPVMHYPHHVQERVNAGVFSTRVPVSRQAAVCALRLPRHVGVHVFALTL--------------
+>UniRef100_A0A938MH69_2026780/	136	0.231	1.393E-31	40	221	233	21	217	906
+----------------------------------------PQQLPLNLVELFDNDGISSEKNRKDGNFDcpdhpahVPGSTYPAEFLPESGAIFTappLPDVSFLFPNkADGEKNNFSCAGHKFEPPVNAYAALYILGTAENGKQeGEIGLNFEDG-QLNLPLKFSDWCEP-AQFGEVEAIAVPFRYswqerGGRMEKEDITCRLWVQKIPLPEKRRLESFVLPYNARMHVFAITLVAA-----------
+>UniRef100_A0A8J3HZW2_2778364/	136	0.232	1.393E-31	51	215	233	965	1144	1149
+---------------------------------------------------YNNMGTSNDNTPGSGNFDGGHMSYSAQALQskgyKPGSVVVFNGTSFVWPaSTPGTVDNYVAQGQVIPVNSVyNANYIAFLGSASHGPlQGNVLVTYTDGTTETVSLGFSDWTLGagkmKPSYGNKVALTTTYRNGPKG-KQNVATYMFYCEATLgALNKQVQSITLPTLPagpgQLHIFA-----------------
+>UniRef100_A0A1B2HKE2_1586287/	135	0.257	1.903E-31	52	215	233	910	1080	1085
+----------------------------------------------------NNVGASDDA-TGDGDFDGGGYSYSRQALAtaglVPGQTGTVDGLTFTWPGSPaGRPDNVTANKQKLTL---SGTKLAFLGSAANGARtRTATVTFTDGTTAPVEIGFSDWTLGgggaAPSYGNVVVANTPYRNQLGGGSEKVATHIFATkTYVAPEGKVLQSVVLPEDVNLHVFA-----------------
+>UniRef100_A0A7G8KM49_2763006/	135	0.264	2.600E-31	15	223	233	138	363	747
+---------------VGPTAAPAgRAEPTAAPAVVPpavgegAPATGRAGRPVPLERLFDNVGTSDDADPGAADLDGAGNSLSARDLAAagwtPGRALTLDATRLEWPrSAPGRPDNVRANGQHVAL-SGTGDTLTFLVTGSSpgrvgpGAGGSGTVHYRDGSRSTYTLTAPDWRGGPLA---TKAVALPHHNTPAGQR-REAVRLYAVSVPLARGAAVASLTLPADPgpdaDLHVFALAVRPPAA---------
+>UniRef100_A0A2T0TAZ4_84725/	135	0.262	2.600E-31	52	216	233	920	1092	1096
+----------------------------------------------------NNIGASDDAGSEVADFDGGGYSYSRQALAAaglsSGATGTVDGLTFTWPNSPNdRADNVVTNGQSVDVTGTKLS--FIGAAADGGRTAAATVTYTDGTTGTVDLGFSDWTLGgggqNPSYGNVVVAKTPYRNLLGGGNEQVVTNIFATkTFTAPEGKVLKSVQLPTNEGLHVFAI----------------
+>UniRef100_S5TLH7_1366598/	134	0.453	3.552E-31	41	220	233	38	216	219
+-----------------------------------------EYFTVDLSGHLDNIGLTMPDQLAAGALNVWGNSLPAGALPA--GAVEVGGVPFVTAGGDGsRPDNVRCAGQLLDLPPVAGSWLHVLATSERRCEEELHVHYADGAVDPEWLRVSDFWPAAAHFGEVAAARTGAMHYPHHIQGDLGGQIWATRVPATRGGTLAALRLPDNPALHLFALTVET------------
+>UniRef100_UPI00218069CC_1654476/	134	0.250	6.629E-31	52	216	233	920	1092	1096
+----------------------------------------------------NNIGVSDDKGSEEADFDGGGYSYSRQALAAagltSGGTGTVDGLAYTWPNSPeDRADNVIAAGQSIDV---SGTKLSFLGAAAGGARtAAGTVTFTDGTSAPIDLGFSDWTlgggSQNPAYGNVVVAKTPYRNQIGGGSEQVVTNIFATkTYTAPDGKVIKSVKLPTNGGLHVFAI----------------
+>UniRef100_UPI001EF8F640_2911966/	133	0.269	9.055E-31	43	217	233	5	184	188
+-------------------------------------------VCVDLSKLFNNKGVSWIGLGIAGSFDHSGISVPGEILP-DGITVTWCDIPFQFPKTSSiENDHICCEEQTIEVDPNSYRQIYVAGFSlYGDYSDRVWIHYEDGSSEDKEFGLSDWYSRTEAgnglkHSEQVAMMIPY-YYENGIKIQAMRGIWIQRLLIDPNKKLHSIRLPDNPYMFIFAIT---------------
+>UniRef100_UPI001A9FE9C4_2530381/	133	0.413	9.055E-31	45	232	233	3	192	221
+---------------------------------------------IDISPYLDNVGATTAGRTATGRLNVWNNSFAAENLPPGGSNVMVGGVPYVMPPFGGiDPDNIRCAGQYLELpgPGRAVDWLHLLATGERRVEDEIAVHFADGSVDFEPVRVSDFWAAPAAFGEVPAFET-LMHYPAHTQFGVPASVWSQRVPVTRRLPLIGIGLPVNAALHVFAVTLQPPDGTRRPAAVST
+>UniRef100_A0A193C823_31958/	133	0.259	9.055E-31	21	221	233	734	943	945
+---------------------PRGKRPDTTIAPVPVSVPAPPWglpalppagdlVPVDLAAVLNSDGVTSEFYLGDGDFDGGGNTYPAAQLPQTGQ-VTDDGVPFLFVNgSEGTPNNVV--GATIPLPAGKYATLHVLGAADtGNAVTTLKVSYVDGS-AEVPLRLTGW-RAAAAFGESEAITTNQLHARAG-VQSVKLAIFHQRVPLDPAREVVSVTLPSaaTPRPHVFAVTLEKG-----------
+>UniRef100_A0A6G3RW39_2706073/	132	0.402	1.690E-30	47	223	233	21	198	199
+-----------------------------------------------IEDFLDSVGVEPSSRSGSGAFNIWGNAFPAGELPC-GTLTAHDRVPFRFPAADGvRPDHLRCRGQRIALPAGRTDWIHVLGAAERRTEDGVLLEYADGSVRRQWLRLSDfWPETGPRFGERLAYRTTAMLYPRHEQYTMSPSIWHQRVPVAVPDGLTALVLPHNPAMHLFALTLVTEAA---------
+>UniRef100_A0A1B1MEJ8_1915/	132	0.285	2.308E-30	50	216	233	931	1111	1115
+--------------------------------------------------YLDNNGVSADDNDPSGDFDGGGGSYSAKALAdqklTPGATVDAGGFSFTWPKvGPGAPDNIVVGGgeQVLDVPGGATKLAILGSASNGPSTGTLTLTFTDGSTQQATVGFSDWTLGggaqKPSYGNVVAARTAYRLY-SGSTDDVDTYVFAtAPIAVPAGKRLASVTLPSStsgGRMHVFGL----------------
+>UniRef100_A0A7X3GHH6_2682849/	132	0.266	3.152E-30	43	222	233	343	522	523
+-------------------------------------------VPIDISGICAIRGI--HNSLGTADVDGDGHSYSREGLPVDG-LLRIGDLSFVFPASQNEAdcDNTACDGQAIPIPPGHYHGISVLASSqYGGSADAFTVEYADGTSEQVQLGFADWWSRFPIAGEKVAWSA-NLNRPSLGKTEEIVHLFANEAPLSRtGSTAVRIVLPNLPNLHVFAVSMWKQA----------
+>UniRef100_A0A7V2U765_2026780/	132	0.279	3.152E-30	34	218	233	722	916	923
+----------------------------------PPPAANVECVHLNaLAGHFNNDGISWRANPADGNFDfpsrASGASFIADLLPKKGALLAVpgnEGVTFRFPDKDDRLrNNVLCDGQRLQLarPYGSFEAAWFLGACHDGArSALLTIDYEDGKAQ-GELRLADWLS-RPAAGEIDVLRLSARHAGDGKEEARDCGLVAWRVPLDPSRKLMALTLPRERNMHVFAVTL--------------
+>UniRef100_UPI00224096B5_202862/	132	0.275	3.152E-30	57	221	233	867	1044	1047
+---------------------------------------------------------TSTATRPVGDFNGYGGSFVAEELAedglVPGQDVTVDGIGYRWPDaAPGSPDNINAHGQTVTVHAAPGqSRLGLLGAGNEGaATGEVTVHYTDGTTRRASVTLGDWhldGATAPPPGNTAAATMPERQMAGGTPEKMTVYIWSTSVPVDPHRTVASVTLPERttgGQMHVFAVGVGEA-----------
+>UniRef100_UPI00068FB531_1463857/	132	0.264	3.152E-30	52	215	233	910	1093	1098
+----------------------------------------------------NSKGVSDDAKP-QGNFDGEGWSYSAQALAAggavPGGTVSAGGFSFTWPDVqPGDPDNIQvtpgqpATGQVVAVqPAAGATKLSLLGsAAEGTAKGTVTLTYTDGTTQQADIGFSDWTlgggSQQPSFGNTVAVKTSYRDTLSSGPDPVGTDVFAtAPIALQAGKQLASVTLPSTVSggvMHVFA-----------------
+>UniRef100_A0A7I8EN04_2717365/	131	0.262	4.305E-30	46	223	233	230	407	968
+----------------------------------------------PLPSLLNNQGIGSAA--GQANFDGSGYGYPSDQVPA-GGIIGLAGVSYLFPtHGSATKDNVVALGQSITLPQGHYQQASLLtASSYGPASGTVTVHYTDGSSSTATLNAPDWYN-----GTSDVINTTYRYTPTGT-DQHAVHIYVSQVWIDASRVAASLTLPqtalpaaNTASLHVFALTLQLPSA---------
+>UniRef100_A0A5A5TI23_2014874/	131	0.229	4.305E-30	49	215	233	103	283	1208
+-------------------------------------------------PAYNNAGSSNDSNPNEGSFDG-NNSYSVQALQGtgllPGQNFTFSNVTFVWPNaAAGTPNNYLVNGQVIPVAPsiaGAANLGFLGASTNGNASGNATVTFTDATTQTFSLGLSDWTlggnpQSTPAFSNQIAATMTYRNTP-VDQQTITTFLFSAQLALPAGKTVQSVTLPtttSSGQMHIFA-----------------
+>UniRef100_A0A3N1SWC4_2485152/	131	0.418	5.880E-30	45	220	233	17	191	194
+---------------------------------------------VDLAPHLNNVALTAMQNLGDGRLNVWGNSLQFETIPS--GRLSVDGVPFeTFNEVDSEPDNIRCDAQYLKLPESKADWLHLLTAAERRCEETVHIHYSSGAVDPEWIRVSDFWPARAHFGESLAATSPSMHYPHHRQGNLSGQLWAVRIPVTRREPVRALRLPDNPALHIFALTMET------------
+>UniRef100_UPI0022597B98_2903819/	131	0.269	5.880E-30	52	215	233	907	1088	1093
+----------------------------------------------------NSTAISTDDDNPQANFDGEGWSYSAKALAAagatPGGTVSSGGFDFTWPKvAAGDPDNIEVAGdtpQVLNVPSAQgATKLSLLGsAAEGSASGTATLTYTDGTTQKADIGFSDWTLGggadKPSFGNTVAVHTPYRDVQGGGTDPVGTEIFAtAPVTLQAGKQLASVTLPSTTDggvLHVFA-----------------
+>UniRef100_A0A6L5AS91_2575830/	130	0.243	8.031E-30	42	219	233	2	182	190
+------------------------------------------YYLVNLEEYYCNCGFSFINQRENGDFTGSGSSYPAEQLPSSEKVIKIHEVPFHFPSKeKGKFNNIEFNEQKIKVKEDSYQAIHVLGAADNGSFlEPISLIDQQGSVSKVMLGFTDWVDYEPKFNDLKAIVCKGVHSAQlGCLEGMQCTIWYQKVKVPTGVLFNEIRLGDNPGMHIFSLTLE-------------
+>UniRef100_UPI000D13FE3E_1463889/	130	0.241	8.031E-30	52	215	233	907	1088	1093
+----------------------------------------------------NSTGISTDDDDPRANFDGEGWSYSAKALAAagvtPGGTVSSGGFDFDWPKvGAGDPDNIEVAGagpQVLNVPSGPAdTKLSLLGsAAEGSASGQVTLTYTDGTTQQAEIGFSDWTLGggtqNPSFGNTVAVHTTYRDVQGGGKDPVGTEIFAtAPITLQAGKQLASVTLPSATDggvIHVFA-----------------
+>UniRef100_A0A543N991_405555/	130	0.437	1.498E-29	45	219	233	17	190	194
+---------------------------------------------VELQRYKNNIALTTLQTLHLGALNVWGNSLPSETMP--HEQITVDGVPFSVSPATGEaPDNIRCAGQYLELPETAADWLHLLATSERRCEETVHIHYSSGAADRERLRVSDFLPARSHFGELLAARSPAMHYPHHRQDNLSGQIWAVRVPVTRRETLRGFRLPDNPAIHIFALSTE-------------
+>UniRef100_UPI001CB70AD5_1896314/	130	0.250	1.498E-29	50	215	233	902	1085	1090
+--------------------------------------------------YVNNNGISADDSNPAANFDGEGWSYSAAALAAagatPGGTVSSGGFDFTWPQvAPGAPDNIVVGGgdQVLDVskSAAGATTLSLLGsASEGPTTGTVTLTYTDGTTQQADIGFSDWTlgggSQQPSYGNVVAVHTAYRDVQGGGKDPVGTEIFStAPIALQAGRQLASVTLPSSTNggdMHIFS-----------------
+>UniRef100_UPI002258EC57_2903886/	130	0.263	1.498E-29	52	215	233	934	1115	1120
+----------------------------------------------------NNTAISADDDNPQANFDGEGWSYSAKALAAagatPGSTVSANGFDFSWPEvTAGDPDNIEVAGstpQVLTVPPAPgATELSLLGsAAEGSASGTLTLTYTDGTTQQADIGFSDWTlgggSDKPSFGNTIAVHTDYRDVQGGGQDPIGTEVFAtAPIALQAGKQLASVTMPSSTKggvIHVFA-----------------
+>UniRef100_UPI001940CD9B_113564/	129	0.462	2.045E-29	60	231	233	1	174	176
+------------------------------------------------------------SNTSSGRFNVWGNSFAAEDLPAGGTGVVVDAVTFTMPPTgTGAPDNVRCAGQYLDLGPQAdlADWLYLLAAGERRVEDEIALHFADGSVDFEPVRVSDFWAAPPAFGETKAFAT-LMHYPIHTQFGVPATIWCQRVPVTRRAPLTGIGLPHNVALHIFAATLQPAAARPAALEVT-
+>UniRef100_A0A2T3VKX0_2135446/	129	0.416	2.045E-29	36	219	233	3	186	198
+------------------------------------AAGTGRHRVLDLTDHLDSTGFTRPDATDAGALNIWGNTFATGDLPAGHPHWLVDGVPFRTAEA-GGPDHLRCRGQYLEVPIGRYDWLHLLATAERRTEDPVLLHFADGAVDPEWLRVSDlWPGGQAHFGEAPALRGSRLHYPRHVQADMRPTLWAQRVAVPRRAPLVGLRLPENPALHVFAVTLE-------------
+>UniRef100_A0A4S2RGE1_2563103/	129	0.241	2.045E-29	52	215	233	907	1088	1093
+----------------------------------------------------NSTGISADDENPQANFDGEGWSYSAEALAAagaePGGTVSSGGFDFAWPQVhAGDPDNIEVVGsgpQVLNVPSAQGdTKIAFLGsAAEGEASGTVTLTYTDGTTQQAEIGFSDWTLGggtqQPSFGNTVAVHTGYRDVQGGGKDPVGTELFAtAPITLQAGKRLASVTLPSNTEggiIHVFA-----------------
+>UniRef100_UPI001CD27338_2877242/	128	0.264	5.209E-29	52	215	233	900	1083	1088
+----------------------------------------------------NSRGISDDTNPT-ANFDGEGWSYSAQALadagAAPGGTVSANGFDFTWPDvKTGDPDNIQvtpgapAPGQAVSVtPVSGATKLSLLGsAAEGSAEGTVTLTYTDGTTQQADVGFSDWTlsggADQPSFGNTVALKTTYRDVQGSTADPVGTDIFAtAPIALQAGKQLASVTLPSAVSggvMHVFA-----------------
+>UniRef100_A0A4U0SM40_2571141/	128	0.254	7.113E-29	50	216	233	920	1104	1108
+--------------------------------------------------YLNNNGVSSDDDSPAANFDGGGYSYSAKALAAagvtSGSTVSSGDFRFTWPKVNaGDPDNIAvgGGGQVLDAPaaPAGASRLSLLGsASNGAASGTVTLTYTDGTTQEEQIGFSDWTLGggsrQPSYGNSVVVRTDHRDVSGGGTQTVETDLFStAPIVLASGEQLQSVTLPDTvsgGTIHVFAM----------------
+>UniRef100_A0A1Q5MVC9_1703920/	127	0.247	9.712E-29	52	215	233	915	1096	1101
+----------------------------------------------------NSTAISTDDDNPQANFDGEGWSYSAEALaaagAAPGGTVSSGGFDFGWPEvAAGDPDNIEVAGtepQVLNVPSASGdTKLSLLGsAAEGSASGQATLTYTDGTTQQAEIGFSDWTLGggaqKPSFGNTVAVHTAYRDVQGGGTDPVGTEIFAtAPIALQAGKQLASVTLPSATEggvIHVFA-----------------
+>UniRef100_A0A1C4K485_1839759/	127	0.244	9.712E-29	50	215	233	916	1099	1104
+--------------------------------------------------YVNNAGISADDQNPAANFDGGGWSYSAKALAAagavPGGTVSAAGFDFTWPQVqPGAPDNIVVGGgdQVLDVsaTSAGHTRLSLLGSADDGDtSGTVTLTYTDGTTQQAQIGFSDWTlgggAGQPSFGNITAVHTTYRDVMDGTTDPVGTDVFAtAPIDLQAGKQLASVTLPattSGGDMHVFA-----------------
+>UniRef100_UPI001575013E_227866/	126	0.233	2.472E-28	40	220	233	1	182	187
+----------------------------------------GKYEMINLEELFNNKGISRMNNPQDANFTGFGSSYISENLPSSGSVLELYGIPFLFPNKDPlVVDNLEFMNQEIQIKEAYYSNIHVLGAADNGSFiEPIKLVGND--IKEVKIGLTDWIESSPKFNNKKGIICEGINsNKSGYTRTVKTNIWYSVVGIPSNNLFKSILLVDNPSMHIFSLTLEK------------
+>UniRef100_UPI00068E7F42_1444769/	126	0.349	2.472E-28	27	231	233	6	214	219
+---------------------------QTAQTVQTAPTDQTAHKVLALEPFMNNQAATTPANLADGRLNVWRNSLPAQDAPLE---LLVDGVPLRTARLDGtGPDNVRCAGQRIEVPERRWDWLYLIGCGERRVRDVLTWHFSDGTVDRDHLALSDLWEGRSDFGEELALRTDVIHYPHHVQERIGITLWCQRVPVTSRKPLTAMSLPRNPAVHLFALTLvgrhlgAGADGEPLIQGAS-
+>UniRef100_UPI000F0856B3_2483798/	126	0.419	3.375E-28	25	221	233	2	194	202
+-------------------------ETTTRVTTAGGSAG----TLVDLSGHRNNLSCTTTDSLREGRLNIWRNSLPQVEMPTAG-LLEIHGVGFSLPRFDGiNPDNVVCSGQHLACASGSYDWIYLLATSERRSEDQFSLHFADGSVDFESFRVSDFWHAEPAFGDRRAFGTTQMHYPFHVQPNLRGDVWFQRVPVTRMVPLSGVTLPDNVAIHLYAMTLIPS-----------
+>UniRef100_UPI001890D6EE_2705253/	126	0.288	3.375E-28	50	217	233	456	631	634
+--------------------------------------------------ALNATVISDDDAATEGCFDRACDSFSADALAAGGATaggkVTVAGQSFDWlDNGSGRFDSITADGQTIDY-YGSGTTLGILGASSGGDtSGTITLTYSDGTTSTATLGFPSWVTGHPtAFGDTTAVTTLHRDTPHGPGQARAAHyvVSYAPVAITPGKSLVSITLPNKPALHVFSIT---------------
+>UniRef100_UPI00203463BB_2888348/	125	0.258	4.608E-28	52	215	233	907	1088	1093
+----------------------------------------------------NSTAVSTDDDNPQANFDGEGWSYSAKALAAagatPGGTVSSGGFDFGWPKvAAGDPDNIEVAGaapQVLNVPSKEGStKLSLLGsAAEGSASGQATLTYTDGTTQQAEIGFSDWTLGggadKPAFGNTVAVHTAYRDVQGGGTDPVGTEIFAtAPIALQAGKQLASVTLPSSTDggvIHVFA-----------------
+>UniRef100_A0A7W9IM19_1816182/	125	0.437	6.291E-28	45	219	233	13	186	190
+---------------------------------------------VDLSEHRNNVAFTTPVALDRGRLNVWGNSLPAGTLPS--GRHLLGDVLFDLPEADGRaPDNVRCAGQFVTLPRVRADWIHLVATSERRCEEFVHIHHSSGAVDVEWLRVSDFWSADPHFGESVAGRSADMHYPHHVQRGLIGLVWLVRVPVPRREEITGIRLPDNPALHVFGLTLE-------------
+>UniRef100_A0A3N1SMM6_2485152/	124	0.252	8.589E-28	52	215	233	930	1111	1116
+----------------------------------------------------NSTAISADDDNPQANFDGEGWSYSAKALAAagatPGGKVSSGGFDFGWPEvAAGDPDNIEVAGtepQVVNVPAAPGdTKLSLLGsAAEGSASGQATLTYTDGTTQQAEIGFSDWTLGggadKPSFGNTVAVHTAYRDVQGGGTDPVGTEIFAtAPIALQAGKQLASVTLPSTTDggvIHVFA-----------------
+>UniRef100_A0A7W3ZVE1_2213162/	124	0.284	1.172E-27	34	223	233	32	231	614
+----------------------------------PAALRAPAAEPRPLRSYFDNRAVSHADRPEAADFDGSGNSLPASGLTAagwtPGSRLLLDATPLTWPDrTPGEPDNVRADGQLVAVDGRGPALTMLLAAtSPHGPTDPVTatgrVHYRDGSSARYTVTAHDWRTGPAA---TSALSLPHHHTPDGVS-TRRARLYAVTVPVDPTRSVRALALPADPgpraDVHVFAVGLRAAAA---------
+>UniRef100_UPI0005AAA057_405782/	124	0.404	1.601E-27	47	218	233	8	177	187
+-----------------------------------------------LEPFLNNQAATTPENLGDGRLNVWRNSLPAQSAPLE---IVVDGVPLRSARLDGRgPDNVLCAGQRIEVPGRRWDWLYVIGCGERRVRDTVTWHFRDGTVDRDHFALSDLWEGRSDFGEELALRTDVIHYPFHVQERIGITLWCQRVPVTSRKPLSAVSLPRNPAVHLFAMTL--------------
+>UniRef100_UPI000FCC90E2_2487275/	123	0.262	2.185E-27	52	216	233	914	1096	1100
+----------------------------------------------------NNKGISADDTNPAANFDGGGYSYSAKALasagATPGATVTSGGFGFTWPKvKPGDPDNIAVSGgdQVLDAPAGsaNATRLSLLGsASNGAADGTMTLAYADGTTQEAQIGFSDWTLGggnrQPSYGNTIALRTAYRDISGGGSQQIATDVFAsAPITLAAGKQLKSVILPTavaGGTLHVFAL----------------
+>UniRef100_A0A553ZJZ9_2595054/	120	0.264	2.631E-26	43	219	233	38	221	606
+-------------------------------------------HALPLTHLYDNTAVGGGSRPGAADFDGAGNALSAPDLSAagwtPGRALDLDAAPLTWPRAtAGRPDNVVANGQTVAV-GGTGPALTFLAAATGtgaPATGNGTVRYRDGSVSGYRLTAPDWRSGPPA---TKAVALPHLVTPHGTVDG-PARLYAVTVPLRPGRAVASVQLPRAAAsgaeLHVFALAVR-------------
+>UniRef100_UPI00225B5EAE_2975715/	119	0.387	6.686E-26	47	223	233	8	182	198
+-----------------------------------------------LDPFLNNQAATTPENLTDGRLNVWRNSLPAQSAPLD---IVVDDVPLRSAPLDGRgPDNVLCSGQRIEVPERRWDWLYVIGCGERRVRDVVTWHFSNGTVDRDQLALSDLWEGRSDFGEDLALRTDVIHYPHHVQERIGITLWCQRVPVTSRKPLGAMSLPRNPAVHLFAMTLVGRQA---------
+>UniRef100_UPI00147FFFB7_81569/	119	0.342	9.123E-26	45	217	233	36	210	220
+---------------------------------------------VPLLSYFNNIAFAGLNDLSKGQLNIWRNSYPQEAVANLPGYIDVGRVKFSFPQTDGEtPDNIRCDGQRIVLPVDQYDWIYMLCSAERRVEDEATLFFSDGSVDFVPFCVSDfWPGAKGRNGEIEALRFDSLNFPRHRQVRIEPAIWRSRIPVARETPLSAIRLPRNVAAHLFAVT---------------
+>UniRef100_A0A1M5CPJ9_1206085/	118	0.451	1.245E-25	44	218	233	10	181	187
+--------------------------------------------PVGLDAIRDNVAMTGADELGAGGLNVWRNSLPAGTYP--GAPVEVDGVPFT-GSPHTGPDNVRCAGQTLPVEIGRWDWLWLLATGERRVEDEIAMLFTDGAVDLEAVRVSDFWAAPAAFGETVAFRSEVMHYPHHVQSRLPGTIWCQRVPITRRADLVAIRLPDNLALHVFAATL--------------
+>UniRef100_UPI0003616C8A_239974/	118	0.437	1.699E-25	45	219	233	17	190	194
+---------------------------------------------VDLSTHRNNIALTTPETLRNGMLNVWGNSLPAETLRTDC--LRVGRVRFAGVRANGtEPDNVRCAGQYVDLPEIEADWIHLLATSERRCEEEVGVHYASGAATTEWVRVSDFLPARARFGELAAARSSALHYPHHRQEDLSGQVWAVRVPVTRWEAVRGLRLPDNPALHVFAISVE-------------
+>UniRef100_UPI000A606C17_1911/	117	0.427	2.317E-25	42	219	233	20	197	201
+------------------------------------------QLPLRLDEFFNNVAFTGPETLGNGRLNVWGNSLPIGTLPT--GRIRVSGVEFDVSAPDGvAPDNVRCTGQLVHLPDGtAADWLHLLITSERRCEETVHLHYASGAVDPEWIRVSDFWPATGHFGEVLAARSAGMHYPHHIQRDLGGQVWSVRVPAVRREPLRSVRLPDNAALHLFAITVE-------------
+>UniRef100_UPI0016035FF4_2448886/	117	0.273	2.317E-25	19	223	233	17	231	611
+-------------------SLPSLVPPAGAAAPGPTGVRAAAAEPRPLHRYFDNRAVSRPDRPDAADFDGAGNSLSASELTaagwAPGSRLLLDATPLTWPDrAPGEADNVRADGQLVTVTgRGPAVTLLLAATSPYGPAAPVTasgrVHYQDGSSTRYTVTAHDWRTGPAA---TSALSLPRHHAPDGVKAGR-ARLYVVTVPVDPTRTVRALALPADPgpdaDVHVFAVGLRASAA---------
+>UniRef100_UPI0020C07DD2_2707767/	117	0.398	3.162E-25	47	218	233	8	177	198
+-----------------------------------------------LEPFLNNQAATTPDNLGEGRLNVWRNSIPAQ--PGPLELV-VDGVPLRSARLDGdGPDNLVCAGQRIEVPERRWDWLYVIGCGERRVRDVITWHFADGSVDRDQLALSDLWEGRSDHGEELALRTDVIHYPYHVQERIGITLWSQRVPITSRQPLTALSLPENPAVHLFAMTL--------------
+>UniRef100_UPI000E22B0D5_871959/	116	0.382	8.028E-25	45	218	233	6	177	181
+---------------------------------------------LPLEPFLNNQAATTPANLADGRLNVWRNSIPAQ--PGPLERV-VDGVPLRSTRLDGnGPDNLVCSGQWIEVPRRRWDWLYVIGCGERRVRDYVTWHFADGSASRDRFELSDLWEGRSDYGEEFALRTDTIHYPQHVQERIGITLWCQRVPVTRRQPLCALSLPENPAVHLFAMTL--------------
+>UniRef100_UPI00068A9E4F_1463917/	115	0.376	1.095E-24	47	223	233	8	182	198
+-----------------------------------------------LEPFLNNQAATTPDNLADGRLNVWRNSIPAQ--PGPLERV-VDGVPLRSARLDGnGPDNVLCAGQRIEVPERRWDWLYVIGCGERRVRDVITWHFSDGSVDRDHLTLSDLWEGRSDQGEELALRTDVIHYPYHVQERIGITLWCQRVPITSRQPLSAMSLPMNPAVHLFAMTLVGQSA---------
+>UniRef100_UPI0003469B67_225762/	114	0.426	3.791E-24	43	219	233	1	176	180
+-------------------------------------------VPVDLSQHLNNIALTDFETLSNGRLNVWSNSLPMETLRADH--IQVGRVGFAGSKATGtEPDNIRCAGQYVDLPEMNADWIHILATSERRCEEEVGVHYTSGAVAGEWIRVSDFLPARAHFGEMAAARSFAMHYPHHRQEDLRGQVWCVRVPVTRWEAVRGLRLPDNPALHIFAASVE-------------
+>UniRef100_V6K9D2_1352941/	113	0.429	5.170E-24	91	221	233	0	134	140
+-------------------------------------------------------------------------------------------MAFEFPaRATGRGDNIRCRGQLLPLPGVRADWLYLLGAAERRTEDEVELHYADGAVRTAWLRMSDfWPETAAWFGEPEAFRGSGLRYPRHTQDGHRPAIWQQRVPVTVPGELTALRLPDNPAMHVFALTavLEPG-----------
+>UniRef100_A0A022MHX4_1883/	112	0.369	1.311E-23	47	218	233	3	172	189
+-----------------------------------------------LEPFLNNQAATTPDNLADGRLNIWRNSLPARSEPLE---AVVDGVPLRSAPLDGRgPDNVLCSGQRIAVPERRWDWLYVIGCGERRVRDVLTWHFTNGSVDRDHLALSDLWEGRSGYGEELALRTDVIHYPYHVQERIGITLWCQRVPITSRQPLGAMSLPKNPAVHLFAMTL--------------
+>UniRef100_UPI001672C615_67368/	111	0.384	4.533E-23	87	227	233	1	143	145
+---------------------------------------------------------------------------------------ELEGTVFAFPaRDTGAGDNVRCRGQLVELPAGRWDWIGLVGAAERRTEDEVELHHADGTVRREWLRMSDfWPQTAPYFGEPLAFSTSGMRYPRHTHRHHAPSLWQQRVPVRVPAPLAAVRLPDNPAMHVFAMTVTADEESRLA-----
+>UniRef100_UPI001C593FAE_2749826/	109	0.259	1.149E-22	35	221	233	12	198	203
+-----------------------------------GRRQSVRYSTVELKSHFNNIGFSYPDIY--GNFTGFGSSYPGDQFPhREDNIVNVKGIPFFLYNAKGRSNNIEFAGQSVEVLPDMYSALHVLGSSDNGSFSEYLKFYLKKSpVGQYKLELSNWVAGVPAYNEHEAYRCSALCAGQQVIETVKPVLWLQSVRFRQPIVFDEISLPDNMCMHLFSLTFEGA-----------
+>UniRef100_A0A5B8M4I2_2599293/	109	0.270	1.149E-22	52	232	233	890	1077	1311
+----------------------------------------------------NTVGTASESDTGVGDFDAAGNSYSREQLAsvglAPGATGKVGSLHFTWPSSPeGAPDAVNPTGQTIDL-QGEVHSIAFIGAGiNGGASDTAVATLDDGSTMPVDFSFGDWVlptsDGSPAFGNSVVAKMSHRN---AVTQVQGAYLFATTpATAPDGRTIVSVQFPTDSKERVFAIATDVAPATNTATQLTT
+>UniRef100_A0A838EJ16_2740538/	109	0.237	2.135E-22	91	217	233	15	153	156
+-------------------------------------------------------------------------------------------VVFTWPDVPaGAPDNYQAAGQVIPVQSmSNATILAFLGSATNGaSSGTATIKYTDGSTQDFTLGFSDWTlngnTNQPSYGNAISYTTSYRNNAHltNGKDTIQTYIFYSSVNLEAGKQVASVTLPTTvtgGQMHVFAVT---------------
+>UniRef100_UPI000B595552_1501230/	107	0.318	1.004E-21	42	219	233	3	182	196
+------------------------------------------FHAMDLRPYFNNRGFTYESRYGEGRLTMGSSSFPAESIRF-GRMYRFGGIPFRY-QASEDGDNIETSGQAVALPwmPGKLDCVHALGvSANGDSFDCVSFVAGDRLLHTARLALSDFVSDRPAFGDRLAMTLPYMHMVSGRYAHVRPNLWICSIPYPgEAGAARALVFEDNPSMHIFAMTLE-------------
+>UniRef100_A0A2T0PYA0_1144618/	105	0.433	3.463E-21	70	218	233	3	150	155
+----------------------------------------------------------------------WRNSLPAEEFPS--GELVIEGVPFHPPRPrRGADDHVTCDGQLLAVAEGGYDWLYLLACSERRVEEEIALHFTGGQVDFEPLRVSDFWAAVPFFGESAAFTSAVMHYPHHVQPRVPGTIWCQRVPVVRRAPLAAVRLPRNAAVHVFAATL--------------
+>UniRef100_A0A838DPV7_2740538/	105	0.260	3.463E-21	52	221	233	3	194	583
+----------------------------------------------------NNIGItgTGYAALTAGGFDTAGDSYSAALLAAltpavtAGSTVTVNGVAFTWpgPDITTNYDNWkTAAAQTITFaPVSNATAVAFLGAASDGsSSGTATINYTTGVPQTFTLGFTDWKTGTPAFSNTLALTLSNYDTSAGVVKSPaaPVYVYYadsSSVTLDPTRIVASVTLPAAVTggglVHVFAAAIKTS-----------
+>UniRef100_A0A081P3V2_1501230/	104	0.296	6.429E-21	42	219	233	3	182	196
+------------------------------------------FHAMDLRPYFNNRGFTYESRCGEGRLTMGSSSFPAESIRF-GRMYRFGGIPFRY-QTSEGGDNIETSGQTVALPwmPGALDCVHALGvSANGDSFDRVSFVAGDRLLHTARLALTDFVSDRPAFGDRLAMTLPCMHMVSGRYAHVRPNLWICSIPYPGEAGAApALVFEDNPSMHIFAMTLE-------------
+>UniRef100_A0A2T6FTL9_189691/	104	0.307	8.759E-21	42	219	233	3	182	196
+------------------------------------------FHAMDLRPYFNNRGFTYESRCGEGRLTMGSSSFPAESVRF-GRMYRFGGIPFRY-QTTEDGDNIETSGQTVALPwmPGTLDCVHALGvSANGDSFDRVSFVAGDRLLHTARLALSDFVSDRPAFGDRLAMTLPYMHMVLGRYAHVRPNLWICSIPyLGEAGAARALVFEDNPSMHIFAMTLE-------------
+>UniRef100_A0A838XCG5_1507437/	103	0.269	1.626E-20	43	218	233	6	185	189
+-------------------------------------------HIIELASIYNTKGVSIQDPKLVAQLDHIHSSIPGEIFP-SDEVISYQGIPFAFPLTEAvDNDVISCDGQIVEVNAQRsFQTLAFLGFSLFGDyQDKFTIHYADGVEEEVRFGLTNWKQyktGTPLFGEQIAMSLPY-YVENMILTELPRTVWLQKVTLQHSGHIKQVILPRNPYLMVIALTL--------------
+>UniRef100_A0A060CMX9_487357/	102	0.278	4.108E-20	44	153	233	73	186	187
+--------------------------------------------YANLAAAYNNVGVTSGDDPKPGNFDGTGNSFNAELLAgqglTPGATVSANGYSFQWPNvAPGVADNVQTAGQLIKL-SGSGNTLAFLGSEAGDRTDTVTVHYTDGTTSTGTVGFP-------------------------------------------------------------------------------
+>UniRef100_UPI0020C7B24C_2810306/	102	0.256	4.108E-20	47	160	233	159	279	401
+-----------------------------------------------LASAADNVGVTEQDDPGPGDIDGGGSSFIAERLAQkgvtPGAAVKANGFSFTWPDaAPGTPDNVTGKGQTIQVSGDeKGNALAFLGTGTSGSaEGTATVHYTDGTTAEAKLGFPNWAVCPP------------------------------------------------------------------------
+>UniRef100_UPI000B9A8B31_1465/	102	0.252	5.595E-20	43	218	233	6	185	189
+-------------------------------------------HIIGLASIFNAKGVSIQDPTLAAQLDHVHSSIPGEIFP-SDEVISYQGIPFAFPLTETvENDVISCDGQIIEVNaPSSFQTLAFLGFSLFGDyQDKFTIQYVDGIEEEARFGLTNWKQyktGTPLFGEQIAMSLPY-YVENMILTELPRTIWLQKVALRHSEHIKQVILPRNPYLIVIALTL--------------
+>UniRef100_UPI001942DCDF_926357/	101	0.233	1.038E-19	52	175	233	739	875	1109
+----------------------------------------------------DNHGISADRTEGQSDYDGWGSGYSRSALAgagvVPGNRFAAGGVSYVWPNTrPGQPDNVVAAGQRLTVaSPAGATRLGLLGSAEGqpaGAAGTLTVHYADGSTTPAEVGFSDWTlaggTATARSDNVVAARMPYRND---------------------------------------------------------
+>UniRef100_A0A652KEP5_1827978/	100	0.395	2.620E-19	90	227	233	2	145	147
+------------------------------------------------------------------------------------------GTAFVFPPrPTAGGDNIRCRGQLVELPdgaaGGRYDWIGLVGAAERRTEDEVELHYRDGSVSRAWLRMSDfWPQTAAYFDEPLAFRTASMRYPRHTHRHHAPALWQQRIAVVRPEPLAAVRLPDNPAMHVFAMTAVVDEESRLA-----
+>UniRef100_A0A931JBU5_114683/	99	0.271	4.857E-19	75	220	233	0	147	150
+---------------------------------------------------------------------------PMAQLPQTGQT-EDDGIAFAFTNgSEGSNNNVIAAGQKVTVAAGGYTKLHVLGAGDTGNvSVPAEAAYADGSTGKLTIQLTAWRSG-PAYGETEAVRTSQIHTRTG-PLGTKAAIFHQVVELDPAKELSAITLgaPSgTARAHIFALSLEK------------
+>UniRef100_A0A942KCA5_2478917/	97	0.304	2.270E-18	114	227	233	0	113	114
+------------------------------------------------------------------------------------------------------------------MPEGRYSELLLLGASEQGSyQATVRFVYQDETSDELTLGLSDWCQ-LPRFGEAIAYEFIQRRGATGAMERITCRIYFQTLPLRPEAVLTRIVLPDRDTMHLFALTLRQAESEETP-----
+>UniRef100_A0A838DN80_2740538/	95	0.283	1.059E-17	51	157	233	41	160	458
+---------------------------------------------------YNNVGItasTSTAAMALGNFDNAGDSYPSENLVAdgfiPGTIVTEYGIDFVWPNvAAGQPDNWKAAGQTIAVNAAPGDSvLAFLGAAtdtfNRGAAGTATIHYRDGSSQNFRLNFTDWLN---------------------------------------------------------------------------
+>UniRef100_A0A973VFE2_1873460/	94	0.295	1.441E-17	45	223	233	5	185	187
+---------------------------------------------VDLSGLVDRIGATYDTDRDSGEFNPWGNSFPAEELPF-GGTTAVGGVPYALVDKPPRgPDHLEALGQVIDCAAtGPAHGLALLAAGEQGPQElRVHVHLDGGRRLSLPVTVPGWSVRPDAPMTPDQLRAGHLHYPGDYGLARlLPALWSRVLRL-PGVPVTAIELTANPLVHVFAVTLEIGAA---------
+>UniRef100_A0A951HER9_2800791/	92	0.273	1.241E-16	43	222	233	879	1050	1255
+-------------------------------------------TPLLLDALFN--------SQSTGDFDTEKRGYDSASLPPPGLYhLGANHIPFRLTGHIGS-DNIACNGQVIQLPPsSRGKTLYLLGAAAPGDQgGLFSVEGTQGHLTRLPVRMNDWVLGGSLHNE-AAFTFERQHTAEGLR-AMTTHFWITSLQLPSDQRPVRLRLPYNTNLHLFAATLAAAS----------
+>UniRef100_UPI001EF5A1EE_1795630/	89	0.271	7.834E-16	31	142	233	879	995	1009
+-------------------------------VTAPGrcAIQTATSCAVDLSGAYNNDGVATLTDPGQGNFDGTGLSFAANLLPAPGAT-TIGGATYQAPPTTGtAKNFVKSTGQAITLPSGNYTSLDIVAAdngSTGSAAATAVVTYSD------------------------------------------------------------------------------------------
+>UniRef100_UPI001EF302F3_2706031/	85	0.282	2.280E-14	82	220	233	8	147	527
+----------------------------------------------------------------------------------PGAELTVAGAPLRLPDpAPGAPDNVRADGQRVRVT-GRGDALAFLVTATGGrALGRGSVEYADGHRSSFRVEAPDWRTGTLA---TSAVALPRISTTDGPRKARAA-LYVVTVPLRHDAAVRAVTLPRDPlgpaSLHVFALGVRP------------
+>UniRef100_UPI001AD6B2B7_67304/	81	0.293	3.568E-13	35	125	233	42	130	243
+-----------------------------------GWVPVPDPVPVPLDSLYDNDGIDTATARG-GGFDGSGYTFPGEELPA--GRVEVDGVPFDFPsSTAGTKNNVVALGQRVDLPRGRYLSAVFL-----------------------------------------------------------------------------------------------------------
+>UniRef100_UPI001C8AAAD7_1490222/	71	0.311	1.299E-09	47	118	233	906	982	993
+-----------------------------------------------IEWYQNNAGISDDGKAGQANFDGGGWSYSAQALAAeglkAGQPVAWNGFTFTWPNrRPGQLDNVQASGQVVDLPSAP------------------------------------------------------------------------------------------------------------------
+>UniRef100_A0A2N5XH94_2593676/	70	0.286	3.213E-09	16	120	233	30	143	151
+----------------APVSATATASPGTARDASPGSGvapTSADPSPLPLHRLFDNTGTAPDGpvAPGQGGLDGAGNALSRDDLAaagwAPGSRLTLDGTPLTWPDSrPGQPDNVVADGQAVR-PDGHGD----------------------------------------------------------------------------------------------------------------
+>UniRef100_A0A4Y8YB55_1883/	61	0.420	3.184E-06	155	221	233	4	72	78
+-----------------------------------------------------------------------------------------------------------------------------------------------------------WPETAAWFGEPEAFRGSGLRYPRHTQDGHRPAIWQQRVPVTVPGELTALRLPDNPAMHVFALTavLEPG-----------
+>UniRef100_A0A942KBR5_2478917/	60	0.275	4.289E-06	34	109	233	642	720	721
+----------------------------------PVSFEEGVFVALDLGGAFNNDAFSDPSNP-RGNFDnrsgVLGATYPAERAPAENSIVEVSGTLFRFPPTSADANNIALKG---------------------------------------------------------------------------------------------------------------------------
+>UniRef100_UPI001F0BFC40_2203210/	57	0.268	4.622E-05	47	108	233	130	196	287
+-----------------------------------------------LAAAYNSVGVTDESNTAPGDFDGGGNSFSAQKLAdvglSPGAAVTALGAELTWPDvPPGVKDNVSSR----------------------------------------------------------------------------------------------------------------------------
+>UniRef100_UPI000A7FA51B_860235/	46	0.307	1.287E-01	33	84	233	723	774	827
+---------------------------------LPPLPDQGTTVTVDLTAAMDNDAFTNEFHMGDGDFDGTGNTYPAAQLPQTGQ----------------------------------------------------------------------------------------------------------------------------------------------------
+>UniRef100_A0A1U9KA27_1471761/	44	0.254	5.502E-01	170	222	233	0	57	146
+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------MPYRNSPSG-QDGLATYVYYTYVPLDhPDKMVRSVTLPdadtiDKGRIHIFDIAIKYAA----------
+>UniRef100_UPI001915FEBF_2778368/	44	0.318	9.823E-01	69	128	233	10	78	79
+---------------------------------------------------------------------GCGESYSAQALlqapphIAPGNAVVVNGVTLTWPNvAAGSQDNYKTKGQTVPVTPvnGATTQAFLEGSS--------------------------------------------------------------------------------------------------------
+>UniRef100_A0A2A3HR12_1938860/	151	0.439	5.047E-37	35	231	233	6	203	212
+-----------------------------------PQASAPRYRVVELADHRNNRAATRVHTTAAGGFNVWRNSFPAEHLPPGGSQVEVGGVPFSFPPVGEGDDNVRCDGQFIAVPAGRYDWVHLLAAAERRTEDTVELHYADGSVDTEWLRVSDFWAAPAWFGELPAYRTPVMHYPYHVQPGVSAHLWAQRVPVPRRTELAGLRLPRNIAVHVFAATAqEPPPGTAGLPAPD-
+>UniRef100_C7PY52_479433/	147	0.267	2.151E-35	47	230	233	1074	1269	1548
+-----------------------------------------------LPAAFNNDAITNDSNRGGADLDGAGASFSAQALAsvgvTPGAPLVHDGLTFTWPDRQvGQSDNVVAAGQTIDI-SGSGSTLGLLGTSTWGaSSGSGTIAYTDGSTQPYTIAFGDWANGTPPTGGDVAIRAPYGNQP-GNQTGWAATIDYFPITLDATKTVQSITLPpgsaqphgGTPAMHIFAMSIKSDQLSVTAPTA--
+>UniRef100_A0A1B4ZDD3_1213862/	141	0.403	1.250E-33	45	228	233	26	210	211
+---------------------------------------------LDLTAFADNVGVTSPDRLSEGAFNIWGNTFPADELPK-GGPVDIHGIPFRFPAvGTGQPDNVRCAGQFIDVPVGRYDWIHVLAAAERRTEDFVRLHYTDGAVDPEWLRVSDfWPETASRFGESAAVSCTRLHYPRHIQRSMGPTLWRQRVAVPREQDLSAIRLPDNPAIHIFAMTLAPATQPETTQ----
+>UniRef100_A0A4R0HF04_1124743/	133	0.394	1.199E-30	25	218	233	35	228	237
+-------------------------MPDQMPDQMPATSVQARCRAVNLAPHRNNVGSTPATDTRGGAFNIWGNSFPAEELPAPGQFV-VDQVAYDFPPTgRGTADNVRAAGQFIEVPSGRYDWLYVLGAAERRVEDELAFHFADGSVDFEQLRLSDFWAAPGWFGETQVRATRSMHYPFHVQAGVPAMLWSQRVPVTRRAALAAVRLPRNPAVHLFAATL--------------
+>UniRef100_A0A2T6FTL9_189691/	98	0.302	1.187E-18	42	219	233	3	182	196
+------------------------------------------FHAMDLRPYFNNRGFTYESRCGEGRLTMGSSSFPAESV-RFGRMYRFGGIPFRYQTTEDG-DNIETSGQTVALPwmPGTLDCVHALGVSANGDSfDRVSFVAGDRLLHTARLALSDFVSDRPAFGDRLAMTLPYMHMVLGRYAHVRPNLWICSIPyLGEAGAARALVFEDNPSMHIFAMTLE-------------

model/Protenix-pxd/examples/7wux/msa/2/non_pairing.a3m

@@ -0,0 +1,436 @@
+>query
+MGSSHHHHHHSQDPNSTTTAPPVELWTRDLGSCLHGTLATALIRDGHDPVTVLGAPWEFRRRPGAWSSEEYFFFAEPDSLAGRLALYHPFESTWHRSDGDGVDDLREALAAGVLPIAAVDNFHLPFRPAFHDVHAAHLLVVYRITETEVYVSDAQPPAFQGAIPLADFLASWGSLNPPDDADVFFSASPSGRRWLRTRMTGPVPEPDRHWVGRVIRENVARYRQEPPADTQTGLPGLRRYLDELCALTPGTNAASEALSELYVISWNIQAQSGLHAEFLRAHSVKWRIPELAEAAAGVDAVAHGWTGVRMTGAHSRVWQRHRPAELRGHATALVRRLEAALDLLELAADAVS
+>B4XYC1	250	1.00	4.608E-69	19	351	352	4	336	337
+-------------------APPVELWTRDLGSCLHGTLATALIRDGHDPVTVLGAPWEFRRRPGAWSSEEYFFFAEPDSLAGRLALYHPFESTWHRSDGDGVDDLREALAAGVLPIAAVDNFHLPFRPAFHDVHAAHLLVVYRITETEVYVSDAQPPAFQGAIPLADFLASWGSLNPPDDADVFFSASPSGRRWLRTRMTGPVPEPDRHWVGRVIRENVARYRQEPPADTQTGLPGLRRYLDELCALTPGTNAASEALSELYVISWNIQAQSGLHAEFLRAHSVKWRIPELAEAAAGVDAVAHGWTGVRMTGAHSRVWQRHRPAELRGHATALVRRLEAALDLLELAADAVS
+>SRR5215472_11685424	196	0.515	1.144E-50	1	346	352	63	412	423
+-GHSRAGRDAGDGAVTAVSIEPLELWTRDLGSCLQAVFATLLLREGQDPVTVLGSAWDFRYEPGDWRSEEFYYPCAGRPLAEALAPLHPLTSVWHRapaDGPDPLRPLRAQLAAGRLPIAAVDNFHLPFRPAFGDVHAAHLLVVAGIDDERgqVLVSDAQPPEFQGPIPVADFLRAWGSANPEDVQDAFFSNSPLDRRWLEVRFTGEFPKPTRAWLAEVLARNVACLRWPDAGQLWSGLPGVERYVDRVLSQ-ACGPGGSAVLEELYVLSWGLQAHADLHAEFLRRHGVAQDLPALREAAEVVDRVAHAWTGFRMTGAHGRLDRPDFGGDLARHGGVLVRAHHEAASALELA-----
+>3300005562.a:Ga0058697_10000188_20	192	0.458	4.730E-49	22	350	352	9	336	338
+----------------------VRQWYRDPLSCLQSTLATVLLGAGVEPLPVLGLAWEFLFKPGDVRREEFYYPCRfEGDVARSLAPYHPIRSSWWSPAPgeDPLAELARRVEDGELPVAGVDNYHLPFRPAFRDVHAAHLVVVYAIDreRDEVGVSDAQPPAFRGSIPTEDFLAAWASPNRADAEDAFFSDSEIGRRCLSVEIEGPIAPLDPVRLEAALAENLARF----GAGGWSGLAGLRRYLDDLS--ARAFAGERRPLEELYPFGWGMQAQTYLHGELLREVGADWSFPELAEAGRAVQEVASAWTGLRMTGAHALAAPAAAAAELRRHGNRLRRRYETALERVAQAVESL-
+>SRR6266536_566964	191	0.460	8.792E-49	21	346	352	170	497	519
+---------------------PVRLWYRDLVSCLQATFATVLLHAGRHPLAALGAAWGFYCWQGEVTTEEFYYGCRHGSLGASLAPHHPVASRWHAGPDGSdpLAPLRDQVGAARLPIAVGDNYHLPFRPAWHDVHAAHLLVVYGFGDGTVEVSDAMPPAFQGPIPVEDFLRSWGSTNPRDEQDDFFSNAAIGRRWLEVTLGEPWPVEDRPWLRSVLQSNLDDLAGGGDglAGGLLGLPGLRGFLDELLARAGRGDSSVLL--ELYVFGWGVQAQASLHGELLRERGRAWDLPALSEAGRAVESVAHAWTGLRITGAHGRRDPAAVAADLARHGRAVEHAYRHAADLVALA-----
+>B5HTY9	190	0.432	1.199E-48	20	350	352	14	349	350
+--------------------PEPELWYRDLISCLQSTFGSVLARAGADPLAVLGAGWRFLHLPGDVRSEEFYYPCPADesggtDLGAALAPHHELHARWWQpaDEDDLWREVRETLAEDRLVIAAVDNFYLPFRPAYQDVHAAHLVIVYGLDETRgvVHVSDAMPPAFRGAVPIEDFLRSWGSANPSDVQDAFFSDSGIGRRCLDVRLDAPAGPLTPELLGGFLRTDVDGFTTATPA--RTGLAGYDEFAAELLDRCRAQDAG--ALRELYPFGWGMQAQASLHGELLRRCGSRWDDPALAAAGRAVESVAHAWTGLRFTGAHGLADPRAAAPDIARHVTRLRGAYACAVDAVGAAAGRL-
+>A0A1G8BDD9	184	0.361	1.702E-46	22	350	352	7	341	344
+----------------------LDFWFHDLCSCLQDCFGTLLLRHGQDPVAVMGAAWEFHHAPGPVATEEFYHPAPRPTLGDNLMPHHPVRATWreQEDVESSWQDIRASIIDGRPAIAAVDNFHMPIRPAYGDVHAAHLMVVWGFDDEagEVYVLESTPPQYSGPVSLADFQRARSSANdsRPDTRDYFFAGAGIRGRWIDVTVDGAFPAVEREWVADVVTANARGFAEPAPGPGWSGLTGLTTWLEGVCDRADDIEDAGVALAELYTAGWAAQSAAALHADFLRDMGNRFGCDPLVHAGRQVDRLANQWTPLRILGAHGSTTGHRHTDQLRDRVRRFTAGHRDAVARLEAAAAAL-
+>GraSoiStandDraft_9_1057307.scaffolds.fasta_scaffold4049564_1	183	0.356	4.309E-46	20	350	352	5	338	339
+--------------------PGIRPWRHDLTHCLHTTFGVLVGFYGLDPLHVLGAGWGFGYRLDDVRREEYYFPCLDGSLLAGLAPHHGLDSHWHEPEDAAhgWEQVRACVAAGQPVAVAADNFHLPFRPAFSDVHTNHLLAVYGFDDEegTVYVADPVPPRFDGPITVDALTNARDSNNPItHERDMFFTANPIANRWLTVELTGPQPTFDRDFVRRVLLSNLDGFARGKVEGPTMrGVAGLREF---LTACLPRIADEPQRIDEVFIVAGVTLAITGLHADFLADSGRRLGLPALVELGREVDRVAHHWTALRIGVANSRSAPIDDLPALLRRGRNLVADQERVLDRMAQTAAQL-
+>SRR5581483_8883662	181	0.405	2.024E-45	21	319	352	13	314	353
+---------------------PMAHWHHDLCSCLQCCMASVMHYYGRDPILTLGAVWDFYYSPEDLRKEEFYSPCRWSGLAESLLPYHPVTSRWHQPDDPevGWLQVKEVVQNGSPVIVAVDNFYLPFRPAYQDIHAGHLILVYGFDEetDQVYVLDSMPPAFIGPIALTDLKASRSSLNPADERDYFFSNAPVANRWLELNIEAPFPQFTEKWVMDVINANLRRFTTPCDGSALSGMSGLARYF-DLLDQNMANPAGHHALEELYVLGWSIQAATALHADFLMQVGKQLNWPRLGSIGRQVAHLAHHWTALRMLGAHGRAHPR--------------------------------
+>K0K7T6	179	0.411	6.974E-45	21	349	352	4	332	334
+---------------------QVEQWYRDPVSCVHATLAEVVRHAGAEPLEVLGLGWEFRHLPGDVRPEEYYWPCRvPGDLAGSVLPHHRVRSVWRTaPEPDPLTALTGPLAVGRLPVLAVDNYHLPFRPAYHDVHAAHLILVRDLDLDRgvALVSDAMPPAHRGELPVADLLRAWRSTMPPDEQDVFFSGRGGQARWLEVIVEAVPPPLTPEALRSALRANVDGFQSQGP--ERTGLAGFGEFLAEVVDRSAAGEAAAP--AEVYTFGWSMQAQSAVHGELLRTCGMRWAEPELAEAGRRVEQVAHHWTALRVTGAHGRTDPVAAAPGLHRHGERLRRSYEQAVESLALASAA--
+>A0A1L7NQD0	179	0.423	1.294E-44	20	350	352	14	344	345
+--------------------PEPELWYRDLISCLQATCGSVLAREGVDPLDVLGAGWQFLHVPGDVRPEEFYYPCSEGELGRALAPHHDLGARWWQPADENdvWREVREHLADDRLVIAAVDNFHLPFRPAYGDVHAAHLVVIYGLDETRgvVYVSDAMPPAFRGAVPIEEFLRSWGSVNPTDVQDAFFSNSKIGRRCLDVSLGTRRGPLTPELLGGYLRTDIEGFTTETSA--RTGLAGYDAFVGELMERCRAGDA--DALRELYPFGWAMQAQASLHGELLRRRGRDWDDAVLAGAGRAVETVAHAWTGLRFTGAHGHGDPRAAAPDIAHHATLLRAAYARAVDAVGAAAARL-
+>SRR5919197_4477474	179	0.452	1.294E-44	21	350	352	224	552	553
+---------------------PPRQWYRDPISCLHSTLAAVVGYEGADPLEVLGLSFEFLYKPGDVRPEEFYFPCRfGDDLARSIAPYPPVRSEWWRaTGEDPLAELAARISNGELPIVAVDNYHLPFRPAYHDVHAAHLVVVYGIDAGRreVSVSDAMPPAFQGAIADGDFLRSWSSPNPRDDQDAFFSDARIDRRCLSVRFETPIPPLDGARLKDALESNSQRLSAG---EGWSGLPGLRRYLDELVGRADAGERRP--LEELYPFGWAMQAQAYVHGELLRVCGADWSVPELREAGRAVESVAYAWTGLWITGAHGLSAPAEATSGLRRHAGRLRRRYEEALEAVEQAVEAL-
+>SRR5215211_2955382	175	0.442	1.534E-43	31	350	352	1	330	348
+-------------------------------SCLQATFATLLLHRGHDPLEVLGAHWEFRYRPGDVRPEEFYFPERvAGDLGASLAPHHPVSSRWASGPAErPLDGIAAELRAGRLVIAAVDNFHLPFRPAFGDVHAAHLLVVYGIDERHGQVHlsDAMPPAFAGPIPVEDFMRSWSSQNPMDAQDAFFSDAGIGRRYLRTTVGEPSRDLDPRHVLACNRRLFDGGAQSAgaqpagaqPAGDWTGRSGRARYLDQLGRRARAAD--TRALEEVYPFGWGMQAQASLHGELLGRWGRQHAVPRLREAGRLVEAVAHGWTGLRMTAAHGRTDPVAAAPDLARHASRLRHAYDLAHEALAEAEAAL-
+>A0A1M5CPU0	173	0.391	7.186E-43	24	343	352	7	328	364
+------------------------GWYRDPLSCLHVTLAVLLERAGRDPLDALSRDFGFRWIPGDVRGEEFYWPVdEPDDPVAGMAPSAGIRSRWRTAAADPLAALASALAAGRPPIVAVDNFHLPFRPAYHDVHAAHLVVVTALDvaGGRAFVVDHMPPAHAGWLPVEHLLAAWGSVNPPDAQDDFFSGEPIERRWLEVDLGPGLAPLTAADAAASAVENCARFgPLLGAPAPSSGRADLHALAA--AAVAAARDADGGALAEVYTFGWSMQAQAAVHGELLRRTGAAAGDLVLAAAGRKVEAVAHVWTGLRVTAAHGRLDPAAVAPAVGRHAARLVTAYETAFAAL--------
+>GraSoi013_1_40cm_1032412.scaffolds.fasta_scaffold160357_1	172	0.404	1.814E-42	20	332	352	5	320	339
+--------------------PGIGHWRHDLTHCLHTTMGVLLGFYGLDPLHALGAGWGFAYPAGDVRREEYYFPTVDRSLLGSLAPHHPLSSSWHEPAGaeQGWHDVREAVSGGVPVAVAVDNFHLPFRPAYSDVHTNHLLAVYGFDDDRheAYVADPVPPRFQGPIPLAALAAARDSANPiRHDRDLFFTANPLANRWLTIHLDGPQPALDLDFVRAAMLRNVAGLADGTAAGaVLRGLAGQRAF---LESALADLDAGEHRVDEVFVVAGAILAVTGLHADFLGAAARRLDRPALAELGREVDRVAHHWTALRIGVANARSRPGAEVPALQARAAAL-------------------
+>SRR5919197_654015	172	0.393	2.471E-42	42	347	352	1	309	311
+------------------------------------------AHRQLDPLVVLGSGWTFAYSPGEWAPAEFFYPALDGSLAATLAPHQPLSIVWREpgSPEEAEQELVAALAGGRPSIVAVDNYWLPFRPAFRDVHAAHLVVVYGHDAERgsFAVLDAVPPAFRGWISRETLARARGSDNPAADDEAFFRGAPIANRWLDVDVDGAVSEVEPEWLGRVVAGNLAHMLGPSGETTWTGLAGVRRYVEWLAERAAAEDGEP-ALKEAYGFGWAPQASAALHGAFLHAAGLRLDAPGLREAARTVDLVAHAWTPLRVGAGHAVSDPPAAAGYLARRGRALVTAYEAAIDRLRELA----
+>A0A1C4Y1U0	170	0.438	1.156E-41	25	350	352	39	368	369
+-------------------------WYRDPLSCLQTTFAAVVDAAGGDPLEVLGAGWEFRHLPGDVRTEEFYHPSRhPEDLGRSIAPHHHVRSRWTTPaaDRDPLSELADEIAAGRLPIAAVDNFHLPFRPAYHDVHAAHLVVVYGVDlaRDLVLVSDAQPPAFTGPIRAEDFLAAWGSVNPADDQDAFFSATRIDRRYLRVEI-GDSRPLDRDGLRAALRANVDGFTAAPASDGgaWTGLAGLRRYLDEVVAAAAAGD--SATVRDVYPFGWSMQAQACLHGELLRTVGVDRDLPCLREAGRAVEAVGHTWSGLRVTAAHGWPAPQAAAESLEHHGARLQQRYQCAVEAVDRAVGRL-
+>SRR5919197_910194	169	0.457	2.916E-41	22	346	352	151	470	475
+----------------------IRQWYRDPVSCLQSTLATVLLAADTEPLPVLGLRWEFLFVPVDVRPEEFYYPCRfADDLARSLAPYHPLRSSWWSPAPEedPLAELARRVEGGELPIAAVDNYHLPFRPAFHDVHAAHLVVVYAVDreKEEVGVSDAQPPAFRGSIPAKDFLAAWGSANPADTEDAFFSDSEIGRRCLSVEIEGPIPPLDAERLRTALEENLAGFVT--------GLADLGRYVDDLE--ARALADERRPLEELYAFGWGMQAQTYLHGELLRETGAGWSVPELAEAGRAVHEVASAWTGLRMTGAHALGARAAAAADLRRHGNRLRRRYEAALEHVAQA-----
+>SRR5919204_1883335	168	0.472	3.969E-41	22	323	352	124	424	427
+----------------------VRQWYRDPLSCLQSTLATVLLAADAEPLPVLGLAWDFLFVPGDVRPEEFYYPCRfEGDVARSLAPYHPVRSSWWSPalDEDPLAELARRVEDGELPVAAVDNYHLPFRPAFHDVHAAHLVVVYAVDreRDEVHVSDATPPAFQGAIAAADFLASWSSANPADDEDAFFSDSRIGPRCLAVEIDGPLPPLDRERLRAALCENLARF----GAVGWSGLAGLRRYVDDLTARAQAGERRP--LEELYAFGWGMQAQTYLHGELLRETGAEWSAPELAEAGRAVQATASAWTGLRVTGAHGPAAPGDPGP----------------------------
+>SRR5919202_365103	167	0.449	1.362E-40	22	350	352	157	480	481
+----------------------VRQWYRDPVSCLQSTLATVLLAAGAEPLPVLGLRWEFLFVPGDVRPEEFYYPCRfEGDVARSLAPYHPLRSSWWSPaaGEDPLAELARRVEGGELPIAAVDNYHLPFRPAFHDVHAAHLVVVYAVDRERgeVAVSDAQPPAFRGAIPAEDFLAASGSPNPADAEDAFFSDSEIGRRCLSVEIDGPIPSLDAERLRAALAENLT--------DFATSLAELGRYVDDLE--ARALDGERRPLEELYAFGWGMQAQTYLHGELLREMGAGGSVRELAEAGRAVQEVASAWTGLRMTGAHGLAAPAAAAADLRRHGNRLRRRYEAALEHVTRAVESL-
+>A0A2A2D0D6	158	0.369	8.748E-38	22	348	352	88	416	422
+----------------------VRPWRHDLGGCLHGCLATLLEHRGVPALPVLGAAWTFRHFPGGVRREEYYYPcADGESLLTALAPHHPVRSVWHEPADAAtgWEQVRDAVAAGTPVAVAVDNYHLPFRPAYRDVHSNHLVVVHGYDEErgTVRVLDAVPPAFHGDITLAELTASRDSGNeLVHERDMFFTGVHIDNRWLSLEldaAPGDFPALDRAEVARVLALNLAHFAAPPDGDACTGLAGQQAF---LEGTVKRLTAGEDIRDELFVAAGAALACTAVHADWLALAGRTLDLPGLVEQARSVERVAHHWSAVRIMAALTRDGGLTP----RRLAGRVHALLKDHESALTALDD---
+>688.fasta_scaffold2401073_1	156	0.357	7.519E-37	22	308	352	11	304	347
+----------------------VVSWRHDLVGCLWTSAATILAFHSAPVLPTLGAAWGFRHQPDDLRREEYYYPCKPGvSLYEAIAPYHPVRSRWHEptDAEQGWIQVRDMVLSGEPVVVAADNFYLPFRPAYQDVHTNHLIVLYGFDTERgsATVLDAVPPRFNGEITITEFTAARDSGNPqLHDRDMFFTANPLGNRWLEVEvETAAFPPFDLDMIKYVIRRNLDGFAASPDGGVRDGYSGMAGQAAYLDDLAGRLEVGENVRDELFLVAGAVLANTALHADWLALAAGVIRIPALAEAGRDVERVAHHWTAIR-------------------------------------------
+>SRR5580658_171216	156	0.357	7.519E-37	22	308	352	56	349	392
+----------------------VVSWRHDLVGCLWTSAATILAFHSAPVLPTLGAAWGFRHQPDDLRREEYYYPCKPGvSLYEAIAPYHPVRSRWHEptDAEQGWIQVRDMVLSGEPVVVAADNFYLPFRPAYQDVHTNHLIVLYGFDTERgsATVLDAVPPRFNGEITITEFTAARDSGNPqLHDRDMFFTANPLGNRWLEVEvETAAFPPFDLDMIKYVIRRNLDGFAASPDGGVRDGYSGMAGQAAYLDDLAGRLEVGENVRDELFLVAGAVLANTALHADWLALAAGVIRIPALAEAGRDVERVAHHWTAIR-------------------------------------------
+>SRR3569833_1969934	149	0.341	1.019E-34	22	308	352	167	457	480
+----------------------VRPWRHDLAGCLHACAGTLLDHQDIPPLDALGAHWGFYYPPGDFRQEEYYFPCRPGtSLLGSLAPYHPISSRWHlpADAEEGWSDVREQRVAGWPTAVGVDNFWLPLRPAHQDVHANHLVIVYGFDDenETVRVMDTVPPRFDGDLPLSVLTAARGSgTEAHHARDMFFADSAIAHRWLEISVNhARRRPPDRPTIAAYLCRNLAGFAAPDDENDHDGLAGLESFLRDMETRLSRGDEIAD-----ELFVVAGAALadTALHADWLAEAGRAVGIPSLTEAGRSVERIAHHWTALR-------------------------------------------
+>SRR6266536_1184334	149	0.466	1.881E-34	38	286	352	2	252	493
+--------------------------------------ATVLLHAGREPLAALGAAWGFYCRPGEVTTEEFYYGCRHGSLGASLAPHHPVASRWHAGPDGSdpLAPLRDQVGAARLPIAVVDNYHLPFRPAWHDVHAAHLLVVYGFGDGTVEVSDAMPPAFQGPIPVEDFLRSWGSTNPRDEQDDFFSNAAIGRRWLEVTLGEPWPVEDRPWLRSVLQSNLDDLAGGGDglAGGLLGLPGLRGFLDELLARAGRGDSSALL--ELYVFGWGVQAQASLHGELLRERGRAWG-----------------------------------------------------------------
+>A0A022MLG6	147	0.352	4.714E-34	23	339	352	23	341	358
+-----------------------PQWYEDPLSCLQTTLGSILLEHGLRPVEVLGRACEFAFAPDDVMCEEFYRPAqSSRGVAADLCPYH--DVESAWTSGKDADDLIGLIEEHAAVIVAVDNYHLPFRPAYHDVHAAHLVVVpawrrTGGGQLEFYVSDAQPPGFQGWLAAEHLVESWTSGNPTDTQDVFFSSREIGGRVLTVKVRPEPGPLTDDQVVRALRGNLDRWDTgtaGPAEGVWTGRSGLRRFVERLAEHSAD----PARLRPAYTFGWAMQAQAYLHGRFAQECALRTRPGHLAEVAASADRVVSAWSNVRLLSAHAAHTP-GAPELIRRRGEELSHAYEQL------------
+>SRR6185503_6371475	140	0.318	1.158E-31	25	293	352	68	340	342
+-------------------------WRHDLVGCLWTCAASILDFYDVPALETLGAAWTFRHCPQDVRREEYYYPCPEGtSLYEAIAPYHPIRSVWHvpADAEEGWQQVRDQVADGTPVVVAVDNFYLPFRPAYQDVHTNHLSIVYGYDEqaGTVRVLDAVPPRFDGDIRIDELTAARNSANPeLHERDMFFTNRPIANRWLEIELdAAAFPPFTLDTVRSTLRRNLQGFYAAASEVEYLGIQGEQEYLASQANWLDKGDDIRDGLFLAAGAAL---ANTALHAEWLALAGRQFYQPRLAEL----------------------------------------------------------
+>4772|scaffold_11782_c1_3|+1184|00	137	0.296	1.329E-30	22	308	352	7	327	369
+----------------------VRPWRHDLAGCLHACLGTLLDHAGRRPLEVLGAGWRFYYRLGDLRAEEYYHPCPdGRSLVASVAPGQGISSRWHRpaDAEQGWQQVREQVLAGVPVAVAVDNFELPFRPAYRDVHSNHLVVVYGFDDErgTVRVLDAIPPFFDGDLPLGVLAAARDSGNRsSHERDMFFADNPIGNRWLELVADGAPSAEPRspagylAANLAALRAGASGNPdssagpnsgagpnssaqpnsdaepdRGAEPNSYAGRDGIARFLTDMSDRLADGHSIADELFVVSGVALAGTA---VHADWVGDTGRRLGLPGWPELARRLDRLAHHWSAVR-------------------------------------------
+>SRR5258708_5638915	137	0.508	1.803E-30	104	347	352	13	257	264
+--------------------------------------------------------------------------------------------------------VRQARGAGRRPTAAVDNSPLPFRPAFGDVHAAHLLVVNGVDDERGLVHvsDAQPPEFQGPIPVADFLRAWGSTNPEDTQDAFFSNSPLDRRWLEVRFTGDFPVADRGWLAGVMAENVRRLRRPEPGPLWSGLAGVERYVERVLEQ-AAGPGRSDALEELYVLSWGLQAQADLHAQFLRGFGVAEDLPAMREASCLVDGVAHAWTGFRMTAAHGRLDRPDFGQELRWHGRRLVRAHDEAVDAIELAL----
+>GraSoi2013_115cm_1033766.scaffolds.fasta_scaffold685313_1	134	0.764	1.521E-29	115	305	352	0	190	191
+-------------------------------------------------------------------------------------------------------------------IAAVDNFHLPFRPAFHDVHAAHLLVVYRITDTDVYVSDAQPPAFQGPIPIADFLRSWDSANPAHDADVFFSSSPSDRRWLHARMRGAGPRTDRGWLAQVIRDNVARFRAGSPDGIETGVEGLRRYLDELCTHEPGTQAADAALSELYVISWNIQAQTGLHAEFLRAQGLHWRIPELAEAAARVDAVAHGWT----------------------------------------------
+>ERR671931_1062055	130	0.480	2.348E-28	21	243	352	108	326	335
+---------------------PPRQWYRDPISCLHSTLAAVVGYEGADPLEVLGLSFEFLYKPGDVRPEEFYFPCRfGDDLARSIAPYHPVRSEWWRaTGEDPLAELAARISNGELPIVAVDNYHLPFRPAYHDVHAAHLVVVYGIDreRDEVGVSDAQPPAFRGSVPAEDFLAAWGSANPADTEDAFFSDSEIGRRCLSVEIEGPIPPLDAERLRTALEENLAGFVT--------GLADLGRYVDDL------------------------------------------------------------------------------------------------------------
+>SRR5439155_7605724	130	0.404	3.181E-28	24	201	352	9	191	192
+------------------------FWFHDLCSCLHDCIATVLIYQDQDPTLTLGASWEFYYSPADVRREEFYHPLPRPTLAESMMPFHPVRSSWHasDDPDAAWSDVKALVADGQPVIVAVDNFYVPFRPAYGDVHAAHLIVVFGFDDatDEVYVLDSTPPTKRGPMPMSEFLRARYSDNPVSGeRDFFFAGAPIANRWLQLEIGTP------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR2546423_1207057	128	0.432	1.071E-27	22	266	352	174	413	417
+----------------------VSQWYRDPVSCLQSTLATVLLAAGAEPLPVLGLAWEFLFIPGDVRPEEFYYPCRfEGDLARSLAPHHPLRSSWWSPAPgeDPLAELARRVERGELPIAAVDNYHLPFRPAFHDVHAAHLVVVYAVDRERgeVGVSDAQPPAFLGSLPAEDFLAAWSSANPADAEDAFFSDAEIGRRCLAVEIEEPIPPLDGERLRAALAENLACFVT--------GLADLRRYVDDLE--ARALAGERPPLEGLYALGLG-------------------------------------------------------------------------------------
+>SRR5215471_7738639	128	0.443	1.451E-27	21	193	352	168	343	344
+---------------------PTRAWRHPLGGCLFAAVGALLWHRGLDPLEALGAAWRFRYRLGDVRREEFYYPCGEDSLVEALAPHHPVRSRWHspSSPAAAWPEVRERLLAGVPVAVVVDNFHVPFRPAFGDVHSSHLVVVTGFDEGTGTVVDAVPPGFQGPLPLAQLALARGSDNRPrHARDMFFAGDPIGARW--------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5919198_860872	128	0.456	1.966E-27	115	344	352	0	226	920
+-------------------------------------------------------------------------------------------------------------------VAGGDTRLLPFRPAYHDVHAAHLVVVYGIDAGRreVSVSDAMPPAFQSAIADGDLLRSWSSPNPRDDQDAFFSDARIDRRCLSVRFETPIPPLDGARLKDALESNAQRLSAG---EGWSGLPGLRRYLDEVVGRAGAGERRP--LEELYPFGWAMQAQAYVHGELLRVCGADWSVPELREAGRAVESVAYAWTGLRMTGAHGLSAPAEATSGLRRHAGRLRRRYEEALEAVE-------
+>ERR1700691_1894743	126	0.322	8.949E-27	4	235	352	55	293	308
+----HRHRTSGMSRPATALIEEVVSWRHDLVGCLWTSAGTVLGFHGAPVLETLGAAWGFHHFPDDLRREEYYYPCPPGmSLYEAIAPYHPVSSRWHEPADAAqgWAQVRDIVLSGSPVVVAADNFYLPFRPAYQDIHTNHMVVVYGFDEasGTARVLDAVPPRFDGDITMEELTAARDSTNPvLHERDMFFTNRPIANRWLEITVdTAAFPPFNLEPARPTLRRNLPGSAAPAPAEAYAGTAG--------------------------------------------------------------------------------------------------------------------
+>DeetaT_8_FD_contig_21_3401058_length_202_multi_3_in_0_out_0_1	122	0.400	1.364E-25	24	203	352	9	193	195
+------------------------FWFHDLCSCLHDCIATVLIYQDQDPTLTLGASWEFYYSPADVRREEFYHPLPRPTLAESMMPFHPVRSSWHasDDPDAAWSDVKALVADGQPVIVAVDNFYVPFRPAYGDVHAAHLIVVFGFDDatDEVYVLDSTPPTKRGPMPISEFLRAIYSDNPVSGeRDFFFADAPSASRSRHLEIGTPSP----------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR6266704_4620549	119	0.447	1.527E-24	22	189	352	1	172	175
+----------------------VRMWRHDLGHCLHATMGVLLGCYGADPLSVLGAAWGFGYRSGDLRREEYYYPLGSESLLGVMAPHHPVSSRWHRPPDaeTAWTEVREAVASGRAVAVAVDNFHLPFRPAYRDVHTNHLLTVYGFDDerDEVLLADPVPPRFQGAITRAEFAAARRSVNPEDHDRDLFFTRNP------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>EndMetStandDraft_4_1072995.scaffolds.fasta_scaffold2302776_1	118	0.370	3.774E-24	108	327	352	0	209	217
+------------------------------------------------------------------------------------------------------------LASGVPVAVAADNFFLPFRPAYRDVHSNHLLLLYGFDDDagHVYVVDPVPPSYQGPIPLETLSLARGSVNPvRHDRDMFFTANPIANRWLTVRVGPVQPVMDRAFVARAIEANVA----------GFGLPGLRAFlAAALAKLPDDGT----VIDEIFLVAGPLLAVTGLHAEFLDRAGQAFGVSALRELGRRVDRIAHHLSALRIAVASARHDRAAAVPGLRR------------------------
+>ERR687887_509227	117	0.470	6.896E-24	22	233	352	115	331	332
+----------------------LRQWYRDPISCLQSTLATVLLAADEEPLPVLGLAWEFLFVPGDVRPEEFYYPCRfEGDVARSLAPYHPLRSSWWSPAPEedPLAELARRAEGGELPIAAVDNYHLPFRPAFHDVHAAHLVVVYAVDrrREEVHVSDATPPAFQGAIAAADFLASWSSTNPADDEDAFFSDSRIGQRCLAVEIDEPLPPFDAERLRTALETNLARFAAEEDDAGRGGL----------------------------------------------------------------------------------------------------------------------
+>SoiMetStandDraft_5_1073268.scaffolds.fasta_scaffold824170_1	116	0.332	1.702E-23	78	328	352	3	256	278
+------------------------------------------------------------------------------SLLGSLAPYHPISSRWHlpAGAEQGWSDVREQLVEGRPTAVGVDNFWLPFRPAHQDVHANHLVIVYGFDDEnkTVRVMDTVPPRFDGDLPLSVLTAARGSGNeAHHDRDMFFADSAIAHRWLEISVNhARLRPPDRPTIAAYLCRNLAGFAAPDDENDHDGLVGLESFLRDMETRLSRGDEIAD-----ELFVVAGAALadTALHADWLAEAGRAVGIPPLTEAGRSVERIAHHWTALRIIAALTRKGDVSTARLRRRH-----------------------
+>SRR5262245_57182801	115	0.435	2.300E-23	31	219	352	2	194	228
+-------------------------------SCLQATVGSVLAYWGHDPLEILGAGWDFTYIPGEVPFEEFYFPSPPGiDLGQSLAPHHPLSVRWATGVrDDPLGELAGAIEAGQLPIVALDKYHLPFRPAYHDVHAAYLLVVYGVDKRRglVLVSDSTPPHFTGPIAAEPFLAAWQSRNPADEQDAFFSESEIGMRYLVVEPRDRIPRLTQRQLGTALRANAA------------------------------------------------------------------------------------------------------------------------------------
+>SRR3954469_16970431	113	0.377	1.034E-22	22	243	352	47	268	283
+----------------------VRQWYRDPVSCLQSTIATLLIEAGWDPVETLGLGWQFPYLPGDVRAEDFYWPCRvPGDPVASMLAHHQVSSSWrQETGSDPLAALEAALDRGQLPVVAVDNFYLPFRPAYHDVHSAHLIVVFDVDrDGTVGISDAMPPAFQGELAVEDLLRSWMSAN-PRENEAFFSGAHIGGRWLDVRLGPAPPRLDPSTLAGAL--LADAVAFRKTDVAGAGLAGLADLSAAI------------------------------------------------------------------------------------------------------------
+>SRR5262249_26821897	112	0.471	2.547E-22	21	158	352	6	147	149
+---------------------PIDHWRHDLGHCLHTTAAVLLAYHRLDPVEVLGAGWGFRYPPGDVRREEYYFPGHPDDLFSGLAPSHGVSSRWrpREGAEDGWRQVRAAHADGAPVAVAVDNFHLPFRPAYRDVHTNHLLAVYGFDDDTgqVFVADPVPPSF-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5688572_1544331	111	0.420	4.641E-22	56	264	352	0	211	212
+--------------------------------------------------------WEFLYKPDDVTAEEFYYPCRVDgDIARSVAPYHEITSRWWraESGGSALDELAGCLNAGALPIAVVDNFHLPFRPAYRDVHAAHLLVVYGVDQQRgeVWVSDAMPPAFSCPIATEEFLASWSSENPLHAGDAFFSGSRIDRRCLLMDVRSQRPPLNRHVAHAALRSNLARFARADDPAGWNGRAGLGRFLQQLLERARAAD--PEALAETYRFG---------------------------------------------------------------------------------------
+>MGYP000725067659	108	0.373	5.102E-21	115	341	352	6	228	245
+-------------------------------------------------------------------------------------------------------------------IVAVNNYHLPFRPAYHDVHAAHLFVLnrLGTPGGVARVHDPQPPAYRGPLSREVLDIARASLRVGDESDPFIAGANPNWRWLEVRVEGPQPSPSLTWVHAIMVENLDALLRQ-----TQGPAALATFLDSLPNRVR--EHGPRALREIYVLGWPAQAEAGLHARFLASVAARHRKPRLAETARAVDHVANGWTGLRVSAAHASTLSAPtAPADVFRQGATLLRRWRRCMD----------
+>SRR5262249_47284095	106	0.432	3.067E-20	25	167	352	10	157	159
+-------------------------WRHELAGCLHACAGALLGFHGIEPLEALGAAWGFHYAPGDARREEYYFPCRPGWsLLRSLAPYHPVGSTWHHPAGdaEGWAEVRSAVASGRPAAVAVDNFHLPFRPAYRDVHSNHLVLVYGFDDDRrlAWVLDAVPPRFDGPIGLHQL----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5690242_2363108	104	0.414	1.364E-19	22	147	352	18	145	148
+----------------------VDHWRHDLTGCLHQSMALLLAHEGLDPLEVLGAAWGFYYDPRDLRREEYYFPTPYESLLSGLAPFHPVRSRWHlpADAAAGWAEVRAAVADGRPVVVAVDNYELPFRPAYQDVHTNHLVTVVGFDDER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5262245_28891133	103	0.492	3.334E-19	21	144	352	23	148	156
+---------------------PVTVWRHDLAGCLHACAATLLAHHGVDPLDAVGAAWGFTYVPGDVRREEYYFPQAGRSLLESLAPYHPVRSEWHRpgSAEEGRRQLLSQLAEGRLVAVAVDNFHLPFRPAFGDVHTNHMVVVYGYD---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5215468_4727865	99	0.449	4.843E-18	21	164	352	181	329	330
+---------------------PVNAWRHDLVGCLWTSAATMLACHGAPVVETLGAAWGFRHLPGDLRREEYYYPTPPGvSLYQAIAPYHPVRSVWHEpaDAGEGWTQVRDEVLAGRPTVVAADNFYLPFRPAYRDVHTNHLVVVHRLDEaaGTVGVLDAVPPHFDGDITL-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5215467_9451402	98	0.413	1.179E-17	161	337	352	0	176	179
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------PITVADFLRAWSSANPPDPQDVFFSDTRIGRRFMTVTAGEPFPRLDAPMLRRILAANLAGFSGEDASDqaGWTGLPGLKLYLMSLLDACAR--PDPAQLASAYPLGWGMQAQASLHAELLRRWGTQAGLPELREAARLVETAAHAWTGLRMTAAHGRGDPRACAGELARHAAGLRRSYE--------------
+>ERR1700761_2897183	97	0.376	2.869E-17	96	294	352	0	202	203
+------------------------------------------------------------------------------------------------TSGKDADDLIGLIEEHAAVIVAVDNYHLPFRPAYHDVHAAHLVVVpawrrTGGGQLEFYVSDAQPPGFQGWLAAEHLVESWTSGNPTDTQDVFFSSREIGGRVLTVKVRPEPGPLTDDQVVRALRGNLDRWDTgtaGPADRVWTGRSGVRRVAERLDEHSAD----PARLRPAYTFGWAMQAQAYLHGRFAQECALRTRPGHLAEVA---------------------------------------------------------
+>SRR3954453_9001413	95	0.398	9.369E-17	25	153	352	6	138	139
+-------------------------WRHDLGHCLQTTMGVLLQHHGLDPLQGLGAAWGFHHIPGEVRREEYYFPLHRGGLLESMAPYHPVRSRWHrpEDAGSGWQQVRAAVLAGSPVAVGADNFLLPVRPAYRDVHTNPLLTVYGFDDERdlVLIADP------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5213080_3547182	95	0.373	9.369E-17	133	295	352	0	164	167
+-------------------------------------------------------------------------------------------------------------------------------------HAAHLIVVFGFDDatDEVYVLDSTPPTKRGPMPMSEFLRARYSDNPVSGeRDFFFAGAPIANRWLQLEIGTPSPELTREWVTEVIATNLRRFREPDASPGWAGMAGLTHYLHSICART-LGADAGDALQELYTVGWTAQGSTALHADFLMLAGRRLGWDRLVEVGR--------------------------------------------------------
+>SRR6266536_4448340	93	0.430	7.400E-16	95	227	352	3	139	147
+-----------------------------------------------------------------------------------------------RDAAEVWAQVRERLAAGVPVAVAVDNFHLPFRPAYQDVHTNHLVVVHGCDErrGTVRVLDAVPPGFDGAIGLEQLTAARSSANPvRHDRDLFFTDSPIANRWLEVEVArERLPRFGPAGVSSGIQGNLAGFATPPPP----------------------------------------------------------------------------------------------------------------------------
+>SRR5215216_3959313	92	0.600	9.936E-16	20	139	352	6	123	124
+--------------------PPVQLWCRDLVSCLQATFATVLLHHGHDPVEVLGAPWQFRYRPGDVRTEEFYFPERAGDLGAAIAPYHPVSSRW--CTGRSLDELDAQLRAGRLVIAAVDNFHLPFRPAFCDVHAAHLLV--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5947209_19054265	92	0.427	9.936E-16	106	229	352	0	123	137
+----------------------------------------------------------------------------------------------------------AAIDAGRPPIVAVDNYHLPFRPAYHDVHAAHLVVVRGYDGDTVQVLDPMPPAFDGPLAGSVLATSRAAATVTDPTDPFFAGSSLRRRWLEVYPTGRQPAWSWAWVQQTLRDNLAALAGPARDDS--------------------------------------------------------------------------------------------------------------------------
+>ERR671931_2548281	89	0.317	7.793E-15	136	349	352	2	215	219
+----------------------------------------------------------------------------------------------------------------------------------------HLLTVYGFDDEarHALVADAVPPRYQGPLALSDFVAARGSSNPiRHDRDLFFTANPIAHRWLEVDVPARMPALDAEFLRFVVESNLRGFGARGADDAYEGIEGAHRFLVDALARLGRGEAVVDEV--FIVSGTALAA-AGVHADYLLLAADRFGSFALLEAARAVERVASHWAALRIALAELRDVSAPRLEGIRRRGEALVRDHRSALARLEHALEA--
+>SRR5205809_3347963	88	0.503	1.880E-14	69	216	352	3	154	156
+---------------------------------------------------------------------EFYFPCSDDDLGRVLAPHHTLEIvtrRAPDDDARALSMLGERLEAGALPIAAVDNLHLPFRPAFGDLHAAHLLVVFGVdtDADAVWVSDAIPPAFQGPIPSATFLRSWGSANPPDGQDPFFSSSPLERRWYDVRLVD-APADNADWIARAIAD---------------------------------------------------------------------------------------------------------------------------------------
+>MGYP000871191451	88	0.370	2.521E-14	21	186	352	11	179	182
+---------------------PLPGWYDDLLSCLQTTIGVSVQAHGWDPVQALAAGWRFSLPAAPVEPVEFYHPA-GDQIGERLCLHHPVQLRWHHPASRAEADagIAAATATGSHSIVAVNNYHLPFRPAYHDVHAAHLFVLnrLGTPGGVARVHDPQPPAYRGPLSREVLDIARASLRVGDESDPFFAG---------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>ERR1051325_7439640	87	0.568	3.380E-14	110	239	352	0	128	129
+--------------------------------------------------------------------------------------------------------------AGELPILAVDNYHLPFRPAYHDVHAAHLLVVYGIDAGRgeVFVSDAMPPAFQGAIACDDLLRSWSSPNPRDDQDAFFSDARIDRRGLSVRFEAAAPPLDRDGLERGLRGNAERL---AAEDEWSGLPGLRRY----------------------------------------------------------------------------------------------------------------
+>SRR5438874_1021933	87	0.443	4.531E-14	126	274	352	1	149	150
+------------------------------------------------------------------------------------------------------------------------------RPAYRDVHAAHLVVVYGveRDRDEVLVSDAVPPAFRGAIPAETFLRAWSSANPRRDEDGFFTDARIDRRCLSVEVDGPFPRLDPDRACEALRANARGFRDRDDGVGWSGLAGIARYLDWLLERARTGGA--RALEELYPLGWAMQAQAYLH-----------------------------------------------------------------------------
+>SRR2546423_1612834	86	0.731	8.139E-14	192	351	352	0	159	163
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RWLRAAMRGPVPDTGLDWLGHVIRENVARYRQGSAGGTQTGVLGLRSYLDELYRAVPGTDAAAELLSELYVISWNIQAQAGLHAEFLRREGVRWRIHELAEAAAGVAAVAHGWTGVRMTGAHSRVWGRHRFDELRRHAVELVRRLDNALDQLELAAEVVS
+>SRR5581483_10036454	86	0.401	1.091E-13	2	131	352	11	141	143
+--CSRSRPSPTRRPAMRVELQPVRYWRHELGHCLHTAAAVLLAHRGLDPVGVLGAAWGFHY-PGDLRREEYYLPGAAGSLFTALAPYHGIRSVWHRpaDAEPGWQQVRAQVIAGNLVAVAADNYHLPFRPAYRD----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>CryGeyStandDraft_13_1057135.scaffolds.fasta_scaffold438374_1	86	0.343	1.091E-13	183	345	352	9	169	184
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FFAGTEIGGRWIDVEIGEPFPKPTEEWVGTVVAENLRGFVEPPIGDGWAGLAGLRRYLADVGDRADDRRD--PVLGELYTVGWASQSVTALHADFLRSTATALGWPEGLEAARRVEHLASLWTPLRILTAHGSTNGIELGDRLRRRMRALIRHYELAIEEVER------
+>GraSoiStandDraft_48_1057284.scaffolds.fasta_scaffold433089_1	83	0.408	1.128E-12	82	217	352	7	148	149
+----------------------------------------------------------------------------------DLAPFHPVRAAWVgpSHPDEAWEQMRAALRDGRPLIAAVDNFHMPNRPAYGDVHAAHLVVVSGFDDDAgmVDVVESTPPAYRGPVPRECFLLAIGSRNDARSATqaVFFAGTEIGGRWIDVEIGEPFPKPTEEWVGTVVAEN--------------------------------------------------------------------------------------------------------------------------------------
+>SRR5919197_3773559	81	0.555	2.704E-12	115	220	352	4	111	119
+-------------------------------------------------------------------------------------------------------------------IVAVDNYHLPFRPAYHDVHAAHLVVVYGIDGSRreVSVSDAIPPAFQGAIAADDLLRSWASANPRDDQDAFFSDARIDRRSLSVRFDAPIPPLDLDRLEGALRSNAER-----------------------------------------------------------------------------------------------------------------------------------
+>SRR5688572_26547208	80	0.366	8.655E-12	138	288	352	1	150	151
+------------------------------------------------------------------------------------------------------------------------------------------LVVYDVDagAGTVGVSDAMPPAYAGPLASDDLLRAWWSANPQDAQDVFFSGEGIGGRWLDVRLGTPFGALTVERLRDAVRANLRELTEPSDPD-TAGLAGLARFAREVAGRARRGEAG--RLAEVYTFGWSMQAQSALHGELLRRCGSAWSLP---------------------------------------------------------------
+>SRR5207248_1268395	79	0.514	1.157E-11	22	156	352	61	200	201
+----------------------VRQWYRDPISCLQSTLATVLLAAGAEPLPVLGLAWELRFQPGRVGREEFAYPCRfEGDVARSLAPYHPIRSSWWSpaDDDDPLVELARRIEGGELPIAAVDNYHLPFRPAFHDVHAAHLVVVYAVDwqRDEVGVSDAQPP---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5882724_12307322	79	0.377	1.547E-11	121	308	352	1	192	205
+-------------------------------------------------------------------------------------------------------------------------YHLPFRPAFHDVHAAHLVVVPGWRRTThgaveFYVSDAQPPQFQGWLSAEHLMNSWTSGNTSDTQDVFFSSREIGGRVLTTKVRSPPDELTTGQVAQALQGNLDRWatgVAGPSDRVWTGRTGLCRFIERLQE----SCDDPEGLRSAYTFGWAMQAQAFLHGRFAQEFAHRSKQTVLLGVAASADRVVSAWSNVR-------------------------------------------
+>SRR5687768_15959820	78	0.362	4.936E-11	148	296	352	0	146	147
+----------------------------------------------------------------------------------------------------------------------------------------------------VYLADAMPPVFHGHMPTENFLRAWTSVNPNDEQDAFFSDTAIDRRYLTVELGRRFPKFDPGFLHRVLDANLAGFAVEDDPAGWGGLRGLDRFLDDLVTRSRAGDAAG--VAAAYPFGWGMQAQASLHGELLRGWGARYEVPEVSEAGRL-------------------------------------------------------
+>SRR4051794_15511058	76	0.471	1.177E-10	114	245	352	0	139	143
+------------------------------------------------------------------------------------------------------------------VIVAVDNYYLPFRPAYQDVHAAHLVVVPAWRRTpgggvEFYVSDAQPPAFQGWLSAEHLVASWTSGNPSDTQDVFFSSREIGGRVLTTKVRQRPEEPTTEQVVRALRGNLDRWDNgvaGPTDRLWTGRSGLRRFVDRLHE----------------------------------------------------------------------------------------------------------
+>SRR3712207_6013657	75	0.379	2.801E-10	141	295	352	0	156	162
+---------------------------------------------------------------------------------------------------------------------------------------------YGFDEeaDEVYVLDSTPPLHKGPITMQDFLAARNSSNPVSGeRDFFFAGAPIANRWLHLEVQSSFPELTRDWVAEVIATNLRRFEASSDGPTFSGMDGLARYLRGVCER-AAGAEGGRALDEMYTVSWVSQAAAGLHADFLMEAGRRLHWYELAEVGR--------------------------------------------------------
+>SRR5919199_5445869	75	0.276	3.740E-10	90	221	352	4	123	149
+------------------------------------------------------------------------------------------RWRHEADPGTAWREVRARIAGGRPVALAVDEFHLPFRPGYRHAHARRALVAYGFDDEAelVFVADPTPPRFQGSLALSALAAAREAEDGQP--------------WLELELAGPQRAFGPTVVGEALERNLRRF----------------------------------------------------------------------------------------------------------------------------------
+>SRR3982074_821911	74	0.432	4.992E-10	24	131	352	26	136	138
+------------------------PWRHDLATCLQSCMATLLDANGVAALDVLGANWSFYHRPAALRRAEYYFPCREGvSLLASLAPYHPVRSQWHEpaDAEQGWSQVRAAVAVGRPVAVAVDNYELPFRPAYHD----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5436305_665040	74	0.325	4.992E-10	150	348	352	6	204	208
+------------------------------------------------------------------------------------------------------------------------------------------------------VSGPVPARSVGCIPRDQLTPARDSGNRsKHERDMFFADQPIGNRWLEAEIdAEHYPAFDRGSIRYAIRRNIDGFTEPGPlgAHRYAGLAGLRAFLDD---SAAKLAAGGQVADEVFVAAGAVLAATALHADWLARAARMLGTIELAEAARQVARVAHHWTAVRIMAALSRDGQVTAPRLARRAANLLADQ-ERALTALGDVLD---
+>SRR5437870_817573	74	0.401	6.662E-10	53	175	352	1	127	131
+-----------------------------------------------------GASWEFFYAAEDVRSEEFYHPAPRPTLGASMMPFHPVSTAWHESTDgeAALAEIEAVIAGGRPVIAAVDNFYMPIRPAFGDVHAAHLVVVTGFDEGTgeVVVLEETPPLYHGPIAVSDFLSARGSGN--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>9576|scaffold_589529_c1_1|-3|11	74	0.299	6.662E-10	102	225	352	3	129	140
+------------------------------------------------------------------------------------------------------DDAFDCVAQGHAVVVAVDSFELPYRPAWRRVNSGRSLIVTAIDRTTGVaqVIDGWMPHYTGSVALADLARARASSVPQDlRREPLYAGTPLRRRWWRIALASEIPHGGRDNVADALAQLTAQATEAP------------------------------------------------------------------------------------------------------------------------------
+>SRR5919199_1533857	74	0.376	6.662E-10	196	341	352	9	148	191
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------VGGGAPTPPLDSERLEAALAENLDGFAGT----GWSGLAGLARYVDALET--RALAGERLPLEELYAFGWGMQAQTYLHGELLRETGAAWSVAELAEAGRAVQEVASAWTGLRMTGAHALGAPAAAAADLRRHGNRLRRRYEAALE----------
+>SRR5581483_6019569	73	0.452	1.582E-09	25	127	352	2	107	108
+-------------------------WRHELSNCLHSCIGVALTRHGFDALVVLGSRWQFYYRPGHLRREEYFWPCPPGvSLAETLMPYHPVSSRWHqpEDAGEGWQQVRDRILAGEPALVAVDNFWLPFRP--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR4029453_12411764	73	0.453	1.582E-09	20	136	352	87	205	207
+--------------------PEPELWSRALISCLQATFGSLLVRVGADPLVVLGAAWRFLHLPGDVRFDEFYYPCHDGDLGAALAPHHELRSRWWQPADEDdvWREVRESLADDRLVIAAVDNFPLPFRPAYGDVHAAH-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5688572_10121371	72	0.428	2.110E-09	126	239	352	1	126	131
+------------------------------------------------------------------------------------------------------------------------------RPAYHDVHAAHLIVVGAIDPAAGTadVSDAMPPAYAGPLALDDLLRAWRSTNPQDGQDVFFSGADIGGRWLDVRFDLPFPDLTADRLADMLRANVRGFVAASGADTapdgtaaetcWSGLAGLRRF----------------------------------------------------------------------------------------------------------------
+>SRR5690348_7358098	72	0.400	2.815E-09	25	123	352	41	140	152
+-------------------------WRHELTGCLHVAMGVLLKHRGHDPLEVLGASWGFYHDPADLRREEYYFPARRGSLLADLAPYHPVSSRWHaATGAEAWSRVRDTIAAGQPVAVAADNYYL------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5258708_3518620	72	0.299	3.753E-09	52	194	352	71	215	216
+----------------------------------------------------LGARWGFAPPRQEAWGElcEYSLPLGSNPYAATLAARTGLQIAQHSGIAAA--DLSGHLASGAPAIVAVDSFYLPYRPAFGRVHSQRTILVRqGQGRTDLRVEDPWPPTYHGSLGAAHLERARRSTVPLDRRaEPVFAGRPIDFEWW-------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5437870_3049837	71	0.420	6.672E-09	20	124	352	36	142	144
+--------------------PEPELWYRDLISCLQATFGSLLLRVGADPLAVLGAGWRFLHLPGDVRSDEFYYPCHDADLGAALAPHHDLRSRWWQPADEDdvWREVRESLGDDRPVIAAVDNFHLP-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>DeetaT_8_FD_contig_31_513410_length_211_multi_4_in_0_out_0_1	71	0.352	6.672E-09	115	239	352	28	180	181
+-------------------------------------------------------------------------------------------------------------------VIQADVFHLPFRPAYHDVHAAHTVIVHGFDDEagTVSVLDSMPPAFDGTVSQEdlanargsgnpseeadpffggtisqrDLANARGSGNPFEEADAFFGGTPIAGRWLRFEVVGEMPSLDREWVGRVVTGNLERFAAATDGPALSGLAGVDRF----------------------------------------------------------------------------------------------------------------
+>SRR5438105_1867171	70	0.453	1.185E-08	210	350	352	1	140	141
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRHVLRENVRALRAPVTGSEWFGLAGLERFVDRLLTR-AAGPDRRTALEEQYVLSWGLQAQADLHAAFLLAAGGRWGLPCLSEAGCLVDRVAHAWTGLRMTGAHGRLDRPEFGLELRWHAGCLVRAHEEAVDAIELALDEL-
+>ERR1700687_5501718	70	0.429	1.580E-08	40	156	352	8	127	128
+----------------------------------------VLQRHGWEPARALGAGWRFVAAKNPVEPVEFYHPA-GEMLADHLCLHHPVLLRWHQPAHDAAAhcDIGESLAHGTAPIVAVNNFHLPFRPAYHDVHAAHLVVVTGYDEhhDNYQILDLMPP---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5262249_51622373	70	0.418	1.580E-08	20	115	352	51	148	149
+--------------------LPVEGWYHDLCSCLQVDAACVLSAFGQEPLAVLGAGWGFQFRPGDWEPVEFYCPAPDGDLARALAPHHRLCCRWHHPDGPeaALAALVEALRAGLPAI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>12671|scaffold1085376_1|-94|01	69	0.310	2.105E-08	169	350	352	0	184	190
+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------AARGSDNPvRHGRDLFFTDNPIGNRWLTIETADVMPAFDQDFVAAAVGRNLADFgdtsTSGASTVSYAGAEGQRRFLGDIADRLAAGDEG--AVDEAFVVAGPVLAQTALHASWLSRAARDFAEPGLAEAARRVERVAHHWSAIRIVVASSRAAPAAAAGPLRRRATALADDHWRALDDIARIIGAV-
+>SRR4051794_8300831	69	0.350	2.804E-08	4	116	352	6	119	120
+----HCRQEYGERAPMNVALSPMTFWYHDLCSCLHNTIATVLHYHHQEPTQTLGAVWDFYYAPAQFHKEEYFFPSRHPTLAENLLPYHPISADWRdSSAADSWPAVREAVARGTPAIV-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5277367_2659287	68	0.500	6.627E-08	21	123	352	29	136	137
+---------------------PVQHWCRDLVSCLLATLATVLLRAGHAPLEVLGAHWEFRYRPGDVRTEEFYYPcAVPGDLAASLAPHHPLSSSWREPgagaGTEALAEISDELAAGRLVIAAVDNFYL------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5579872_5282090	67	0.350	1.175E-07	136	246	352	1	114	115
+----------------------------------------------------------------------------------------------------------------------------------------HIILVYGVDQHRglVWLCDPTPPGFNGPLPIGDFQQARNSANPADVQDAFFSASEIRGRYLRIVADPGLAPLSPLELGAALKANLAAFGADSPADgPWTGNIGLRRYLDSVTSH---------------------------------------------------------------------------------------------------------
+>SRR5205809_7151332	66	0.289	2.082E-07	104	209	352	0	106	107
+--------------------------------------------------------------------------------------------------------LREYLHAGRTAIVAVDSYYLPYRPAFGHVHSSRTILVRRGDSQAAEVEDVWSPGYSGPLGWDHLERARYSCMPYAAlTEPVFSGCPLSGEWFAVDLEPVMLPDPTVW----------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5919204_5113640	66	0.452	2.082E-07	21	124	352	194	299	301
+---------------------PVRLWCRDTISCLHATLATVADHHGWSPLSAVGPLWEFRYFPGDDRGEEFYYPLCGRPPGEALMPYHPvsIEWRAAKSARQGLAELRVALAEDVLPIVAVDNYHLP-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5690242_5973043	66	0.305	2.771E-07	69	200	352	4	135	139
+---------------------------------------------------------------------EYSLPGGVLSFSERIASRTGVKIVQQDGAHSS--SLYSFLATGQTAIAVVDSFHLPYRPAFGRVHSHRTILVRqGLDPTDVLVEDEWPPAYHGPVPVRSLEAARYSAVPLDPvREPVFAGGKIRGEWFHLEMDG-------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5882724_5907471	66	0.394	2.771E-07	20	121	352	93	196	197
+--------------------PEPELWCRDLISCLQATFGTLLARLGADPLAVLGAGWRFLHLPGDVRFDEFYYPCPDADLGAALAPHHELRARWWQPADEDdvWREVRESLVDDRPVIAAVDNF--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5919198_2188180	65	0.556	3.688E-07	115	193	352	5	83	99
+-------------------------------------------------------------------------------------------------------------------IVAVDNYHLPFRPAFRDVHAGHLVVLCAVEDDAVVVSDALSPAFQGRVALADFARSWESANGARGESGFFSGSPIGGAL--------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR4051794_17814528	65	0.418	3.688E-07	103	226	352	0	128	136
+-------------------------------------------------------------------------------------------------------ELIELIEAHASVIVAVDNYHLPFRPAYHDVHAAHLIVVpawrRTVDGDvEFYVSDAQPPRFQGWLSEEHVMNACTSGNPADHQDVFFSSQAIGGRVLTVQVRSQPAELTVDRFTEAIAGNVQRWITSEG-----------------------------------------------------------------------------------------------------------------------------
+>ERR1700744_2712043	65	0.342	4.908E-07	21	124	352	5	108	109
+---------------------PVP-WYRPAINCLAAGVGTVLATAGHDPLDILGSGWDFTHVPGQLPFEEFYWSVTEAsDLGSRLAPHHRVTVEWSDDDAGDLSGLMSELEQDRIPVAAVDKYFLP-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>ERR1051325_11437074	64	0.327	1.156E-06	62	179	352	4	120	127
+--------------------------------------------------------------PLRSQLVEYSLPFGPSSFIEALLFRTGLRICSHTGPDP--NNLRRYLAEGGEAIIAVDSFLLPYRPAFGRVHSHRTIIVRkGQNGDEVWVEDAWPPSYEGSLPLAVIENAQHSQVSLDP----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR6266404_4313130	63	0.313	1.537E-06	100	197	352	2	100	112
+----------------------------------------------------------------------------------------------------SESELRQHLALSEPAIVAVDSFYLPYRPAFGKVHSHRTLLVVSSREDLVWVEDDWPPCYQGPLQWSCLQRARYGDVPLQPRFePVFAGGTLSGIWFSVR----------------------------------------------------------------------------------------------------------------------------------------------------------
+>MGYP000377277604	63	0.341	2.044E-06	100	175	352	8	89	135
+----------------------------------------------------------------------------------------------------SVDDLRAMLDAGKPVIIGLDSDDLygaGDAPFTDDVVAGHAVVITGIDDETglVYINDPGFPDGAGVaIPLETFEDAWQDAD--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5690242_18701050	63	0.616	2.044E-06	1	105	352	51	157	158
+-GDRHRRAPRGRRAGMIETAPQVQLRPRDLRRCLHGSLATALLHDGHDPVTVLGAPWEFRRRAGAWTTEEYYYLPEPDSLAKRLAPYHPFESTWHrgDGPGDPLDELR------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>DeetaT_20_FD_contig_41_1501015_length_280_multi_3_in_0_out_0_1	63	0.335	2.044E-06	188	348	352	0	159	163
+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PIGNRWLEAEIdAEHYPAFDRGSIRYAIRRNIDGFTEPGPlgAHSYAGLAGLRAFLDD---SAAKLAAGGQVADEVFVAAGAVLAATALHADWLARAARVLGTIELAEAARQVERVAHHWTAVRIMAALSRDGQVTAPRLARRAANLLADQ-ERALTALGDVLD---
+>SRR5256714_1899555	63	0.418	2.044E-06	232	348	352	2	116	218
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GPAALRRYVDDLE--ARALAGERRPLEELYAFGWGMQAQTYLHGELLRETGAGWSVAELAEAGRGVQEVASAWTGLRMTGAHGLGAPAVAAADLRPHGNPLRRRHQEALQRVGRAGG---
+>SRR4051794_37091874	63	0.333	2.718E-06	189	323	352	1	133	134
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDRRCLLMHVQSVQPPLQRDAVGAALRSNLARFARSDAPEGWNGRAGIDRFLEQLVERARAGD--RQALSDAYRFGWSMQAQSYLHGELLRTKGREWQVAALSEAGRVVESVASAWSGLRVTAAHGRNAPAGVAA----------------------------
+>SRR5215218_1112994	62	0.319	3.614E-06	204	344	352	0	139	145
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PLTREWLTEVIATNLRRFREPDAGAGWAGMAGLTHYLQSICER-SLGPDAGDALQELYTVGWTAQGSTALHADFLMLAGRQLGWDRLVEVGRHVDRLANEWTALRMFGAHGFTRPAEIAERLRRRTIIFLSNYEQTLQLLE-------
+>SRR5215216_6411204	61	0.281	8.489E-06	101	171	352	27	93	106
+-----------------------------------------------------------------------------------------------------LEQLIAHLETGLPAIAFVNTAHLSHW----NHETGHAVVVIGMDEQSVFIHDPAIDEPAKAIPIPEFEAAW------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>MGYP000919097685	60	0.303	1.499E-05	100	171	352	5	83	138
+----------------------------------------------------------------------------------------------------TVDDLRAALDAGEPVIVGIDSadvYSGGGGPFDPGMESGHAVVVTGIDngpPGVLYINDPGFPdGAGVEIPLELFEDAW------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5205814_1734864	60	0.336	1.992E-05	136	243	352	0	112	114
+----------------------------------------------------------------------------------------------------------------------------------------HLVTVVGFDDERgeAFVIDPVPPRFSGAIPVEVLTAARSSGNPiVGERDLFFTGNPIGNRWLDIEVEADVPAHDLDFVREVVACNRDAFEATSESGSPvrTGLSGERRFLDSI------------------------------------------------------------------------------------------------------------
+>ERR1700722_17685023	59	0.402	2.647E-05	25	118	352	15	111	112
+-------------------------WCRDLISCLQSTFAAVLDRAGEDPLAVLGAGWQFRQIPGDVRPEEFYYPCSgEGDLGAALAPRHALHSRWWQpaDPDDPWQEIRAELDEDRLVIAAV-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5690348_3972261	59	0.380	2.647E-05	19	115	352	22	121	122
+-------------------APPLPRWYRDYVSCLQSTMATLLLAAGEDPVDTLGLGWEFLHIEGDVRAEEFYWPCRkPGDVAGSLLPHHAATSRWLQaDADDPLAPLEAALAEGRlPVL--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>MGYP000822340748	59	0.274	2.647E-05	113	200	352	49	137	210
+-----------------------------------------------------------------------------------------------------------------PIIVGADTYFLPYSANHKKRHAKHTLILCGFDltRNVVYVIDWYsPWFYKGEIDIEIFLQARNSKNEKD--DSFYSGTPIKNNWAYIEKIP-------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5215831_14536786	59	0.487	3.516E-05	230	350	352	10	129	138
+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WSGLRGVERYVDHVLSKAP-GPDGLAVLEELYVLSWGLQAQADLHAEFLRRHGVAQDLPALREAAAVVDRVAHAWTGFRMTGAHGRLDRPDFGGELAWHGSVLVRAHHEAADALELALEEL-
+>OM-RGC.v1.007693089	59	0.259	4.671E-05	101	171	352	0	76	148
+-----------------------------------------------------------------------------------------------------LDELRTLLDADTPVIIGLDAddlYGTGDSPFADDLVSGHAVVITGIDDEAglVYINDPGFPDGAGVaISISEFEDAW------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR6185436_5620841	58	0.392	6.204E-05	136	244	352	2	113	117
+----------------------------------------------------------------------------------------------------------------------------------------HLVVTYGFDEeaDEVYVLDSTPPVFQGAIAVRDFLAARGSTVPREGeQDFFFSGTPIANRWLHLEVGADFPELTREWVSEVVAAHVRGFRATRETASGAALSGLAGLGRYLR-----------------------------------------------------------------------------------------------------------
+>SRR5262245_38567583	58	0.340	8.239E-05	158	290	352	1	132	133
+--------------------------------------------------------------------------------------------------------------------------------------------------------------FQGPIPLAALTAARDSANPvRHERDLFFTANPLANRWLTIHLHGPQPVLDLDLVRRALLGNATGLLDGAADgDRLRGLAGQRWF---LQSLLADLAAGAHRVDEVFIVAGALLATTGLHADFLAAAASRLDRPEL-------------------------------------------------------------
+>3300027819.a:Ga0209514_10000001_1266	58	0.188	8.239E-05	94	171	352	222	311	431
+----------------------------------------------------------------------------------------------FSSVSEAIRQLEIVINSGRPIMVHLDSYYVKeefaktsefWKNNVGDSHSSHFMVVTGYNESHVYINDPTEPNlsiKNVEVPIEIFKEAW------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5688500_5242141	57	0.301	1.094E-04	100	181	352	29	110	113
+----------------------------------------------------------------------------------------------------SLGKLRQALTSGPVLVGPLDMSQLTYMPNHERlVGADHFVVLYGIDHEHVFLHDPAGFAY-VALPLNDFRRAWRAENIEYRPD--------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR4051794_22847671	57	0.238	1.453E-04	100	175	352	10	96	106
+----------------------------------------------------------------------------------------------------SLDGIKSEIAQGRPVIVLVDNSRyirseggkqVPY-PSGQGFEAPHIVVVTGYDADNVYLNDPlaiTVSGKDFRVPTASFQAAAGAKG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5512142_3069760	56	0.355	3.400E-04	180	286	352	2	106	108
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RDYFFAGSQIGCRWIDVKLGDPFPKPTTAWVGEVIAENLRGFVEPSVPDRRIGLAGLRWYLTDLSERVDSED--GNVLGELYTVGWAAQSVTALHADFLRQTASAFG-----------------------------------------------------------------
+>SRR5215510_68064	55	0.326	4.513E-04	148	245	352	4	107	115
+----------------------------------------------------------------------------------------------------------------------------------------------------IYVCDSMPPRFRGPIPITDFINAWSSINQRTENDEVFSGAGIDRRWLSVELGAAFPAVDAAFLCRTLAANREQWHRTTPPqsaserDSWTGAQGLWQFLDALLE----------------------------------------------------------------------------------------------------------
+>SRR5215472_923646	55	0.569	4.513E-04	21	99	352	76	154	157
+---------------------PVQLWTRDLGSCLQAVFATLLLRERQDPVTVLGAAWDFRYEPGDWRSEEFYYPCAGRPLAEALAPLHPLTSTWHRAPTD------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5262249_44885629	55	0.361	5.989E-04	26	116	352	65	158	160
+--------------------------RHDLAGCLPACAASLLGARGLDPLETLGASWSSLHARGEVRRVEYSSPSPPGaSLLGALAPYHPTRSRWHEpaDAEQGWAQVRAAVAAGTPVAV-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>MGYP000859423510	55	0.312	7.949E-04	95	171	352	82	161	324
+-----------------------------------------------------------------------------------------------PSGDNGLYDVLQIVNDGVPCIVNVDGYFLSYHPLFKTEHENHAAVLYGYNMNlhTIYISDYMPPYfFNGEISISEFLEAR------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5580693_9259363	53	0.469	1.857E-03	21	100	352	23	103	111
+---------------------PIQHWCRDLVSCLQATFATVLAHAGHDPLDALGAHWEFRYRPGDVRTEEFYYPcAVPGDLAASLAPHHPLSSSWRQPAEGT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5690349_8663926	53	0.305	1.857E-03	92	173	352	44	126	150
+--------------------------------------------------------------------------------------------TSFPDFRQASDYLKELLARRKLVFVWGDEYYLPYRkEAFHAIHSTHSFVVTDYDGENkaYYVEDWD--GLYGYLPAAHVEAAFDS----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR6266851_2378427	53	0.386	2.464E-03	127	224	352	0	100	101
+-------------------------------------------------------------------------------------------------------------------------------PAFGDVHTNHLLSVFGLDEERgcAYVVDDIPPAFRGWIPIAMLDAARGSANrAEHGRDRFFTNEAIRWRWLEIRCSAQLPRLSDEAIDAVLGQNLAGFRQP-------------------------------------------------------------------------------------------------------------------------------
+>SaaInlV_150m_DNA_4_1039716.scaffolds.fasta_scaffold159517_1	53	0.262	2.464E-03	85	175	352	0	99	177
+-------------------------------------------------------------------------------------EHYGVD--THQGAGAGIESLMSELVQGHAVIVAVDADDM-WNPGslfrglFGEDGADHAVVVTGLdlsdpDHPQVYINDPgDPNGAGKAYPLEQFLAAWSDSG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5919198_383436	53	0.382	2.464E-03	22	113	352	254	347	351
+----------------------VEPWYDDLASCLHSTLASVVAQRQLDPLVVLGSGWTFAYSPGEWAPAEFFYPALDGSLAATLAPHqpLSIAWREPGSPEEAEQELVAALAGGGP----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5436853_446621	53	0.283	3.268E-03	136	238	352	0	97	123
+----------------------------------------------------------------------------------------------------------------------------------------HLLTVYGFDDDagTALLADPVPPSFAGPVPRSLLAAARDSDNPvLHERDMFFTANPIANRWLDVRVGPVQPAFGPAFVRDAVAAAR--------PDPPSAAASLRR-----------------------------------------------------------------------------------------------------------------
+>SRR5215204_5524451	52	0.283	4.335E-03	103	162	352	1	59	117
+-------------------------------------------------------------------------------------------------------HLVDKLDKGMPVCLPVDIYFLPFTSHFQRLHMAHYVNVFGYNDTQYYIISPYY-RYQGWV---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR3954452_13515641	52	0.349	4.335E-03	219	341	352	0	119	120
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGMLAISTETAWTGMNGLDRYLTRLT--VRAEEKDADALADVYPFGWAMQAQAYMHAELLRACAVRWRRPVLGEAARRLAAVSHAWTGVPISAGHGGAD-TRVAETVERHCRRLRRCHEQAVE----------
+>SRR5271163_123213	52	0.265	5.750E-03	100	175	352	2	79	120
+----------------------------------------------------------------------------------------------------SVDDLQQYLDQGRSVIVSVDPDPI-WYPGQPDQGEGHAVMITAIDETTgmVTLDDTgSPQGNEEQVPISEFQQAWAEHD--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>GraSoiStandDraft_4_1057263.scaffolds.fasta_scaffold8820481_1	52	0.270	5.750E-03	99	171	352	122	191	210
+---------------------------------------------------------------------------------------------------PTLKTIRDFLRKGYIAIVNVNYYPLYRQPGY----SGHFVIVLSIDKRSVRLHDPGLPRKdNMRIPLRQFLAAW------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR3990172_4137688	52	0.270	5.750E-03	99	171	352	128	197	216
+---------------------------------------------------------------------------------------------------PTLKTIRDFLRKGYIAIVNVNYYPLYRQPGY----SGHFVIVLSIDKRSVRLHDPGLPRKdNMRIPLRQFLAAW------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5215467_2164624	51	0.316	7.626E-03	152	289	352	0	137	138
+--------------------------------------------------------------------------------------------------------------------------------------------------------DASPPSFKGSIPIHALQAARGSENPAiHNRDLFFTNVPIANRWLEVEIGNTFPCITKQWVKEVLSTNTQRFAAPTSEVALSGTEGMVRYFGDF-GLDQVRERGTPAMDELVLVSVAFQEATALHADFLRAMGQRLDWRE--------------------------------------------------------------
+>MGYP000895684420	51	0.301	7.626E-03	100	171	352	80	151	152
+----------------------------------------------------------------------------------------------------SLARLRGLVARGPVVVGPLDMSKLTYIPGHEHlVGADHFVLVHDVTDEEVFMHDPGGSPY-VSLPIADFLAAW------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5919197_1036140	51	0.415	7.626E-03	22	119	352	166	266	267
+----------------------VRQWYRDPISCLQSTLATVLLAAGAEPLPVLGLAWEFRFQRGRVGREEFAYPCRfEGDVARSLAPYHPLRSSWWSPalDEDPLGELARRVEDGELPVAAVD----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>2286|Ga0268252_1295275_1|+2|10	51	0.373	1.011E-02	274	348	352	2	76	87
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HGELLRWCGRRWIDAALAEAGRRVERVAHLWTGVRVVCAHLRDDPAPHGRTLARHTNRLQHAYEDAVEAVARAAG---
+>SRR5947208_11376747	51	0.406	1.011E-02	226	343	352	2	118	122
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PARGRAGLAGLACYLDGICER-AAGPHGRAALDEIYTVGWQMQAATALHADFLRLAGRSLDWDELAEAGRQVDRLANAWTPLRIMGAHAGTRDLDVTGELRRRATRLVADHELTLELL--------
+>ERR671937_651557	51	0.397	1.011E-02	22	111	352	66	158	160
+----------------------VRQWYRDPVSCLQSTLATVVLAAGAEPLPVLGLGWEFLFEPGDVRPEEFYYPCRfEGDLARSLAPYHPIRSRWWspEPDEDPLAELARRVEAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5215472_1733542	51	0.384	1.341E-02	156	269	352	0	114	118
+------------------------------------------------------------------------------------------------------------------------------------------------------------PGFDGPMASRDFLLAWGSANPADTRDAFFSDSGIGRRCLITRVTGPgRGPVGRDGLAAALRANLNDLTAPlaTSQLPWTGLAGLHRYLDDLRQRAAAGD--QEVLADAYAFGWPMQA----------------------------------------------------------------------------------
+>SRR4051812_10767532	51	0.393	1.341E-02	20	106	352	55	143	145
+--------------------PEPELWYRDLISCLQATFGSLLVRDGADPLVVLGAGWRFLHLPGDVRFDEFYYPCRDGDLGAALAPHHDLHSRWWQPGDEGdvWREIRE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>MGYP000929587384	50	0.285	1.778E-02	115	172	352	1	63	84
+-------------------------------------------------------------------------------------------------------------------IVPVDTALLPYWLTRSDvpeteRGTDHAVVVVAVDEQHVYVNDPDFAQAPQVVELGWFLDAWR-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5713101_4123152	50	0.337	1.778E-02	52	140	352	9	92	103
+----------------------------------------------------LGARWSFGFPRDDRELQEYTL---PDYLAAKLRTRTGIVIRSHSDPAGL--ELRRHLADEQPAAIAVDSFYLPYRPAFQRVHSSRTILV-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5206468_3369128	50	0.358	1.778E-02	224	343	352	7	123	124
+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GEPAPAYRGLAGLRGF---LTAVADALAEGRPASDEGFVVAGPILAITGLHADWLARAARMFDDPRLLEAARVVERVAHHWTAFRIAVATARADPPGAAESLRARGRALVDDHERALALL--------
+>SRR5437879_4950898	50	0.301	2.358E-02	141	239	352	1	106	113
+---------------------------------------------------------------------------------------------------------------------------------------------YGVDDGHklVWVLDAIPPAFQGPISRATFDAGRDSSNRsRQERDMFFADNPIANRWLELDIEPDRNADgalgDRDRLRQILEGNLRGFTQERKSGPFEGVRGVDRF----------------------------------------------------------------------------------------------------------------
+>GraSoiStandDraft_27_1057306.scaffolds.fasta_scaffold00573_2	50	0.252	2.358E-02	101	171	352	0	77	154
+-----------------------------------------------------------------------------------------------------LDDLKKFIDNGQPPIALVKYANLPDRVDKGST-GGQYVVVVGYDDaaQNIFINDPDMfpwnhaAGFQKAYPYQTWLSAW------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>A0A2H2XNW3	50	0.271	2.358E-02	101	180	352	125	201	208
+-----------------------------------------------------------------------------------------------------IEDIRQLLACGYLIICLVNWCKLNAHIGYE----GHYVLVYDISETHIYLHDPGLPTYiSQALTITEFEQAWAAPTQRDRN---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR3954466_6934608	49	0.329	3.126E-02	88	175	352	0	87	132
+----------------------------------------------------------------------------------------GIPVSIENSD---VSGLIDALDSGKGIIVAVDSGEYWTGEATEDNAPDHAVVVAAIDEENgiVYLSDTGtPDGNMLAVPLDAFLDAWGDSG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>ERR1700752_922602	49	0.304	3.126E-02	100	175	352	3	84	182
+----------------------------------------------------------------------------------------------------TLTDLETYLDEGRSIILGVDSsdiWNEPEDPAEPVDQADHALVITAIDKEQGLVvlSDPgDPDGNQSIVPLSDFTEAWSDSG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR2546423_3336499	49	0.373	3.126E-02	24	111	352	176	266	268
+------------------------QWYRDPISCLQSTLATVLLAAGVEPLPVLGLAWEFLFRPGRIGREEFAYPCRfEGDVARSLAPYHPLRSHWWSPAPEedALAELARRVERG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5947209_18303409	49	0.482	4.144E-02	20	75	352	68	123	125
+--------------------PGVEFWRHDLSSCLQDCLATLLVQRRHDPVPALGAAWDFYYPPGDLRPEEYYYPCR------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR6185503_18933790	49	0.450	4.144E-02	20	99	352	52	131	136
+--------------------PEPELWYRDLISCLQATFGSLLLRAGADPLTVLGAGWRFLHVPGDVRSEEFYYPAEDADLGAALAPHHELHSRWWQPADE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>ERR1700687_2983525	49	0.379	5.494E-02	232	318	352	22	106	109
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLAALADLLADLASRLEREGAWP--LRDIYVLGWSAQAEASLHSRFLAGAARDLQRPDVAEAARWVDAVAHAWTGFRVAAAHGAAAP---------------------------------
+>SRR5579862_9683268	49	0.357	5.494E-02	213	337	352	4	127	133
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALKANLAAFSADSPADaPWTGNIGLRRYLDHVISHAEA--GHADAVRQVYPFAWSAQASAAMHGELLRTRGGQWRIPELTEAGRAVEAVASAWTPVRVLAAHGWQSPASIASSLRSYGIDLARQYR--------------
+>SRR5215471_6261074	49	0.308	5.494E-02	197	327	352	0	128	147
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EVTGPARALDRVFLRRVLADNGRRFRSGSGAGPeLTGLAGLERF----CEWaAAALAAAQPVVDEVFVVAGVVLADTALHADYLAHAAARLGAARLLEAARRVERLAHHWTAVRIAVATARGAEPTAAPRLGR------------------------
+>SRR5213076_2182558	48	0.551	7.282E-02	115	161	352	0	48	116
+-------------------------------------------------------------------------------------------------------------------IVAVDNYHLPFRPAYGDVHTNHLVVVYGFDDEagEVHVLDSKPPRYRGP----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5207237_9007299	48	0.259	7.282E-02	100	171	352	27	106	120
+----------------------------------------------------------------------------------------------------GVDRLKAEVAAGNPVVVWITAGkYVQRTPvvasyngeTFKLVAGEHAVVVYGYDSGGVYIMDVSNGSFTYT-EWSSFLTRW------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>4958|scaffold10375_5|+5204|00	48	0.285	7.282E-02	95	175	352	87	169	196
+-----------------------------------------------------------------------------------------------SSPDKAWEANKTAIKT-KPIIVLTDIYHLKFRNEYLKQHGAHFIILFYYDElsNSVGVLDWYePHFYKGEILLNDFLSARYSEN--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>EndMetStandDraft_8_1072994.scaffolds.fasta_scaffold5616288_1	48	0.285	7.282E-02	95	175	352	87	169	196
+-----------------------------------------------------------------------------------------------SSPDKAWEANKTAIKT-KPIIVLTDIYHLKFRNEYLKQHGAHFIILFYYDElsNSVGVLDWYePHFYKGEILLNDFLSARYSEN--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5262249_50530649	48	0.330	7.282E-02	1	105	352	93	204	205
+-GGGRGMTSDVTARTYMIIGPEPELWYRDLVSCLRATFGSLLARACADPLTVLGAGWRFLHLPGDVRSEEFYYPCPADesggaDLGAALAPHHGLHSRWWQpaDEDDLWREVR------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5437667_7529899	48	0.381	9.652E-02	235	344	352	0	108	114
+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLRDYLAGVAARARDARD-PGVMDELYVAGWAAQQSAGLHADFLAAAGCRLGRTRLAEAGREVDRLAHHWSDLRMLGAHCRAEPAAAASRIRRRAAQLVTDTERVLAQLE-------
+>SRR2546430_2482901	48	0.346	9.652E-02	146	269	352	4	127	134
+--------------------------------------------------------------------------------------------------------------------------------------------------GKVRVLDEVPPRFDGEIELAELAAARHSVNPiVHGRDKFFTANPIAGRWLSVRATASPPytVDDRERISALLRANIERFDQ-SQADVYSGLSGQARFLAEGARRLDTDPAAKDEL--FVVAGTALAA----------------------------------------------------------------------------------
+>SRR4030042_1077736	48	0.232	9.652E-02	117	172	352	7	59	215
+---------------------------------------------------------------------------------------------------------------------WRDRTDVPWTETWDD---GHYMVLLGMDAANLYFEDPSLLGARGVIPRAEFVDRWH-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>MGYP000240722769	48	0.333	1.279E-01	113	145	352	42	74	91
+-----------------------------------------------------------------------------------------------------------------PIIVLVDVYYLPYRKEYHKYHASHAVLLVGYDE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5205814_4332124	48	0.359	1.279E-01	194	296	352	0	101	104
+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LQVSIGEDFPAPAPGWVDGVIRQNVERFRAGGDGGSFSGLAGLRDYLAGVAARARDARD-PGVMDELYVAGWAAQQSAGLHADFLAAAGCRLGRTRLAEAGRE-------------------------------------------------------
+>SRR6266542_2363188	47	0.509	1.695E-01	21	73	352	49	101	105
+---------------------PVRLWCRDLVSCLQATFATVLLHAGRDPLAALGAAWGFYYLPGDVTSEEFYYP--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5688572_6867596	47	0.298	1.695E-01	49	150	352	41	139	141
+-------------------------------------------------PELLGARWTFAlpHDERRAELTEYSLPFHPLGFVAAIDRRTGLRLQEGR-----AEELDGTVAGGTPVIAAVDSFHLPYRPAFGRVHSHRTVIVRRVLRDAVEV---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR3989344_2091767	47	0.222	2.247E-01	125	175	352	7	60	146
+-----------------------------------------------------------------------------------------------------------------------------WVKSWEKVHSSHFMTVTGYDDDYVYINDPtdhDLTIKNMKVPNNNFLSAWSNGN--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5216683_1865760	47	0.315	2.247E-01	101	172	352	126	194	216
+-----------------------------------------------------------------------------------------------------LDDLKRELSLGSLAIVNVNYFRL----LEKVGYAGHFVVVEAVDEEEVLLQNPGLPPIPnQRVAMATFLAAWH-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR3569832_2248283	46	0.377	2.977E-01	134	178	352	21	65	133
+--------------------------------------------------------------------------------------------------------------------------------------GDHWFSVYGIDESGVRIYDPIPSKFTGTIPLEDFKRAWGGNALVA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR4051812_39536360	46	0.300	2.977E-01	104	172	352	70	137	138
+--------------------------------------------------------------------------------------------------------VAAQLAAGLPPIALIpDWRALPAEQTY-ATGNAHAVVITGVTDSDVTFIDPW-PGKSFAMSTTRFEAAWS-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5688572_24881951	46	0.294	2.977E-01	104	171	352	6	62	140
+--------------------------------------------------------------------------------------------------------LEEALGAGLPPIVLIEVAPARW----------HYVVVVGVTDNAVHVHDPARAP-DLRIERAEFLSRW------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR2546423_2718336	46	0.417	2.977E-01	22	99	352	74	152	162
+----------------------IRQWYRDPISCLQSTLAAVLLAAGAEPLPVLGLAWEFRFQPGRVGREEFAYPCRfEGDLAGSLAPYHPLRSSWWSPAPE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5688500_13065661	46	0.325	3.944E-01	271	313	352	2	44	130
+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RGLYADFLTEAAALLGDPRVAEAASGWRAAADLWEDLSDAVIP--------------------------------------
+>SRR4051812_2527260	46	0.279	3.944E-01	178	313	352	4	132	135
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HDRDRFFTNQPIAHRWLDVGLESPRPRPSTASI---VRGNLAAFRKVSDGHIFRGSSGLAQFLDTAAGAIAGGKPPDELF---VVAGTALAAS-SLHAEWLSREGMRTGTPVWCELGRAVDRISHHWTALRIAAAR--------------------------------------
+>SRR4051812_40660863	46	0.407	3.944E-01	1	76	352	78	153	154
+-GGGRGMTSVVMARTYMITGPEPELWYRDLISCLQATFGSLLARAGADPLTVLGAGWRFLHLPGDVRSEEFYYPCPP-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5207244_1963219	46	0.405	3.944E-01	22	99	352	88	166	171
+----------------------IRQWYRDPISCLQSTLATVLLAAGAEPLPVLGLAWEFLFVPGDVRPEEFYYPCRfKGDPARSLAPYHPIRSHWWRPAEE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>A0A2B0WVF8	46	0.236	3.944E-01	93	171	352	79	171	362
+---------------------------------------------------------------------------------------------VYSDFGNGLQFIKECLNRQEVFIALGSTFFLPYSNDYlnpkfikshidihtDKYVTDHYLAINKLTEDSVFVQDPVPNKYMGEISLEEFHSFW------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>MGYP001339385609	46	0.295	5.226E-01	129	172	352	3	46	60
+---------------------------------------------------------------------------------------------------------------------------------YWDQVTSHVVVVIGCDKQGVVINDPSLPDGGRAISWDVFLAAWA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR6185295_5817841	46	0.388	5.226E-01	252	318	352	41	107	118
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DSAGVRQELYVLGWWMQAMTAVHARFLAEAGRALGRPELVEIARRVELVAHEWTGLRITAVHGPADD---------------------------------
+>SRR4051812_38390578	46	0.280	5.226E-01	104	153	352	45	94	119
+--------------------------------------------------------------------------------------------------------IRAELAASGTVIVVANTYHLPWSPAYQQSATPHWLLVTDTHDGLWHLVDP------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>UPI000845F276	46	0.256	5.226E-01	100	169	352	85	156	167
+----------------------------------------------------------------------------------------------------TFQDIASALRNGEVPIVLISTYRL------HRVRAPHWVVVTGFDRHYIYFHDPYegfyernkRQAQHISIPINEFLR--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>MGYP001050378313	46	0.526	5.226E-01	87	160	352	109	178	179
+---------------------------------------------------------------------------------------HGLRRESIDADDGAL------VARGELPIAAVDNFHLPFRPAFHDVHAAHLVVVYGVDRARGLVNvsDAMPPAFSG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>ERR671931_602696	45	0.323	6.924E-01	203	304	352	0	98	99
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PALTRKWLHEVVEQNRERLL--ADDDPFCGLVALRAYMEDLLAYCGTPFGGRALVGA-YRLGWPMQAQADLHGELLRLAGARFDDAALCEAAAEVRGVGHAW-----------------------------------------------
+>SRR5882724_1744776	45	0.295	6.924E-01	94	154	352	41	95	101
+----------------------------------------------------------------------------------------------YRIGARGLDELRGDLADGAVPVVLVSMDYI------HKDPTAHWVVVTGVDDENVTVNDPW-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR6478752_1188215	45	0.400	6.924E-01	20	99	352	50	134	137
+--------------------PEPELWYRDLISCLQATFGSLLARLGADPLAVLGAGWRFLHLPGDVRSEEFYYPCPADesggtDLGAALAPHHQLHSLWWQPADE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR6185437_13975043	45	0.282	6.924E-01	135	173	352	14	51	246
+---------------------------------------------------------------------------------------------------------------------------------------DHYVVVTGVEDGIVRFHDPHGHPYA-TLPADDFIAAWAS----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5215467_3611681	45	0.365	9.172E-01	255	347	352	9	101	110
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HMLGELYTVGWAAQSVAALHADFLRRHAMAFGWSEGLEAARSVDQLANLWTPLRIFAAHASTNGIEVSDRLRQRMRVVVDHYELALEELDRAA----
+>SRR6185312_7446242	45	0.341	9.172E-01	268	308	352	11	51	138
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGRLLYADFLDVASVVLDEPALERAAAGFREAGDRWSKLA-------------------------------------------
+>SRR5205085_3472310	45	0.430	9.172E-01	22	99	352	58	136	150
+----------------------VSQWYRDPISCLQSTLATVLLAAGAEPLPVLGLAWELRFQPGRVGREEFAYTCRfEGDLARSLAPYHPISSRWWSPAED------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SaaInl7_100m_RNA_FD_contig_21_4047958_length_241_multi_3_in_0_out_0_1	45	0.217	9.172E-01	85	171	352	72	172	360
+-------------------------------------------------------------------------------------KIYTMERKFYRSLEEGLYGIHEHLSQNDFFISLGTTYYLPYSRDYKNPKyieshvksnsnkyvTDHYLSVYGLHNENIFINDPVPNKYIGAISLKDFSDFW------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR6185312_10924508	44	0.395	1.215E+00	232	327	352	5	95	127
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GMSGLARYFDLLRERTAA-PDGHQALEELYVLGWSLQASTALHADFLMKAGKQLDWYQLTTVGRQVARIAHHWTPLRMLGAHG----RARPDEIRE------------------------
+>MGYP001029765960	44	0.279	1.215E+00	110	152	352	91	133	258
+--------------------------------------------------------------------------------------------------------------QKQPIMAFVDAFDCDWLPFYRKHHIKHTIIVYSINKDDIYFYD-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>18595|scaffold4953588_1|+69|01	44	0.323	1.609E+00	86	152	352	25	95	99
+--------------------------------------------------------------------------------------RAGATVTLHETSGrvAAVKHLQEALAAGTPPLAWVDQAHMPYlqLPEVLKGHIGHLVAIAGQTGDSYLIDD-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5215208_421555	44	0.275	1.609E+00	188	295	352	1	106	107
+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PIRNRWFEIEWSGAVPVLPSlGRVRCVVNRNLETFDRPPVDGWTFGQAGLRLMFDVLAG---SAAPGVRESDEMFVVAGAALAKTALHAEYLRQAGRRWGVPSLSEASR--------------------------------------------------------
+>SRR5215213_5558053	44	0.298	1.609E+00	101	175	352	49	114	117
+-----------------------------------------------------------------------------------------------------LDDLKEELARGLYPIVYLElvSGQLRYV---------HSVVVVEITDDQVQVLDPEIGERAFNI--EDFNRAWSAKN--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5919202_3634501	44	0.400	1.609E+00	22	90	352	119	188	191
+----------------------VAHWYRDPLSCLQSTLASVLLHAGAEPLPVLGLAWEFLFKPGEVPREEFAYPCRfEGDVARSLEPYHPIR---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>MGYP000886274396	44	0.291	2.132E+00	101	148	352	21	68	69
+-----------------------------------------------------------------------------------------------------WKQNLKKLQEGIPLIILVDLFYLPYTIYLGKEHAAHAIIVYEYCDNKI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5581483_1739624	44	0.382	2.132E+00	25	92	352	42	109	110
+-------------------------WYRDLISCLQATFGTLVARLGADPLAVLGAGWRFLHLPGDVRFDEFYYPCPDGDLGAALAPHHELRAR-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>ERR1700741_1246718	44	0.491	2.132E+00	20	78	352	52	110	120
+--------------------PEPELWYRDLISCLQATFGSIVARAGADPLTVLGAGWRFLHLPGDVRSEEFYYPCPPDD---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR4051794_34888363	44	0.322	2.132E+00	4	62	352	75	133	134
+----HAAAGRPGRRIAAMRLPRMEPWRHDLVGCLHTAIGSVMANHGFDPLVTLGASWGFYYRP-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>5940|scaffold5088856_1|+3|11	43	0.366	2.824E+00	22	81	352	21	80	81
+----------------------LKRWYADPMSCLQACLGTVLIFPGADPLETLGTSWEFRYVPGDVRREEFYYPCRFKDDPA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>ERR1700729_2025172	43	0.463	3.739E+00	23	63	352	65	105	111
+-----------------------PMWYRDTVSCLPATIGSVLAYHGYDPLEVLGAGWDFTFIPG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5206468_2692918	42	0.328	4.952E+00	1	64	352	41	104	110
+-GRAQPAGRRGRGARVKVELTPLSYWFHDLCSCLHDCLGTVLTYHGQSPIEVMGASWEFFHSPDD-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR3954452_12164045	42	0.481	4.952E+00	20	73	352	70	123	125
+--------------------PEPQWWYRDLVSCLQATFGTVLARAGIDPLSVLGAGWRFLHLPGDVRSEEFYYP--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5579862_4067062	42	0.341	4.952E+00	268	308	352	13	53	130
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGRPLYGDFLDVAASVLREPSLERAAAGFRDAGRRWTGLA-------------------------------------------
+>ERR1051325_11233650	42	0.454	4.952E+00	21	75	352	72	126	131
+---------------------PVRQWYRDPVSCLQSTLSTVLLDVGADPLAVLGLGFEFRYLPGEVRPEEFYYPGR------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>ERR1700712_5093054	42	0.252	4.952E+00	98	174	352	75	169	193
+--------------------------------------------------------------------------------------------------DQALNDLKAALAAGKATMVGVNNTALykdfPHQDQPgQTPAANHQVVVIGYDtaTDTVYIDDGGWPPDPedagrpeggqkMPVKLDTFLAAWKAD---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR3712207_5935252	42	0.292	6.558E+00	268	308	352	0	40	104
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GNLRALYADFLEQAAARLHAPELVPVAGLFRAAAEAWQSVA-------------------------------------------
+>SRR5579872_692970	42	0.280	6.558E+00	76	146	352	32	106	111
+----------------------------------------------------------------------------PDVGIGKALELLGFAVaeRAHDDGADApFDDLRHALASGPVVLGPLDMGHLTYIPYHEALGGaDHFVLAYAMDEE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR2546430_4736840	42	0.270	6.558E+00	106	167	352	7	80	145
+----------------------------------------------------------------------------------------------------------EALGGGDPVLVVGDAFHLPWVPYHGRQHLDHGFVIEGLEPGAmpvvAHVVDAYDNatqwghavPLATTLPLADL----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR5256885_6193825	42	0.359	8.684E+00	1	98	352	12	114	119
+-GRSPDMTVDVPARTYMITGPEPEWWYRDLVSCLQATFGSLLIREGADPLSVLGAGWRFLHLPGEVRSEEFYYPCPTDesgaiDLGAALAPHHQLHSRRLPPAG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR3954469_21777195	42	0.431	8.684E+00	20	77	352	32	89	121
+--------------------PEPEWWYRDLISCLQATFGSVLANAGADPLAVLGAGWRFLHLPGEVRSEEFYYPCPAG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>SRR3546814_4326061	42	0.311	8.684E+00	100	160	352	66	120	151
+----------------------------------------------------------------------------------------------------GVAELEERFRAGWLPMVLVSTFYVHG------DHVAHWVVVTGFGPDAVYINDPWVDRKGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

model/Protenix-pxd/examples/dimer.fasta

@@ -0,0 +1,2 @@
+>dimer
+FPTIPLSRLFDNAMLRAHRLHQLAFDTYQEFEEAYIPKEQKYSFLQNPQTSLCFSESIPTPSNREETQQKSNLELLRISLLLIQSWLEPVQFLRSVFANSLVYGASDSNVYDLLKDLEERIQTLMGRLEDGSPRTGQIFKQTYSKFDTNSHNDDALLKNYGLLYCFRKDMDKVETFLRIVQCRSVEGSCGF:FSGSEATAAILSRAPWSLQSVNPGLKTNSSKEPKFTKCRSPERETFSCHWTDEVHHGTKNLGPIQLFYTRRNTQEWTQEWKECPDYVSAGENSCYFNSSFTSIWIPYCIKLTSNGGTVDEKCFSVDEIVQPDPPIALNWTLLNVSLTGIHADIQVRWEAPRNADIQKGWMVLEYELQYKEVNETKWKMMDPILTTSVPVYSLKVDKEYEVRVRSKQRNSGNYGEFSEVLYVTLPQMSQ

model/Protenix-pxd/examples/example.json

@@ -0,0 +1,104 @@
+[{
+    "sequences": [
+        {
+            "proteinChain": {
+                "sequence": "MGSSHHHHHHSSGLVPRGSHMSGKIQHKAVVPAPSRIPLTLSEIEDLRRKGFNQTEIAELYGVTRQAVSWHKKTYGGRLTTRQIVQQNWPWDTRKPHDKSKAFQRLRDHGEYMRVGSFRTMSEDKKKRLLSWWKMLRDNDLVLEFDPSIEPYEGMAGGGFRYVPRDISDDDLLIRVNEHTQLTAEGELLWSWPDDIEELLSEP",
+                "count": 1,
+                "msa": {
+                    "precomputed_msa_dir": "./examples/7r6r/msa/1",
+                    "pairing_db": "uniref100"
+                }
+            }
+        },
+        {
+            "dnaSequence": {
+                "sequence": "TTTCGGTGGCTGTCAAGCGGG",
+                "count": 1
+            }
+        },
+        {
+            "dnaSequence": {
+                "sequence": "CCCGCTTGACAGCCACCGAAA",
+                "count": 1
+            }
+        }
+    ],
+    "name": "7r6r"
+},
+{
+    "sequences": [
+        {
+            "proteinChain": {
+                "sequence": "MASWSHPQFEKGGTHVAETSAPTRSEPDTRVLTLPGTASAPEFRLIDIDGLLNNRATTDVRDLGSGRLNAWGNSFPAAELPAPGSLITVAGIPFTWANAHARGDNIRCEGQVVDIPPGQYDWIYLLAASERRSEDTIWAHYDDGHADPLRVGISDFLDGTPAFGELSAFRTSRMHYPHHVQEGLPTTMWLTRVGMPRHGVARSLRLPRSVAMHVFALTLRTAAAVRLAEGATT",
+                "count": 2,
+                "msa": {
+                    "precomputed_msa_dir": "./examples/7wux/msa/1",
+                    "pairing_db": "uniref100"
+                }
+            }
+        },
+        {
+            "proteinChain": {
+                "sequence": "MGSSHHHHHHSQDPNSTTTAPPVELWTRDLGSCLHGTLATALIRDGHDPVTVLGAPWEFRRRPGAWSSEEYFFFAEPDSLAGRLALYHPFESTWHRSDGDGVDDLREALAAGVLPIAAVDNFHLPFRPAFHDVHAAHLLVVYRITETEVYVSDAQPPAFQGAIPLADFLASWGSLNPPDDADVFFSASPSGRRWLRTRMTGPVPEPDRHWVGRVIRENVARYRQEPPADTQTGLPGLRRYLDELCALTPGTNAASEALSELYVISWNIQAQSGLHAEFLRAHSVKWRIPELAEAAAGVDAVAHGWTGVRMTGAHSRVWQRHRPAELRGHATALVRRLEAALDLLELAADAVS",
+                "count": 2,
+                "msa": {
+                    "precomputed_msa_dir": "./examples/7wux/msa/2",
+                    "pairing_db": "uniref100"
+                }
+            }
+        },
+        {
+            "ligand": {
+                "ligand": "CCD_P4G",
+                "count": 1
+            }
+        },
+        {
+            "ligand": {
+                "ligand": "CCD_6OI",
+                "count": 2
+            }
+        },
+        {
+            "ligand": {
+                "ligand": "CCD_MG",
+                "count": 3
+            }
+        }
+    ],
+    "name": "7wux"
+},
+{
+    "sequences": [
+        {
+            "proteinChain": {
+                "sequence": "MAEVIRSSAFWRSFPIFEEFDSETLCELSGIASYRKWSAGTVIFQRGDQGDYMIVVVSGRIKLSLFTPQGRELMLRQHEAGALFGEMALLDGQPRSADATAVTAAEGYVIGKKDFLALITQRPKTAEAVIRFLCAQLRDTTDRLETIALYDLNARVARFFLATLRQIHGSEMPQSANLRLTLSQTDIASILGASRPKVNRAILSLEESGAIKRADGIICCNVGRLLSIADPEEDLEHHHHHHHH",
+                "count": 2,
+                "msa": {
+                    "precomputed_msa_dir": "./examples/7pzb/msa/1",
+                    "pairing_db": "uniref100"
+                }
+            }
+        },
+        {
+            "dnaSequence": {
+                "sequence": "CTAGGTAACATTACTCGCG",
+                "count": 2
+            }
+        },
+        {
+            "dnaSequence": {
+                "sequence": "GCGAGTAATGTTAC",
+                "count": 2
+            }
+        },
+        {
+            "ligand": {
+                "ligand": "CCD_PCG",
+                "count": 2
+            }
+        }
+    ],
+    "name": "7pzb"
+}
+]

model/Protenix-pxd/examples/example_constraint_msa.json

@@ -0,0 +1,162 @@
+[
+    {
+        "sequences": [
+            {
+                "proteinChain": {
+                    "sequence": "YMLDLQPETTDLYCGGGGSGGGGSGGGGSIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDMGGGGSGGGGSGGGGSGGGGSGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGCYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMCAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEHHHHHH",
+                    "count": 1,
+                    "msa": {
+                        "precomputed_msa_dir": "./examples/7st3/msa/1/",
+                        "pairing_db": "uniref100"
+                    }
+                }
+            },
+            {
+                "proteinChain": {
+                    "sequence": "EVKLVESGGGLVQPGGSLRLSCAASGSIFSINTMGWYRQTPGKQRDLVADISSGGSTKYGDSVKGRFTISRDNTKNTVYLQMNSLKPEDTAVYYCYGLSYSNDDYWGQGTQVTVSS",
+                    "count": 1,
+                    "msa": {
+                        "precomputed_msa_dir": "./examples/7st3/msa/2/",
+                        "pairing_db": "uniref100"
+                    }
+                }
+            }
+        ],
+        "modelSeeds": [],
+        "name": "7st3_base"
+    },
+    {
+        "sequences": [
+            {
+                "proteinChain": {
+                    "sequence": "YMLDLQPETTDLYCGGGGSGGGGSGGGGSIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDMGGGGSGGGGSGGGGSGGGGSGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGCYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMCAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEHHHHHH",
+                    "count": 1,
+                    "msa": {
+                        "precomputed_msa_dir": "./examples/7st3/msa/1/",
+                        "pairing_db": "uniref100"
+                    }
+                }
+            },
+            {
+                "proteinChain": {
+                    "sequence": "EVKLVESGGGLVQPGGSLRLSCAASGSIFSINTMGWYRQTPGKQRDLVADISSGGSTKYGDSVKGRFTISRDNTKNTVYLQMNSLKPEDTAVYYCYGLSYSNDDYWGQGTQVTVSS",
+                    "count": 1,
+                    "msa": {
+                        "precomputed_msa_dir": "./examples/7st3/msa/2/",
+                        "pairing_db": "uniref100"
+                    }
+                }
+            }
+        ],
+        "modelSeeds": [],
+        "name": "7st3_pocket_1_8",
+        "constraint": {
+            "pocket": {
+                "binder_chain": [
+                    "2",
+                    1
+                ],
+                "contact_residues": [
+                    [
+                        "1",
+                        1,
+                        69
+                    ]
+                ],
+                "max_distance": 8
+            }
+        }
+    },
+    {
+        "sequences": [
+            {
+                "proteinChain": {
+                    "sequence": "YMLDLQPETTDLYCGGGGSGGGGSGGGGSIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDMGGGGSGGGGSGGGGSGGGGSGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGCYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMCAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEHHHHHH",
+                    "count": 1,
+                    "msa": {
+                        "precomputed_msa_dir": "./examples/7st3/msa/1/",
+                        "pairing_db": "uniref100"
+                    }
+                }
+            },
+            {
+                "proteinChain": {
+                    "sequence": "EVKLVESGGGLVQPGGSLRLSCAASGSIFSINTMGWYRQTPGKQRDLVADISSGGSTKYGDSVKGRFTISRDNTKNTVYLQMNSLKPEDTAVYYCYGLSYSNDDYWGQGTQVTVSS",
+                    "count": 1,
+                    "msa": {
+                        "precomputed_msa_dir": "./examples/7st3/msa/2/",
+                        "pairing_db": "uniref100"
+                    }
+                }
+            }
+        ],
+        "modelSeeds": [],
+        "name": "7st3_token_1_15",
+        "constraint": {
+            "contact": [
+                {
+                    "residue1": [
+                        "1",
+                        1,
+                        72
+                    ],
+                    "residue2": [
+                        "2",
+                        1,
+                        103
+                    ],
+                    "max_distance": 15
+                }
+            ]
+        }
+    },
+    {
+    "sequences": [
+      {
+        "proteinChain": {
+          "sequence": "MSSPLKNALVTAMLAGGALSSPTKQHVGIPVNASPEVGPGKYSFKQVRNPNYKFNGPLSVKKTYLKYGVPIPAWLEDAVQNSTSGLAERSTGSATTTPIDSLDDAYITPVQIGTPAQTLNLDFDTGSSDLWVFSSETTASEVDGQTIYTPSKSTTAKLLSGATWSISYGDGSSSSGDVYTDTVSVGGLTVTGQAVESAKKVSSSFTEDSTIDGLLGLAFSTLNTVSPTQQKTFFDNAKASLDSPVFTADLGYHAPGTYNFGFIDTTAYTGSITYTAVSTKQGFWEWTSTGYAVGSGTFKSTSIDGIADTGTTLLYLPATVVSAYWAQVSGAKSSSSVGGYVFPCSATLPSFTFGVGSARIVIPGDYIDFGPISTGSSSCFGGIQSSAGIGINIFGDVALKAAFVVFNGATTPTLGFASK", 
+          "count": 1, 
+          "msa": {
+            "precomputed_msa_dir": "./examples/5sak/1/", 
+            "pairing_db": "uniref100"
+          }
+        }
+      }, 
+      {
+        "ligand": {"ligand": "CCD_ZRY", "count": 1}
+      }
+    ], 
+    "modelSeeds": [], 
+    "name": "5sak_base"
+  },
+    {
+    "sequences": [
+      {
+        "proteinChain": {
+          "sequence": "MSSPLKNALVTAMLAGGALSSPTKQHVGIPVNASPEVGPGKYSFKQVRNPNYKFNGPLSVKKTYLKYGVPIPAWLEDAVQNSTSGLAERSTGSATTTPIDSLDDAYITPVQIGTPAQTLNLDFDTGSSDLWVFSSETTASEVDGQTIYTPSKSTTAKLLSGATWSISYGDGSSSSGDVYTDTVSVGGLTVTGQAVESAKKVSSSFTEDSTIDGLLGLAFSTLNTVSPTQQKTFFDNAKASLDSPVFTADLGYHAPGTYNFGFIDTTAYTGSITYTAVSTKQGFWEWTSTGYAVGSGTFKSTSIDGIADTGTTLLYLPATVVSAYWAQVSGAKSSSSVGGYVFPCSATLPSFTFGVGSARIVIPGDYIDFGPISTGSSSCFGGIQSSAGIGINIFGDVALKAAFVVFNGATTPTLGFASK", 
+          "count": 1, 
+          "msa": {
+            "precomputed_msa_dir": "./examples/5sak/1/", 
+            "pairing_db": "uniref100"
+          }
+        }
+      }, 
+      {
+        "ligand": {"ligand": "CCD_ZRY", "count": 1}
+      }
+    ], 
+    "modelSeeds": [], 
+    "name": "5sak_atom_1_3_5", 
+    "constraint": {
+      "contact": [
+        {
+          "atom1": ["1", 1, 311, "CG2"], 
+          "atom2": ["2", 1, 1, "C10"], 
+          "max_distance": 5, 
+          "min_distance": 3
+        }
+      ]
+    }
+  }
+
+]

model/Protenix-pxd/examples/example_without_msa.json

@@ -0,0 +1,30 @@
+[{
+    "sequences": [
+        {
+            "proteinChain": {
+                "sequence": "MAEVIRSSAFWRSFPIFEEFDSETLCELSGIASYRKWSAGTVIFQRGDQGDYMIVVVSGRIKLSLFTPQGRELMLRQHEAGALFGEMALLDGQPRSADATAVTAAEGYVIGKKDFLALITQRPKTAEAVIRFLCAQLRDTTDRLETIALYDLNARVARFFLATLRQIHGSEMPQSANLRLTLSQTDIASILGASRPKVNRAILSLEESGAIKRADGIICCNVGRLLSIADPEEDLEHHHHHHHH",
+                "count": 2
+            }
+        },
+        {
+            "dnaSequence": {
+                "sequence": "CTAGGTAACATTACTCGCG",
+                "count": 2
+            }
+        },
+        {
+            "dnaSequence": {
+                "sequence": "GCGAGTAATGTTAC",
+                "count": 2
+            }
+        },
+        {
+            "ligand": {
+                "ligand": "CCD_PCG",
+                "count": 2
+            }
+        }
+    ],
+    "name": "7pzb_need_search_msa"
+}
+]

model/Protenix-pxd/examples/finetune_subset.txt

@@ -0,0 +1,5 @@
+6hvq
+5mqc
+5zin
+3ew0
+5akv

model/Protenix-pxd/examples/ligands/7wux_smiles.smi

@@ -0,0 +1 @@
+Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)[C@@H](O)[C@H]1O

model/Protenix-pxd/examples/ligands/compounds-3d-R.sdf

@@ -0,0 +1,123 @@
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+M  END
+>  <Name>
+S
+
+$$$$

model/Protenix-pxd/examples/ligands/compounds-3d-RS.sdf

@@ -0,0 +1,246 @@
+mol_R
+  MOE2022           3D
+
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+ 53 55  1  0  0  0  0
+M  END
+>  <Name>
+S
+
+$$$$
+mol_S
+  MOE2022           3D
+
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+ 53 55  1  0  0  0  0
+M  END
+>  <Name>
+R
+
+$$$$

model/Protenix-pxd/examples/prot.fasta

@@ -0,0 +1,4 @@
+>A|protein
+MASWSHPQFEKGGTHVAETSAPTRSEPDTRVLTLPGTASAPEFRLIDIDGLLNNRATTDVRDLGSGRLNAWGNSFPAAELPAPGSLITVAGIPFTWANAHARGDNIRCEGQVVDIPPGQYDWIYLLAASERRSEDTIWAHYDDGHADPLRVGISDFLDGTPAFGELSAFRTSRMHYPHHVQEGLPTTMWLTRVGMPRHGVARSLRLPRSVAMHVFALTLRTAAAVRLAEGATT
+>B|protein
+MGSSHHHHHHSQDPNSTTTAPPVELWTRDLGSCLHGTLATALIRDGHDPVTVLGAPWEFRRRPGAWSSEEYFFFAEPDSLAGRLALYHPFESTWHRSDGDGVDDLREALAAGVLPIAAVDNFHLPFRPAFHDVHAAHLLVVYRITETEVYVSDAQPPAFQGAIPLADFLASWGSLNPPDDADVFFSASPSGRRWLRTRMTGPVPEPDRHWVGRVIRENVARYRQEPPADTQTGLPGLRRYLDELCALTPGTNAASEALSELYVISWNIQAQSGLHAEFLRAHSVKWRIPELAEAAAGVDAVAHGWTGVRMTGAHSRVWQRHRPAELRGHATALVRRLEAALDLLELAADAVS

model/Protenix-pxd/finetune_demo.sh

@@ -0,0 +1,42 @@
+# Copyright 2024 ByteDance and/or its affiliates.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+export LAYERNORM_TYPE=fast_layernorm
+export USE_DEEPSPEED_EVO_ATTENTION=true
+# wget -P /af3-dev/release_model/ https://af3-dev.tos-cn-beijing.volces.com/release_model/protenix_base_default_v0.5.0.pt
+checkpoint_path="/af3-dev/release_model/protenix_base_default_v0.5.0.pt"
+
+python3 ./runner/train.py \
+--model_name "protenix_base_constraint_v0.5.0" \
+--run_name protenix_finetune \
+--seed 42 \
+--base_dir ./output \
+--dtype bf16 \
+--project protenix \
+--use_wandb false \
+--diffusion_batch_size 48 \
+--eval_interval 400 \
+--log_interval 50 \
+--checkpoint_interval 400 \
+--ema_decay 0.999 \
+--train_crop_size 384 \
+--max_steps 100000 \
+--warmup_steps 2000 \
+--lr 0.001 \
+--sample_diffusion.N_step 20 \
+--load_checkpoint_path ${checkpoint_path} \
+--load_ema_checkpoint_path ${checkpoint_path} \
+--data.train_sets weightedPDB_before2109_wopb_nometalc_0925 \
+--data.weightedPDB_before2109_wopb_nometalc_0925.base_info.pdb_list examples/finetune_subset.txt \
+--data.test_sets recentPDB_1536_sample384_0925,posebusters_0925

model/Protenix-pxd/inference_demo.sh

@@ -0,0 +1,49 @@
+# Copyright 2024 ByteDance and/or its affiliates.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+export LAYERNORM_TYPE=fast_layernorm
+export USE_DEEPSPEED_EVO_ATTENTION=true
+
+N_sample=5
+N_step=200
+N_cycle=10
+seed=101
+
+input_json_path="./examples/example.json"
+dump_dir="./output"
+model_name="protenix_base_default_v0.5.0"
+
+python3 runner/inference.py \
+--model_name ${model_name} \
+--seeds ${seed} \
+--dump_dir ${dump_dir} \
+--input_json_path ${input_json_path} \
+--model.N_cycle ${N_cycle} \
+--sample_diffusion.N_sample ${N_sample} \
+--sample_diffusion.N_step ${N_step}
+
+# The following is a demo to use DDP for inference
+# torchrun \
+#     --nproc_per_node $NPROC \
+#     --master_addr $WORKER_0_HOST \
+#     --master_port $WORKER_0_PORT \
+#     --node_rank=$ID \
+#     --nnodes=$WORKER_NUM \
+#     runner/inference.py \
+#     --seeds ${seed} \
+#     --dump_dir ${dump_dir} \
+#     --input_json_path ${input_json_path} \
+#     --model.N_cycle ${N_cycle} \
+#     --sample_diffusion.N_sample ${N_sample} \
+#     --sample_diffusion.N_step ${N_step}

model/Protenix-pxd/protenix/config/__init__.py

@@ -0,0 +1,14 @@
+# Copyright 2024 ByteDance and/or its affiliates.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+from .config import load_config, parse_configs, parse_sys_args, save_config

model/Protenix-pxd/protenix/config/config.py

@@ -0,0 +1,290 @@
+# Copyright 2024 ByteDance and/or its affiliates.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import argparse
+import copy
+import sys
+from typing import Any, Optional, Union
+
+import yaml
+from ml_collections.config_dict import ConfigDict
+
+from protenix.config.extend_types import (
+    DefaultNoneWithType,
+    GlobalConfigValue,
+    ListValue,
+    RequiredValue,
+    ValueMaybeNone,
+    get_bool_value,
+)
+
+
+class ArgumentNotSet(object):
+    pass
+
+
+class ConfigManager(object):
+    def __init__(self, global_configs: dict, fill_required_with_null: bool = False):
+        """
+        Initialize the ConfigManager instance.
+
+        Args:
+            global_configs (dict): A dictionary containing global configuration settings.
+            fill_required_with_null (bool, optional):
+                A boolean flag indicating whether required values should be filled with `None` if not provided. Defaults to False.
+        """
+        self.global_configs = global_configs
+        self.fill_required_with_null = fill_required_with_null
+        self.config_infos, self.default_configs = self.get_config_infos()
+
+    def get_value_info(
+        self, value
+    ) -> tuple[Any, Optional[Any], Optional[bool], Optional[bool]]:
+        """
+        Return the type, default value, whether it allows None, and whether it is required for a given value.
+
+        Args:
+            value: The value to determine the information for.
+
+        Returns:
+            tuple: A tuple containing the following elements:
+                - dtype: The type of the value.
+                - default_value: The default value for the value.
+                - allow_none: A boolean indicating whether the value can be None.
+                - required: A boolean indicating whether the value is required.
+        """
+        if isinstance(value, DefaultNoneWithType):
+            return value.dtype, None, True, False
+        elif isinstance(value, ValueMaybeNone):
+            return value.dtype, value.value, True, False
+        elif isinstance(value, RequiredValue):
+            if self.fill_required_with_null:
+                return value.dtype, None, True, False
+            else:
+                return value.dtype, None, False, True
+        elif isinstance(value, GlobalConfigValue):
+            return self.get_value_info(self.global_configs[value.global_key])
+        elif isinstance(value, ListValue):
+            return (value.dtype, value.value, False, False)
+        elif isinstance(value, list):
+            if not value:
+                return (str, value, False, False)
+            return (type(value[0]), value, False, False)
+        else:
+            return type(value), value, False, False
+
+    def _get_config_infos(self, config_dict: dict) -> dict:
+        """
+        Recursively extracts configuration information from a given dictionary.
+
+        Args:
+            config_dict (dict): The dictionary containing configuration settings.
+
+        Returns:
+            tuple: A tuple containing two dictionaries:
+                - all_keys: A dictionary mapping keys to their corresponding configuration information.
+                - default_configs: A dictionary mapping keys to their default configuration values.
+
+        Raises:
+            AssertionError: If a key contains a period (.), which is not allowed.
+        """
+        all_keys = {}
+        default_configs = {}
+        for key, value in config_dict.items():
+            assert "." not in key
+            if isinstance(value, (dict)):
+                children_keys, children_configs = self._get_config_infos(value)
+                all_keys.update(
+                    {
+                        f"{key}.{child_key}": child_value_type
+                        for child_key, child_value_type in children_keys.items()
+                    }
+                )
+                default_configs[key] = children_configs
+            else:
+                value_info = self.get_value_info(value)
+                all_keys[key] = value_info
+                default_configs[key] = value_info[1]
+        return all_keys, default_configs
+
+    def get_config_infos(self):
+        return self._get_config_infos(self.global_configs)
+
+    def _merge_configs(
+        self,
+        new_configs: dict,
+        global_configs: dict,
+        local_configs: dict,
+        prefix="",
+    ) -> ConfigDict:
+        """Overwrite default configs with new configs recursively.
+        Args:
+            new_configs: global flattern config dict with all hierarchical config keys joined by '.', i.e.
+                {
+                    'c_z': 32,
+                    'model.evoformer.c_z': 16,
+                    ...
+                }
+            global_configs: global hierarchical merging configs, i.e.
+                {
+                    'c_z' 32,
+                    'c_m': 128,
+                    'model': {
+                        'evoformer': {
+                            ...
+                        }
+                    }
+                }
+            local_configs: hierarchical merging config dict in current level, i.e. for 'model' level, this maybe
+                {
+                    'evoformer': {
+                        'c_z': GlobalConfigValue("c_z"),
+                    },
+                    'embedder': {
+                        ...
+                    }
+                }
+            prefix (str, optional): A prefix string to prepend to keys during recursion. Defaults to an empty string.
+
+        Returns:
+            ConfigDict: The merged configuration dictionary.
+
+        Raises:
+            Exception: If a required config value is not allowed to be None.
+        """
+        # Merge configs in current level first, since these configs maybe referenced by lower level
+        for key, value in local_configs.items():
+            if isinstance(value, dict):
+                continue
+            full_key = f"{prefix}.{key}" if prefix else key
+            dtype, default_value, allow_none, required = self.config_infos[full_key]
+            if full_key in new_configs and not isinstance(
+                new_configs[full_key], ArgumentNotSet
+            ):
+                if allow_none and new_configs[full_key] in [
+                    "None",
+                    "none",
+                    "null",
+                ]:
+                    local_configs[key] = None
+                elif dtype == bool:
+                    local_configs[key] = get_bool_value(new_configs[full_key])
+                elif isinstance(value, (ListValue, list)):
+                    local_configs[key] = (
+                        [dtype(s) for s in new_configs[full_key].strip().split(",")]
+                        if new_configs[full_key].strip()
+                        else []
+                    )
+                else:
+                    local_configs[key] = dtype(new_configs[full_key])
+            elif isinstance(value, GlobalConfigValue):
+                local_configs[key] = global_configs[value.global_key]
+            else:
+                if not allow_none and default_value is None:
+                    raise Exception(f"config {full_key} not allowed to be none")
+                local_configs[key] = default_value
+        for key, value in local_configs.items():
+            if not isinstance(value, dict):
+                continue
+            self._merge_configs(
+                new_configs, global_configs, value, f"{prefix}.{key}" if prefix else key
+            )
+
+    def merge_configs(self, new_configs: dict) -> ConfigDict:
+        configs = copy.deepcopy(self.global_configs)
+        self._merge_configs(new_configs, configs, configs)
+        return ConfigDict(configs)
+
+
+def parse_configs(
+    configs: dict, arg_str: str = None, fill_required_with_null: bool = False
+) -> ConfigDict:
+    """
+    Parses and merges configuration settings from a dictionary and command-line arguments.
+
+    Args:
+        configs (dict): A dictionary containing initial configuration settings.
+        arg_str (str, optional): A string representing command-line arguments. Defaults to None.
+        fill_required_with_null (bool, optional):
+            A boolean flag indicating whether required values should be filled with `None` if not provided. Defaults to False.
+
+    Returns:
+        ConfigDict: The merged configuration dictionary.
+    """
+    manager = ConfigManager(configs, fill_required_with_null=fill_required_with_null)
+    parser = argparse.ArgumentParser()
+    # Register arguments
+    for key, (
+        dtype,
+        default_value,
+        allow_none,
+        required,
+    ) in manager.config_infos.items():
+        # All config use str type, strings will be converted to real dtype later
+        parser.add_argument(
+            "--" + key, type=str, default=ArgumentNotSet(), required=required
+        )
+    # Merge user commandline pargs with default ones
+    merged_configs = manager.merge_configs(
+        vars(parser.parse_args(arg_str.split())) if arg_str else {}
+    )
+    return merged_configs
+
+
+def parse_sys_args() -> str:
+    """
+    Check whether command-line arguments are valid.
+    Each argument is expected to be in the format `--key value`.
+
+    Returns:
+        str: A string formatted as command-line arguments.
+
+    Raises:
+        AssertionError: If any key does not start with `--`.
+    """
+    args = sys.argv[1:]
+    arg_str = ""
+    for k, v in zip(args[::2], args[1::2]):
+        assert k.startswith("--")
+        arg_str += f"{k} {v} "
+    return arg_str
+
+
+def load_config(path: str) -> dict:
+    """
+    Loads a configuration from a YAML file.
+
+    Args:
+        path (str): The path to the YAML file containing the configuration.
+
+    Returns:
+        dict: A dictionary containing the configuration loaded from the YAML file.
+    """
+    with open(path, "r") as f:
+        return yaml.safe_load(f)
+
+
+def save_config(config: Union[ConfigDict, dict], path: str) -> None:
+    """
+    Saves a configuration to a YAML file.
+
+    Args:
+        config (ConfigDict or dict): The configuration to be saved.
+            If it is a ConfigDict, it will be converted to a dictionary.
+        path (str): The path to the YAML file where the configuration will be saved.
+    """
+    with open(path, "w") as f:
+        if isinstance(config, ConfigDict):
+            config = config.to_dict()
+        yaml.safe_dump(config, f)

model/Protenix-pxd/protenix/config/extend_types.py

@@ -0,0 +1,55 @@
+# Copyright 2024 ByteDance and/or its affiliates.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+class DefaultNoneWithType(object):
+    def __init__(self, dtype):
+        self.dtype = dtype
+
+
+class ValueMaybeNone(object):
+    def __init__(self, value):
+        assert value is not None
+        self.dtype = type(value)
+        self.value = value
+
+
+class GlobalConfigValue(object):
+    def __init__(self, global_key):
+        self.global_key = global_key
+
+
+class RequiredValue(object):
+    def __init__(self, dtype):
+        self.dtype = dtype
+
+
+class ListValue(object):
+    def __init__(self, value, dtype=None):
+        if value is not None:
+            self.value = value
+            self.dtype = dtype or type(value[0])
+        else:
+            self.value = None
+            self.dtype = dtype
+
+
+def get_bool_value(bool_str: str):
+    bool_str_lower = bool_str.lower()
+    if bool_str_lower in ("false", "f", "no", "n", "0"):
+        return False
+    elif bool_str_lower in ("true", "t", "yes", "y", "1"):
+        return True
+    else:
+        raise ValueError(f"Cannot interpret {bool_str} as bool")

model/Protenix-pxd/protenix/data/ccd.py

@@ -0,0 +1,450 @@
+# Copyright 2024 ByteDance and/or its affiliates.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import functools
+import logging
+import pickle
+from collections import defaultdict
+from pathlib import Path
+from typing import Any, Optional, Union
+
+import biotite
+import biotite.structure as struc
+import biotite.structure.io.pdbx as pdbx
+import numpy as np
+from biotite.structure import AtomArray
+from rdkit import Chem
+
+from configs.configs_data import data_configs
+from protenix.data.substructure_perms import get_substructure_perms
+
+logger = logging.getLogger(__name__)
+
+COMPONENTS_FILE = data_configs["ccd_components_file"]
+RKDIT_MOL_PKL = Path(data_configs["ccd_components_rdkit_mol_file"])
+
+
+@functools.lru_cache
+def biotite_load_ccd_cif() -> pdbx.CIFFile:
+    """biotite load CCD components file
+
+    Returns:
+        pdbx.CIFFile: ccd components file
+    """
+    return pdbx.CIFFile.read(COMPONENTS_FILE)
+
+
+def _map_central_to_leaving_groups(component) -> Optional[dict[str, list[list[str]]]]:
+    """map each central atom (bonded atom) index to leaving atom groups in component (atom_array).
+
+    Returns:
+        dict[str, list[list[str]]]: central atom name to leaving atom groups (atom names).
+    """
+    comp = component.copy()
+    # Eg: ions
+    if comp.bonds is None:
+        return {}
+    central_to_leaving_groups = defaultdict(list)
+    for c_idx in np.flatnonzero(~comp.leaving_atom_flag):
+        bonds, _ = comp.bonds.get_bonds(c_idx)
+        for l_idx in bonds:
+            if comp.leaving_atom_flag[l_idx]:
+                comp.bonds.remove_bond(c_idx, l_idx)
+                group_idx = struc.find_connected(comp.bonds, l_idx)
+                if not np.all(comp.leaving_atom_flag[group_idx]):
+                    return None
+                central_to_leaving_groups[comp.atom_name[c_idx]].append(
+                    comp.atom_name[group_idx].tolist()
+                )
+    return central_to_leaving_groups
+
+
+@functools.lru_cache
+def get_component_atom_array(
+    ccd_code: str, keep_leaving_atoms: bool = False, keep_hydrogens=False
+) -> AtomArray:
+    """get component atom array
+
+    Args:
+        ccd_code (str): ccd code
+        keep_leaving_atoms (bool, optional): keep leaving atoms. Defaults to False.
+        keep_hydrogens (bool, optional): keep hydrogens. Defaults to False.
+
+    Returns:
+        AtomArray: Biotite AtomArray of CCD component
+            with additional attribute: leaving_atom_flag (bool)
+    """
+    ccd_cif = biotite_load_ccd_cif()
+    if ccd_code not in ccd_cif:
+        logger.warning(f"Warning: get_component_atom_array() can not parse {ccd_code}")
+        return None
+    try:
+        comp = pdbx.get_component(ccd_cif, data_block=ccd_code, use_ideal_coord=True)
+    except biotite.InvalidFileError as e:
+        # Eg: UNL without atom.
+        logger.warning(
+            f"Warning: get_component_atom_array() can not parse {ccd_code} for {e}"
+        )
+        return None
+    atom_category = ccd_cif[ccd_code]["chem_comp_atom"]
+    leaving_atom_flag = atom_category["pdbx_leaving_atom_flag"].as_array()
+    comp.set_annotation("leaving_atom_flag", leaving_atom_flag == "Y")
+
+    for atom_id in ["alt_atom_id", "pdbx_component_atom_id"]:
+        comp.set_annotation(atom_id, atom_category[atom_id].as_array())
+    if not keep_leaving_atoms:
+        comp = comp[~comp.leaving_atom_flag]
+    if not keep_hydrogens:
+        # EG: ND4
+        comp = comp[~np.isin(comp.element, ["H", "D"])]
+
+    # Map central atom index to leaving group (atom_indices) in component (atom_array).
+    comp.central_to_leaving_groups = _map_central_to_leaving_groups(comp)
+    if comp.central_to_leaving_groups is None:
+        logger.warning(
+            f"Warning: ccd {ccd_code} has leaving atom group bond to more than one central atom, central_to_leaving_groups is None."
+        )
+    return comp
+
+
+@functools.lru_cache(maxsize=None)
+def get_one_letter_code(ccd_code: str) -> Union[str, None]:
+    """get one_letter_code from CCD components file.
+
+    normal return is one letter: ALA --> A, DT --> T
+    unknown protein: X
+    unknown DNA or RNA: N
+    other unknown: None
+    some ccd_code will return more than one letter:
+    eg: XXY --> THG
+
+    Args:
+        ccd_code (str): _description_
+
+    Returns:
+        str: one letter code
+    """
+    ccd_cif = biotite_load_ccd_cif()
+    if ccd_code not in ccd_cif:
+        return None
+    one = ccd_cif[ccd_code]["chem_comp"]["one_letter_code"].as_item()
+    if one == "?":
+        return None
+    else:
+        return one
+
+
+@functools.lru_cache(maxsize=None)
+def get_mol_type(ccd_code: str) -> str:
+    """get mol_type from CCD components file.
+
+    based on _chem_comp.type
+    http://mmcif.rcsb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.type.html
+
+    not use _chem_comp.pdbx_type, because it is not consistent with _chem_comp.type
+    e.g. ccd 000 --> _chem_comp.type="NON-POLYMER" _chem_comp.pdbx_type="ATOMP"
+    https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v5_next.dic/Items/_struct_asym.pdbx_type.html
+
+    Args:
+        ccd_code (str): ccd code
+
+    Returns:
+        str: mol_type, one of {"protein", "rna", "dna", "ligand"}
+    """
+    ccd_cif = biotite_load_ccd_cif()
+    if ccd_code not in ccd_cif:
+        return "ligand"
+
+    link_type = ccd_cif[ccd_code]["chem_comp"]["type"].as_item().upper()
+
+    if "PEPTIDE" in link_type and link_type != "PEPTIDE-LIKE":
+        return "protein"
+    if "DNA" in link_type:
+        return "dna"
+    if "RNA" in link_type:
+        return "rna"
+    return "ligand"
+
+
+def get_all_ccd_code() -> list:
+    """get all ccd code from components file"""
+    ccd_cif = biotite_load_ccd_cif()
+    return list(ccd_cif.keys())
+
+
+_ccd_rdkit_mols: dict[str, Chem.Mol] = {}
+
+
+def get_component_rdkit_mol(ccd_code: str) -> Union[Chem.Mol, None]:
+    """get rdkit mol by PDBeCCDUtils
+    https://github.com/PDBeurope/ccdutils
+
+    preprocessing all ccd components in _components_file at first time run.
+
+    Args:
+        ccd_code (str): ccd code
+
+    Returns
+        rdkit.Chem.Mol: rdkit mol with ref coord
+    """
+    global _ccd_rdkit_mols
+    # _ccd_rdkit_mols is not empty
+    if _ccd_rdkit_mols:
+        return _ccd_rdkit_mols.get(ccd_code, None)
+
+    rdkit_mol_pkl = RKDIT_MOL_PKL
+    if rdkit_mol_pkl.exists():
+        with open(rdkit_mol_pkl, "rb") as f:
+            _ccd_rdkit_mols = pickle.load(f)
+        return _ccd_rdkit_mols.get(ccd_code, None)
+    else:
+        raise FileNotFoundError(
+            f"CCD components file {rdkit_mol_pkl} not found, please download it to your DATA_ROOT_DIR before running."
+            "See https://github.com/bytedance/Protenix"
+        )
+
+
+@functools.lru_cache
+def get_ccd_ref_info(ccd_code: str, return_perm: bool = True) -> dict[str, Any]:
+    """
+    Ref: AlphaFold3 SI Chapter 2.8
+    Reference features. Features derived from a residue, nucleotide or ligand’s reference conformer.
+    Given an input CCD code or SMILES string, the conformer is typically generated
+    with RDKit v.2023_03_3 [25] using ETKDGv3 [26]. On error, we fall back to using the CCD ideal coordinates,
+    or finally the representative coordinates
+    if they are from before our training date cut-off (2021-09-30 unless otherwise stated).
+    At the end, any atom coordinates still missing are set to zeros.
+
+    Get reference atom mapping and coordinates.
+
+    Args:
+        name (str): CCD name
+        return_perm (bool): return atom permutations.
+
+    Returns:
+        Dict:
+            ccd: ccd code
+            atom_map: atom name to atom index
+            coord: atom coordinates
+            charge: atom formal charge
+            perm: atom permutation
+    """
+    mol = get_component_rdkit_mol(ccd_code)
+    if mol is None:
+        return {}
+    if mol.GetNumAtoms() == 0:  # eg: "UNL"
+        logger.warning(
+            f"Warning: mol {ccd_code} from get_component_rdkit_mol() has no atoms,"
+            "get_ccd_ref_info() return empty dict"
+        )
+        return {}
+    conf = mol.GetConformer(mol.ref_conf_id)
+    coord = conf.GetPositions()
+    charge = np.array([atom.GetFormalCharge() for atom in mol.GetAtoms()])
+
+    results = {
+        "ccd": ccd_code,  # str
+        "atom_map": mol.atom_map,  # dict[str,int]: atom name to atom index
+        "coord": coord,  # np.ndarray[float]: atom coordinates, shape:(n_atom,3)
+        "mask": mol.ref_mask,  # np.ndarray[bool]: atom mask, shape:(n_atom,)
+        "charge": charge,  # np.ndarray[int]: atom formal charge, shape:(n_atom,)
+    }
+
+    if return_perm:
+        try:
+            Chem.SanitizeMol(mol)
+            perm = get_substructure_perms(mol, MaxMatches=1000)
+
+        except:
+            # Sanitize failed, permutation is unavailable
+            perm = np.array(
+                [
+                    [
+                        i
+                        for i, atom in enumerate(mol.GetAtoms())
+                        if atom.GetAtomicNum() != 1
+                    ]
+                ]
+            )
+        # np.ndarray[int]: atom permutation, shape:(n_atom_wo_h, n_perm)
+        results["perm"] = perm.T
+
+    return results
+
+
+# Modified from biotite to use consistent ccd components file
+def _connect_inter_residue(
+    atoms: AtomArray, residue_starts: np.ndarray
+) -> struc.BondList:
+    """
+    Create a :class:`BondList` containing the bonds between adjacent
+    amino acid or nucleotide residues.
+
+    Parameters
+    ----------
+    atoms : AtomArray or AtomArrayStack
+        The structure to create the :class:`BondList` for.
+    residue_starts : ndarray, dtype=int
+        Return value of
+        ``get_residue_starts(atoms, add_exclusive_stop=True)``.
+
+    Returns
+    -------
+    BondList
+        A bond list containing all inter residue bonds.
+    """
+
+    bonds = []
+
+    atom_names = atoms.atom_name
+    res_names = atoms.res_name
+    res_ids = atoms.res_id
+    chain_ids = atoms.chain_id
+
+    # Iterate over all starts excluding:
+    #   - the last residue and
+    #   - exclusive end index of 'atoms'
+    for i in range(len(residue_starts) - 2):
+        curr_start_i = residue_starts[i]
+        next_start_i = residue_starts[i + 1]
+        after_next_start_i = residue_starts[i + 2]
+
+        # Check if the current and next residue is in the same chain
+        if chain_ids[next_start_i] != chain_ids[curr_start_i]:
+            continue
+        # Check if the current and next residue
+        # have consecutive residue IDs
+        # (Same residue ID is also possible if insertion code is used)
+        if res_ids[next_start_i] - res_ids[curr_start_i] > 1:
+            continue
+
+        # Get link type for this residue from RCSB components.cif
+        curr_link = get_mol_type(res_names[curr_start_i])
+        next_link = get_mol_type(res_names[next_start_i])
+
+        if curr_link == "protein" and next_link in "protein":
+            curr_connect_atom_name = "C"
+            next_connect_atom_name = "N"
+        elif curr_link in ["dna", "rna"] and next_link in ["dna", "rna"]:
+            curr_connect_atom_name = "O3'"
+            next_connect_atom_name = "P"
+        else:
+            # Create no bond if the connection types of consecutive
+            # residues are not compatible
+            continue
+
+        # Index in atom array for atom name in current residue
+        # Addition of 'curr_start_i' is necessary, as only a slice of
+        # 'atom_names' is taken, beginning at 'curr_start_i'
+        curr_connect_indices = np.where(
+            atom_names[curr_start_i:next_start_i] == curr_connect_atom_name
+        )[0]
+        curr_connect_indices += curr_start_i
+
+        # Index in atom array for atom name in next residue
+        next_connect_indices = np.where(
+            atom_names[next_start_i:after_next_start_i] == next_connect_atom_name
+        )[0]
+        next_connect_indices += next_start_i
+
+        if len(curr_connect_indices) == 0 or len(next_connect_indices) == 0:
+            # The connector atoms are not found in the adjacent residues
+            # -> skip this bond
+            continue
+
+        bonds.append(
+            (curr_connect_indices[0], next_connect_indices[0], struc.BondType.SINGLE)
+        )
+
+    return struc.BondList(atoms.array_length(), np.array(bonds, dtype=np.uint32))
+
+
+def add_inter_residue_bonds(
+    atom_array: AtomArray,
+    exclude_struct_conn_pairs: bool = False,
+    remove_far_inter_chain_pairs: bool = False,
+) -> AtomArray:
+    """
+    add polymer bonds (C-N or O3'-P) between adjacent residues based on auth_seq_id.
+
+    exclude_struct_conn_pairs: if True, do not add bond between adjacent residues already has non-standard polymer bonds
+                  on atom C or N or O3' or P.
+
+    remove_far_inter_chain_pairs: if True, remove inter chain (based on label_asym_id) bonds that are far away from each other.
+
+    returns:
+        AtomArray: Biotite AtomArray merged inter residue bonds into atom_array.bonds
+    """
+    res_starts = struc.get_residue_starts(atom_array, add_exclusive_stop=True)
+    inter_bonds = _connect_inter_residue(atom_array, res_starts)
+
+    if atom_array.bonds is None:
+        atom_array.bonds = inter_bonds
+        return atom_array
+
+    select_mask = np.ones(len(inter_bonds._bonds), dtype=bool)
+    if exclude_struct_conn_pairs:
+        for b_idx, (atom_i, atom_j, b_type) in enumerate(inter_bonds._bonds):
+            atom_k = atom_i if atom_array.atom_name[atom_i] in ("N", "O3'") else atom_j
+            bonds, types = atom_array.bonds.get_bonds(atom_k)
+            if len(bonds) == 0:
+                continue
+            for b in bonds:
+                if (
+                    # adjacent residues
+                    abs((res_starts <= b).sum() - (res_starts <= atom_k).sum()) == 1
+                    and atom_array.chain_id[b] == atom_array.chain_id[atom_k]
+                    and atom_array.atom_name[b] not in ("C", "P")
+                ):
+                    select_mask[b_idx] = False
+                    break
+
+    if remove_far_inter_chain_pairs:
+        if not hasattr(atom_array, "label_asym_id"):
+            logging.warning(
+                "label_asym_id not found, far inter chain bonds will not be removed"
+            )
+        for b_idx, (atom_i, atom_j, b_type) in enumerate(inter_bonds._bonds):
+            if atom_array.label_asym_id[atom_i] != atom_array.label_asym_id[atom_j]:
+                coord_i = atom_array.coord[atom_i]
+                coord_j = atom_array.coord[atom_j]
+                if np.linalg.norm(coord_i - coord_j) > 2.5:
+                    select_mask[b_idx] = False
+
+    # filter out removed_inter_bonds from atom_array.bonds
+    remove_bonds = inter_bonds._bonds[~select_mask]
+    remove_mask = np.isin(atom_array.bonds._bonds[:, 0], remove_bonds[:, 0]) & np.isin(
+        atom_array.bonds._bonds[:, 1], remove_bonds[:, 1]
+    )
+    atom_array.bonds._bonds = atom_array.bonds._bonds[~remove_mask]
+
+    # merged normal inter_bonds into atom_array.bonds
+    inter_bonds._bonds = inter_bonds._bonds[select_mask]
+    atom_array.bonds = atom_array.bonds.merge(inter_bonds)
+    return atom_array
+
+
+def res_names_to_sequence(res_names: list[str]) -> str:
+    """convert res_names to sequences {chain_id: canonical_sequence} based on CCD
+
+    Return
+        str: canonical_sequence
+    """
+    seq = ""
+    for res_name in res_names:
+        one = get_one_letter_code(res_name)
+        one = "X" if one is None else one
+        one = "X" if len(one) > 1 else one
+        seq += one
+    return seq

model/Protenix-pxd/protenix/data/compute_esm.py

@@ -0,0 +1,230 @@
+# Copyright 2024 ByteDance and/or its affiliates.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import argparse
+import os
+
+import pandas as pd
+import torch
+from esm import FastaBatchedDataset, pretrained
+from tqdm.auto import tqdm
+
+ESM_CONFIG = {
+    "esm2-3b": {
+        "type": "esm2",
+        "model_path": "esm2_t36_3B_UR50D.pt",
+        "emb_dim": 2560,
+        "n_layers": 36,
+    },
+    "esm2-3b-ism": {
+        "type": "esm2",
+        "model_path": "esm2_t36_3B_UR50D_ism.pt",
+        "emb_dim": 2560,
+        "n_layers": 36,
+    },  # https://www.biorxiv.org/content/10.1101/2024.11.08.622579v2
+}
+
+
+def _load_esm2_model(model_path):
+    if os.path.exists(model_path):
+        model, alphabet = pretrained.load_model_and_alphabet_local(model_path)
+    else:
+        model, alphabet = pretrained.load_model_and_alphabet(
+            os.path.splitext(os.path.basename(model_path))[0]
+        )
+    return model, alphabet
+
+
+def load_esm_model(model_name, local_esm_dir="release_data/checkpoint"):
+    local_model_path = os.path.join(local_esm_dir, ESM_CONFIG[model_name]["model_path"])
+    if os.path.exists(local_model_path):
+        print("Try to load ESM language model from ", local_model_path)
+
+    if "ism" in model_name and not os.path.exists(local_model_path):
+        raise RuntimeError(
+            f"esm2-3b-ism model: {local_model_path} does not exist \n"
+            + "this model can not be download from fair-esm, \n"
+            + "download it from https://af3-dev.tos-cn-beijing.volces.com/release_model/esm2_t36_3B_UR50D_ism.pt"
+        )
+    if model_name.startswith("esm2"):
+        model, alphabet = _load_esm2_model(local_model_path)
+    model.eval()
+    if torch.cuda.is_available():
+        model = model.cuda()
+
+    return model, alphabet
+
+
+def _check_files_exist(save_dir, labels):
+    return all(
+        [os.path.exists(os.path.join(save_dir, label + ".pt")) for label in labels]
+    )
+
+
+def compute_ESM_embeddings(
+    model_name,
+    model,
+    alphabet,
+    labels,
+    sequences,
+    save_dir,
+    toks_per_batch=4096,
+    truncation_seq_length=1022,
+):
+    if model_name.startswith("esm2"):
+        embeddings = compute_esm2_embeddings(
+            model,
+            alphabet,
+            labels,
+            sequences,
+            save_dir,
+            toks_per_batch,
+            truncation_seq_length,
+        )
+    return embeddings
+
+
+# Adapt from Corso, Gabriele, et al. "Diffdock: Diffusion steps, twists, and turns for molecular docking."
+# URL: https://github.com/gcorso/DiffDock/blob/main/utils/inference_utils.py
+def compute_esm2_embeddings(
+    model,
+    alphabet,
+    labels,
+    sequences,
+    save_dir,
+    toks_per_batch=4096,
+    truncation_seq_length=1022,
+):
+    dataset = FastaBatchedDataset(labels, sequences)
+    batches = dataset.get_batch_indices(toks_per_batch, extra_toks_per_seq=1)
+    data_loader = torch.utils.data.DataLoader(
+        dataset,
+        collate_fn=alphabet.get_batch_converter(truncation_seq_length),
+        batch_sampler=batches,
+    )
+    repr_layer = model.num_layers
+    embeddings = {}
+    with torch.no_grad():
+        for batch_idx, (labels, strs, toks) in enumerate(tqdm(data_loader)):
+            print(
+                f"Processing {batch_idx + 1} of {len(batches)} batches ({toks.size(0)} sequences)"
+            )
+            if _check_files_exist(save_dir, labels):
+                continue
+            if torch.cuda.is_available():
+                toks = toks.to(device="cuda", non_blocking=True)
+            out = model(toks, repr_layers=[repr_layer], return_contacts=False)
+            representation = out["representations"][repr_layer].to(device="cpu")
+            for i, label in enumerate(labels):
+                truncate_len = min(truncation_seq_length, len(strs[i]))
+                embeddings[label] = representation[i, 1 : truncate_len + 1].clone()
+                save_path = os.path.join(save_dir, label + ".pt")
+                torch.save(embeddings[label], save_path)
+    return embeddings
+
+
+def pdb_sequences_iterator(
+    input_path="./scripts/msa/data/pdb_seqs/pdb_seq.csv",
+    save_path="./scripts/msa/data/pdb_seqs/pdb_labels_seqs.csv",
+    start_id=0,
+    end_id=-1,
+):
+    if os.path.exists(save_path):
+        df_seq = pd.read_csv(save_path)
+    else:
+        df = pd.read_csv(input_path)
+        # Protein only
+        df = df[df["mol_type"] == "protein"]
+        # Sequence name
+        df["pdb_entity_id"] = df["pdb_id"] + "_" + df["entity_id"].astype(str)
+        # Group by 'seq'
+        df_seq = (
+            df.groupby("seq")["pdb_entity_id"]
+            .apply(lambda x: ",".join(x))
+            .reset_index()
+        )
+        # Use the first pdb_entity_id as the label
+        df_seq["seq_label"] = df_seq["pdb_entity_id"].apply(lambda x: x.split(",")[0])
+        assert df_seq["seq_label"].nunique() == len(df_seq)
+        # Get a part id
+        df_seq["part_id"] = df_seq["pdb_entity_id"].apply(lambda x: x[1:3])
+        df_seq.to_csv(save_path)
+
+    if end_id == -1:
+        end_id = len(df_seq)
+    df_seq = df_seq[start_id:end_id]
+
+    part_counts = dict(df_seq["part_id"].value_counts())
+    for part_id, count in part_counts.items():
+        df_part = df_seq[df_seq["part_id"] == part_id]
+        print(f"Part {part_id}: {len(df_part)} sequences.")
+        yield part_id, df_part["seq_label"].tolist(), df_part["seq"].tolist()
+
+
+def process_pdb_dataset(
+    model_name, root_save_dir, pdb_seq_path, pdb_seq_label_path, start_id=0, end_id=-1
+):
+
+    model, alphabet = load_esm_model(model_name)
+    seq_iterator = pdb_sequences_iterator(
+        pdb_seq_path, pdb_seq_label_path, start_id, end_id
+    )
+    error_parts = []
+    for part_id, labels, sequences in seq_iterator:
+        save_dir = os.path.join(root_save_dir, f"{part_id}")
+
+        if not os.path.exists(save_dir):
+            os.makedirs(save_dir)
+        print(f"[{part_id}] Generating ESM language model embeddings")
+        lm_embeddings = compute_ESM_embeddings(
+            model_name,
+            model,
+            alphabet,
+            labels,
+            sequences,
+            save_dir,
+            truncation_seq_length=4094,
+            toks_per_batch=16384,
+        )
+        print(f"[{part_id}] Processed {len(lm_embeddings)} sequences in total. Done!")
+
+    print("Error parts: ", error_parts)
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--model_name", type=str, choices=list(ESM_CONFIG.keys()))
+    parser.add_argument("--start_id", type=int, default=0)
+    parser.add_argument("--end_id", type=int, default=-1)
+    args = parser.parse_args()
+
+    save_dir = f"./esm_embeddings/{args.model_name}"
+    pdb_seq_path = "./scripts/msa/data/pdb_seqs/pdb_seq.csv"
+    pdb_seq_label_path = "./scripts/msa/data/pdb_seqs/pdb_labels_seqs.csv"
+
+    if not os.path.exists(save_dir):
+        print("Make dir: ", save_dir)
+        os.makedirs(save_dir)
+    process_pdb_dataset(
+        args.model_name,
+        save_dir,
+        pdb_seq_path,
+        pdb_seq_label_path,
+        args.start_id,
+        args.end_id,
+    )
+
+
+if __name__ == "__main__":
+    main()

model/Protenix-pxd/protenix/data/constants.py

@@ -0,0 +1,977 @@
+# Copyright 2024 ByteDance and/or its affiliates.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from rdkit.Chem import GetPeriodicTable
+
+EvaluationChainInterface = [
+    "intra_ligand",
+    "intra_dna",
+    "intra_rna",
+    "intra_prot",
+    "ligand_prot",
+    "rna_prot",
+    "dna_prot",
+    "prot_prot",
+    "antibody_antigen",
+    "antibody",
+]
+
+EntityPolyTypeDict = {
+    "nuc": [
+        "peptide nucleic acid",
+        "polydeoxyribonucleotide",
+        "polydeoxyribonucleotide/polyribonucleotide hybrid",
+        "polyribonucleotide",
+    ],
+    "protein": ["polypeptide(D)", "polypeptide(L)"],
+    "ligand": ["cyclic-pseudo-peptide", "other"],
+}
+
+CRYSTALLIZATION_METHODS = {
+    "X-RAY DIFFRACTION",
+    "NEUTRON DIFFRACTION",
+    "ELECTRON CRYSTALLOGRAPHY",
+    "POWDER CRYSTALLOGRAPHY",
+    "FIBER DIFFRACTION",
+}
+
+### Protein Constants ###
+# https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_entity_poly.pdbx_seq_one_letter_code_can.html
+
+mmcif_restype_1to3 = {
+    "A": "ALA",
+    "R": "ARG",
+    "N": "ASN",
+    "D": "ASP",
+    "C": "CYS",
+    "Q": "GLN",
+    "E": "GLU",
+    "G": "GLY",
+    "H": "HIS",
+    "I": "ILE",
+    "L": "LEU",
+    "K": "LYS",
+    "M": "MET",
+    "F": "PHE",
+    "P": "PRO",
+    "S": "SER",
+    "T": "THR",
+    "W": "TRP",
+    "Y": "TYR",
+    "V": "VAL",
+    "B": "ASX",  # additional
+    "Z": "GLX",  # additional
+    # "X": "UNK",
+}
+
+mmcif_restype_3to1 = {v: k for k, v in mmcif_restype_1to3.items()}
+
+"""
+vdw table from rdkit; indices match those of the ligand atom_types.
+https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/atomic_data.cpp#L46
+"""
+
+rdkit_vdws = [
+    1.2,
+    1.4,
+    2.2,
+    1.9,
+    1.8,
+    1.7,
+    1.6,
+    1.55,
+    1.5,
+    1.54,
+    2.4,
+    2.2,
+    2.1,
+    2.1,
+    1.95,
+    1.8,
+    1.8,
+    1.88,
+    2.8,
+    2.4,
+    2.3,
+    2.15,
+    2.05,
+    2.05,
+    2.05,
+    2.05,
+    2.0,
+    2.0,
+    2.0,
+    2.1,
+    2.1,
+    2.1,
+    2.05,
+    1.9,
+    1.9,
+    2.02,
+    2.9,
+    2.55,
+    2.4,
+    2.3,
+    2.15,
+    2.1,
+    2.05,
+    2.05,
+    2.0,
+    2.05,
+    2.1,
+    2.2,
+    2.2,
+    2.25,
+    2.2,
+    2.1,
+    2.1,
+    2.16,
+    3.0,
+    2.7,
+    2.5,
+    2.48,
+    2.47,
+    2.45,
+    2.43,
+    2.42,
+    2.4,
+    2.38,
+    2.37,
+    2.35,
+    2.33,
+    2.32,
+    2.3,
+    2.28,
+    2.27,
+    2.25,
+    2.2,
+    2.1,
+    2.05,
+    2.0,
+    2.0,
+    2.05,
+    2.1,
+    2.05,
+    2.2,
+    2.3,
+    2.3,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.4,
+    2.0,
+    2.3,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+    2.0,
+]
+
+
+"""
+atom37 vdw table. Orders match atom37 indices. Note: the vdw's for N and O are different from rdkit_van_der_waals in this file. 
+We used the rdkit values for consistency.
+Ref to https://github.com/aqlaboratory/openfold/blob/80c85b54e1a81d9a66df3f1b6c257ff97f10acd3/openfold/utils/loss.py#L1208C5-L1211C6
+rdkit_van_der_waals_radius = {
+    "C": 1.7,
+    "N": 1.6,
+    "O": 1.55,
+    "S": 1.8,
+}
+
+atom37_vdw = [
+        rdkit_van_der_waals_radius[name[0]]
+        for name in residue_constants.atom_types
+    ]
+
+"""
+atom37_vdw = [
+    1.55,
+    1.7,
+    1.7,
+    1.7,
+    1.52,
+    1.7,
+    1.7,
+    1.7,
+    1.52,
+    1.52,
+    1.8,
+    1.7,
+    1.7,
+    1.7,
+    1.55,
+    1.55,
+    1.52,
+    1.52,
+    1.8,
+    1.7,
+    1.7,
+    1.7,
+    1.7,
+    1.55,
+    1.55,
+    1.55,
+    1.52,
+    1.52,
+    1.7,
+    1.55,
+    1.55,
+    1.52,
+    1.7,
+    1.7,
+    1.7,
+    1.55,
+    1.52,
+]
+
+
+# Standard residues (AlphaFold3 SI Talbe 13)
+PRO_STD_RESIDUES = {
+    "ALA": 0,
+    "ARG": 1,
+    "ASN": 2,
+    "ASP": 3,
+    "CYS": 4,
+    "GLN": 5,
+    "GLU": 6,
+    "GLY": 7,
+    "HIS": 8,
+    "ILE": 9,
+    "LEU": 10,
+    "LYS": 11,
+    "MET": 12,
+    "PHE": 13,
+    "PRO": 14,
+    "SER": 15,
+    "THR": 16,
+    "TRP": 17,
+    "TYR": 18,
+    "VAL": 19,
+    "UNK": 20,
+}
+
+RNA_STD_RESIDUES = {
+    "A": 21,
+    "G": 22,
+    "C": 23,
+    "U": 24,
+    "N": 25,
+}
+
+DNA_STD_RESIDUES = {
+    "DA": 26,
+    "DG": 27,
+    "DC": 28,
+    "DT": 29,
+    "DN": 30,
+}
+
+GAP = {"-": 31}
+STD_RESIDUES = PRO_STD_RESIDUES | RNA_STD_RESIDUES | DNA_STD_RESIDUES
+STD_RESIDUES_WITH_GAP = STD_RESIDUES | GAP
+STD_RESIDUES_WITH_GAP_ID_TO_NAME = {
+    idx: res_type for res_type, idx in STD_RESIDUES_WITH_GAP.items()
+}
+
+rna_order_with_x = {
+    "A": 0,
+    "G": 1,
+    "C": 2,
+    "U": 3,
+    "N": 4,
+}
+
+RNA_NT_TO_ID = {
+    "A": 0,
+    "G": 1,
+    "C": 2,
+    "U": 3,
+    "N": 4,
+    "R": 4,  # A or G
+    "Y": 4,  # C or U
+    "S": 4,  # G or C
+    "W": 4,  # A or U
+    "K": 4,  # G or U
+    "M": 4,  # A or C
+    "B": 4,  # C, G, U
+    "D": 4,  # A, G, U
+    "H": 4,  # A, C, U
+    "V": 4,  # A, C, G
+    "X": 4,
+    "I": 4,
+    "T": 4,
+    "-": 5,
+}
+
+# Partial inversion of RNA_NT_TO_ID
+RNA_ID_TO_NT = {
+    0: "A",
+    1: "G",
+    2: "C",
+    3: "U",
+    4: "N",  # Also R, Y, S, W, K, M, B, D, H
+    5: "-",
+}
+
+
+def get_all_elems():
+    """
+    Retrieve a list of all element symbols from the RDKit periodic table up to a specified cutoff.
+
+    Returns:
+        list: A list of element symbols strings.
+    """
+    elem_list = []
+    pt = GetPeriodicTable()
+    for i in range(1, 119):
+        elem_list.append(pt.GetElementSymbol(i).upper())
+
+    # 128 elements in the AlphaFold3 SI Table 5 ref_element
+    elem_list += [f"UNK_ELEM_{i}" for i in range(119, 129)]
+    return elem_list
+
+
+# len(STD_RESIDUES) + Atomic number up to 118 + 10 UNK_ELEM
+ELEMS = dict([(i, len(STD_RESIDUES) + idx) for idx, i in enumerate(get_all_elems())])
+
+RES_ATOMS_DICT = {
+    "ALA": {"N": 0, "CA": 1, "C": 2, "O": 3, "CB": 4, "OXT": 5},
+    "ARG": {
+        "N": 0,
+        "CA": 1,
+        "C": 2,
+        "O": 3,
+        "CB": 4,
+        "CG": 5,
+        "CD": 6,
+        "NE": 7,
+        "CZ": 8,
+        "NH1": 9,
+        "NH2": 10,
+        "OXT": 11,
+    },
+    "ASN": {
+        "N": 0,
+        "CA": 1,
+        "C": 2,
+        "O": 3,
+        "CB": 4,
+        "CG": 5,
+        "OD1": 6,
+        "ND2": 7,
+        "OXT": 8,
+    },
+    "ASP": {
+        "N": 0,
+        "CA": 1,
+        "C": 2,
+        "O": 3,
+        "CB": 4,
+        "CG": 5,
+        "OD1": 6,
+        "OD2": 7,
+        "OXT": 8,
+    },
+    "CYS": {"N": 0, "CA": 1, "C": 2, "O": 3, "CB": 4, "SG": 5, "OXT": 6},
+    "GLN": {
+        "N": 0,
+        "CA": 1,
+        "C": 2,
+        "O": 3,
+        "CB": 4,
+        "CG": 5,
+        "CD": 6,
+        "OE1": 7,
+        "NE2": 8,
+        "OXT": 9,
+    },
+    "GLU": {
+        "N": 0,
+        "CA": 1,
+        "C": 2,
+        "O": 3,
+        "CB": 4,
+        "CG": 5,
+        "CD": 6,
+        "OE1": 7,
+        "OE2": 8,
+        "OXT": 9,
+    },
+    "GLY": {"N": 0, "CA": 1, "C": 2, "O": 3, "OXT": 4},
+    "HIS": {
+        "N": 0,
+        "CA": 1,
+        "C": 2,
+        "O": 3,
+        "CB": 4,
+        "CG": 5,
+        "ND1": 6,
+        "CD2": 7,
+        "CE1": 8,
+        "NE2": 9,
+        "OXT": 10,
+    },
+    "ILE": {
+        "N": 0,
+        "CA": 1,
+        "C": 2,
+        "O": 3,
+        "CB": 4,
+        "CG1": 5,
+        "CG2": 6,
+        "CD1": 7,
+        "OXT": 8,
+    },
+    "LEU": {
+        "N": 0,
+        "CA": 1,
+        "C": 2,
+        "O": 3,
+        "CB": 4,
+        "CG": 5,
+        "CD1": 6,
+        "CD2": 7,
+        "OXT": 8,
+    },
+    "LYS": {
+        "N": 0,
+        "CA": 1,
+        "C": 2,
+        "O": 3,
+        "CB": 4,
+        "CG": 5,
+        "CD": 6,
+        "CE": 7,
+        "NZ": 8,
+        "OXT": 9,
+    },
+    "MET": {
+        "N": 0,
+        "CA": 1,
+        "C": 2,
+        "O": 3,
+        "CB": 4,
+        "CG": 5,
+        "SD": 6,
+        "CE": 7,
+        "OXT": 8,
+    },
+    "PHE": {
+        "N": 0,
+        "CA": 1,
+        "C": 2,
+        "O": 3,
+        "CB": 4,
+        "CG": 5,
+        "CD1": 6,
+        "CD2": 7,
+        "CE1": 8,
+        "CE2": 9,
+        "CZ": 10,
+        "OXT": 11,
+    },
+    "PRO": {"N": 0, "CA": 1, "C": 2, "O": 3, "CB": 4, "CG": 5, "CD": 6, "OXT": 7},
+    "SER": {"N": 0, "CA": 1, "C": 2, "O": 3, "CB": 4, "OG": 5, "OXT": 6},
+    "THR": {"N": 0, "CA": 1, "C": 2, "O": 3, "CB": 4, "OG1": 5, "CG2": 6, "OXT": 7},
+    "TRP": {
+        "N": 0,
+        "CA": 1,
+        "C": 2,
+        "O": 3,
+        "CB": 4,
+        "CG": 5,
+        "CD1": 6,
+        "CD2": 7,
+        "NE1": 8,
+        "CE2": 9,
+        "CE3": 10,
+        "CZ2": 11,
+        "CZ3": 12,
+        "CH2": 13,
+        "OXT": 14,
+    },
+    "TYR": {
+        "N": 0,
+        "CA": 1,
+        "C": 2,
+        "O": 3,
+        "CB": 4,
+        "CG": 5,
+        "CD1": 6,
+        "CD2": 7,
+        "CE1": 8,
+        "CE2": 9,
+        "CZ": 10,
+        "OH": 11,
+        "OXT": 12,
+    },
+    "VAL": {"N": 0, "CA": 1, "C": 2, "O": 3, "CB": 4, "CG1": 5, "CG2": 6, "OXT": 7},
+    "UNK": {"N": 0, "CA": 1, "C": 2, "O": 3, "CB": 4, "CG": 5, "OXT": 6},
+    "DA": {
+        "OP3": 0,
+        "P": 1,
+        "OP1": 2,
+        "OP2": 3,
+        "O5'": 4,
+        "C5'": 5,
+        "C4'": 6,
+        "O4'": 7,
+        "C3'": 8,
+        "O3'": 9,
+        "C2'": 10,
+        "C1'": 11,
+        "N9": 12,
+        "C8": 13,
+        "N7": 14,
+        "C5": 15,
+        "C6": 16,
+        "N6": 17,
+        "N1": 18,
+        "C2": 19,
+        "N3": 20,
+        "C4": 21,
+    },
+    "DC": {
+        "OP3": 0,
+        "P": 1,
+        "OP1": 2,
+        "OP2": 3,
+        "O5'": 4,
+        "C5'": 5,
+        "C4'": 6,
+        "O4'": 7,
+        "C3'": 8,
+        "O3'": 9,
+        "C2'": 10,
+        "C1'": 11,
+        "N1": 12,
+        "C2": 13,
+        "O2": 14,
+        "N3": 15,
+        "C4": 16,
+        "N4": 17,
+        "C5": 18,
+        "C6": 19,
+    },
+    "DG": {
+        "OP3": 0,
+        "P": 1,
+        "OP1": 2,
+        "OP2": 3,
+        "O5'": 4,
+        "C5'": 5,
+        "C4'": 6,
+        "O4'": 7,
+        "C3'": 8,
+        "O3'": 9,
+        "C2'": 10,
+        "C1'": 11,
+        "N9": 12,
+        "C8": 13,
+        "N7": 14,
+        "C5": 15,
+        "C6": 16,
+        "O6": 17,
+        "N1": 18,
+        "C2": 19,
+        "N2": 20,
+        "N3": 21,
+        "C4": 22,
+    },
+    "DT": {
+        "OP3": 0,
+        "P": 1,
+        "OP1": 2,
+        "OP2": 3,
+        "O5'": 4,
+        "C5'": 5,
+        "C4'": 6,
+        "O4'": 7,
+        "C3'": 8,
+        "O3'": 9,
+        "C2'": 10,
+        "C1'": 11,
+        "N1": 12,
+        "C2": 13,
+        "O2": 14,
+        "N3": 15,
+        "C4": 16,
+        "O4": 17,
+        "C5": 18,
+        "C7": 19,
+        "C6": 20,
+    },
+    "DN": {
+        "OP3": 0,
+        "P": 1,
+        "OP1": 2,
+        "OP2": 3,
+        "O5'": 4,
+        "C5'": 5,
+        "C4'": 6,
+        "O4'": 7,
+        "C3'": 8,
+        "O3'": 9,
+        "C2'": 10,
+        "C1'": 11,
+    },
+    "A": {
+        "OP3": 0,
+        "P": 1,
+        "OP1": 2,
+        "OP2": 3,
+        "O5'": 4,
+        "C5'": 5,
+        "C4'": 6,
+        "O4'": 7,
+        "C3'": 8,
+        "O3'": 9,
+        "C2'": 10,
+        "O2'": 11,
+        "C1'": 12,
+        "N9": 13,
+        "C8": 14,
+        "N7": 15,
+        "C5": 16,
+        "C6": 17,
+        "N6": 18,
+        "N1": 19,
+        "C2": 20,
+        "N3": 21,
+        "C4": 22,
+    },
+    "C": {
+        "OP3": 0,
+        "P": 1,
+        "OP1": 2,
+        "OP2": 3,
+        "O5'": 4,
+        "C5'": 5,
+        "C4'": 6,
+        "O4'": 7,
+        "C3'": 8,
+        "O3'": 9,
+        "C2'": 10,
+        "O2'": 11,
+        "C1'": 12,
+        "N1": 13,
+        "C2": 14,
+        "O2": 15,
+        "N3": 16,
+        "C4": 17,
+        "N4": 18,
+        "C5": 19,
+        "C6": 20,
+    },
+    "G": {
+        "OP3": 0,
+        "P": 1,
+        "OP1": 2,
+        "OP2": 3,
+        "O5'": 4,
+        "C5'": 5,
+        "C4'": 6,
+        "O4'": 7,
+        "C3'": 8,
+        "O3'": 9,
+        "C2'": 10,
+        "O2'": 11,
+        "C1'": 12,
+        "N9": 13,
+        "C8": 14,
+        "N7": 15,
+        "C5": 16,
+        "C6": 17,
+        "O6": 18,
+        "N1": 19,
+        "C2": 20,
+        "N2": 21,
+        "N3": 22,
+        "C4": 23,
+    },
+    "U": {
+        "OP3": 0,
+        "P": 1,
+        "OP1": 2,
+        "OP2": 3,
+        "O5'": 4,
+        "C5'": 5,
+        "C4'": 6,
+        "O4'": 7,
+        "C3'": 8,
+        "O3'": 9,
+        "C2'": 10,
+        "O2'": 11,
+        "C1'": 12,
+        "N1": 13,
+        "C2": 14,
+        "O2": 15,
+        "N3": 16,
+        "C4": 17,
+        "O4": 18,
+        "C5": 19,
+        "C6": 20,
+    },
+    "N": {
+        "OP3": 0,
+        "P": 1,
+        "OP1": 2,
+        "OP2": 3,
+        "O5'": 4,
+        "C5'": 5,
+        "C4'": 6,
+        "O4'": 7,
+        "C3'": 8,
+        "O3'": 9,
+        "C2'": 10,
+        "O2'": 11,
+        "C1'": 12,
+    },
+}
+
+CRYSTALLIZATION_AIDS = (
+    "SO4",
+    "GOL",
+    "EDO",
+    "PO4",
+    "ACT",
+    "PEG",
+    "DMS",
+    "TRS",
+    "PGE",
+    "PG4",
+    "FMT",
+    "EPE",
+    "MPD",
+    "MES",
+    "CD",
+    "IOD",
+)
+
+PROT_STD_RESIDUES_ONE_TO_THREE = {
+    "A": "ALA",
+    "R": "ARG",
+    "N": "ASN",
+    "D": "ASP",
+    "C": "CYS",
+    "Q": "GLN",
+    "E": "GLU",
+    "G": "GLY",
+    "H": "HIS",
+    "I": "ILE",
+    "L": "LEU",
+    "K": "LYS",
+    "M": "MET",
+    "F": "PHE",
+    "P": "PRO",
+    "S": "SER",
+    "T": "THR",
+    "W": "TRP",
+    "Y": "TYR",
+    "V": "VAL",
+    "X": "UNK",
+}
+
+CRYSTALLIZATION_AIDS = (
+    "SO4",
+    "GOL",
+    "EDO",
+    "PO4",
+    "ACT",
+    "PEG",
+    "DMS",
+    "TRS",
+    "PGE",
+    "PG4",
+    "FMT",
+    "EPE",
+    "MPD",
+    "MES",
+    "CD",
+    "IOD",
+)
+
+
+### Molecule Constants ###
+# AlphaFold3 SI Tabel 9
+LIGAND_EXCLUSION = {'144', 'SEP', 'PG0', 'BEN', 'NH4', 'PO4', '3SY', 'BO3', 'UNL', 'MES', 'FLC', 'PGR', '15P', 'MYR', 
+                    'POL', 'CIT', 'N', 'SPD', 'CAQ', 'IPA', 'EGL', 'SAR', 'NO3', 'STU', 'NHE', 'BU1', 'OXA', 'TPO', 
+                    'EEE', 'CAD', 'CBM', 'SPM', 'BCN', 'FMT', 'PEP', 'CM', 'BAM', 'ETF', 'IOD', 'MLI', 'MRD', 'SCN', 
+                    'GSH', 'CCN', 'SR', '1PE', 'ACY', 'STE', '9JE', 'SEO', 'IHS', 'MLA', 'TBU', 'DEP', 'STO', 'ACE', 
+                    'NA', 'TRS', 'CPT', 'OHE', 'TME', 'CL', 'BME', 'DN', '3HR', 'LDA', 'SO4', 'MPD', 'OLC', 'DOD', 
+                    'PE4', 'DOX', 'CMO', 'POP', 'PG4', '2F2', 'DMS', 'IMD', 'NH2', 'EOX', 'IPH', 'ACT', '7PE', 'UNX', 
+                    'GTT', '7N5', 'AZI', 'FCY', 'SIN', 'AAE', 'BTB', 'BTC', 'PGE', 'PE3', 'MB3', 'EDO', 'PLM', 'BCT', 
+                    'EOH', 'P6G', 'ACN', 'D10', 'EPE', 'DIO', 'CO3', 'PVO', 'TAR', 'URE', 'BDN', 'GOL', 'MSE', 'HED', 
+                    'CLR', 'MEG', 'IHP', 'PEO', 'CXS', 'MOH', 'GYF', 'PEG', 'FJO', 'FW5', 'OLA', '2JC', 'ABA', 'O4B', 
+                    'UPL', 'OME', 'C8E', 'OMB', 'UNK'}  # fmt: skip
+
+
+# AlphaFold3 SI Tabel 11
+GLYCANS = {'79J', 'LXZ', 'KO1', 'Z57', 'XDX', '8OQ', 'G0S', '14T', 'ZB3', '9PG', 'BGL', 'GYU', 'AHG', 'SUC', 'ADA', 'NGR', 
+           '4R1', 'EBQ', 'GAF', 'NAA', 'GYP', 'NDG', 'U2D', 'ISL', '9GP', 'KDM', 'HSX', 'NYT', 'V3P', '4NN', 'Z3L', 'ZCZ', 
+           'D5E', 'RIP', '3LR', 'GL1', 'K99', 'MQG', 'RAM', 'TUP', 'KDB', 'SIO', 'Z5L', 'GUL', 'GU2', 'EQV', '0V4', 'ABD', 
+           'RY7', '5II', 'GAL', '2GL', 'DR5', '4RS', 'MNA', 'DFX', '0WK', 'HTG', 'RP5', 'A1Q', 'B1N', 'GUF', 'NGA', 'TMR', 
+           'C3X', '9S7', 'XLS', 'MAG', 'RST', 'SDY', 'HSH', 'GN4', 'GTR', 'KBA', '6YR', 'CKB', 'DDA', 'RHC', 'OPM', 'SIZ', 
+           'GE3', 'TS8', 'Z6W', 'BZD', '56N', 'RIB', 'GL6', '8GA', 'GLC', 'TAG', 'QIF', 'TA6', 'UAP', 'TVY', 'GC1', 'ARW', 
+           'GU3', 'LBS', 'KDD', 'NPF', '49V', 'CDR', '12E', '6LA', '2M4', 'SA0', 'HNW', 'AOG', 'G8Z', '8LR', 'GPH', 'XXX', 
+           'GPM', 'MTT', 'JFZ', 'LOG', 'LMO', '5TH', '8I4', 'GUP', '5KQ', 'R2G', 'SSG', 'P8E', 'RF5', 'TOC', 'CT3', '2FL', 
+           '73E', 'VJ4', '0H0', 'ERI', 'AMG', '3GR', 'BO1', 'AFD', 'FYJ', 'IDF', 'NBY', 'DOM', 'MBF', 'QDK', 'TDG', '6GR', 
+           'MAV', '1X4', 'AF1', 'EEN', 'ZB1', 'Z2D', '445', 'KHP', 'LKS', '10M', '491', 'OTU', 'BNG', 'AY9', 'KDR', 'LEC', 
+           'FFX', 'AFO', 'SGA', '16F', 'X34', 'SEJ', 'LAG', 'DNO', '6PZ', 'LBT', 'OSU', '3BU', '6K3', 'SFU', 'YDR', 'SIA', 
+           '2WP', '25E', 'SMD', 'NBG', 'DO8', 'LGU', 'S81', 'Z3Q', 'TWA', 'G6S', '2WS', 'G6D', '18D', 'IN1', '64K', 'QPS', 
+           'PTQ', 'FX1', 'RVM', '8GP', 'NLC', 'FCA', 'JLT', 'AH8', 'MFB', 'RRJ', 'SOL', 'TM5', 'TCB', 'GU5', 'TWY', 'ETT', 
+           '8YV', 'SG6', 'XMM', '17T', 'BGC', 'MLR', 'Z6J', '9SJ', 'R2B', 'BBK', 'BEM', 'LTG', '0NZ', 'DKZ', '3YW', 'ASO', 
+           'FUB', '4GL', 'GLT', 'KTU', 'CBF', 'ARI', 'FIF', 'LCN', 'SG5', 'AC1', 'SUP', 'ZMR', 'GU8', 'YYH', 'XKJ', 'JSV', 
+           'DQR', 'M6D', 'FBP', 'AFP', 'F6P', 'GLG', 'JZR', 'DLG', '9C1', 'AAL', 'RRY', 'ZDC', 'TVS', 'B1H', 'XXM', '8B7', 
+           'RCD', 'UBO', '7D1', 'XYT', 'WZ2', 'X1X', 'LRH', 'GDA', 'GLS', 'G6P', '49A', 'NM9', 'DVC', 'MG5', 'SCR', 'MAF', 
+           '149', 'LFC', 'FMF', 'FRU', 'BG8', 'GP4', 'GU1', 'XXR', '4V5', 'MA2', '293', '6KH', 'GAA', 'MXY', 'QV4', 'MSX', 
+           'GU6', '95Z', 'Z9M', 'ARB', 'FNY', 'H1S', 'VG1', 'VTB', 'Z61', 'H6Z', '7K3', 'XGP', 'SOE', 'Z6H', 'GYV', 'MLB', 
+           'DR3', 'ISD', 'BGN', 'AXR', 'SCG', 'Z8T', '6UD', 'KDF', 'GLA', 'BNX', '3MG', 'BDP', 'KFN', 'Z9N', '2FG', 'PNA', 
+           'MUB', 'ZDO', '9WJ', 'GMB', 'LER', 'TVM', '89Y', 'Z4Y', '9SM', 'NGS', 'LAO', 'KGM', 'FKD', 'M1F', 'BG6', 'LAK', 
+           '8GG', '6LS', 'GBH', 'CEG', 'BDR', 'RR7', 'SOG', 'AZC', 'AMU', 'BS7', '3S6', 'MXZ', 'Z3U', 'MDP', '6MJ', 'M3M', 
+           'DT6', 'PRP', 'TUG', 'Z16', 'IDG', 'TUR', 'Z4S', 'GM0', 'A0K', 'GCN', 'ZEE', 'UEA', 'HVC', 'CE5', 'FUD', 'NAG', 
+           'GPO', '22S', '3J4', 'DKX', 'FMO', 'BXP', 'NSQ', '50A', 'MAT', '5TM', '0MK', '9OK', 'RI2', 'SZZ', 'IDS', 'JRV', 
+           '18O', '1CF', 'RAO', 'P53', '27C', 'Z3K', 'Z4U', 'Z4R', 'B4G', '6KU', 'HBZ', '07E', 'KBG', '98U', 'GFP', 'LFR', 
+           'G2F', '51N', 'FUF', 'LGC', '6S2', 'E3M', 'G7P', 'OTN', 'MVP', 'TVD', 'BBV', 'E5G', 'MJJ', 'IEM', 'FSA', 'CE8', 
+           'U1Y', '1FT', 'HTM', 'DLD', 'YO5', 'W9T', '5N6', 'PNG', 'NGY', 'DSR', 'M3N', 'GP0', '3MK', 'RBL', 'GTM', 'FSW', 
+           '4JA', 'YYM', 'Z4V', '3HD', '2DR', 'AIG', 'GL0', 'BND', 'TM6', 'TUJ', 'DAN', '5GF', '4QY', '3FM', '6KW', 'LNV', 
+           '289', 'BFN', 'PSG', 'U9J', 'YX0', 'EQP', 'YZ0', '0BD', 'GAT', 'LVZ', 'FUL', '22O', 'DLF', 'MA1', 'BXY', 'C3G', 
+           'CR6', 'GNS', 'EEQ', 'IDY', 'FFC', 'NBX', 'SID', '9KJ', '9WZ', 'M2F', 'FK9', 'SSH', 'TWG', 'RVG', 'BXX', '24S', 
+           'FSM', 'GDL', 'F1X', '3R3', 'ALX', '4GC', 'GL2', 'DL6', 'GS1', 'AMV', 'TVV', '2DG', 'RGG', 'TFU', '1GN', 'N3U', 
+           'SOR', 'MA3', 'GCT', 'H1M', '16G', '49T', 'BCD', 'GPW', 'DAG', 'GN1', 'IAB', 'EBG', 'GPU', '38J', '1LL', 'DR2', 
+           'YIO', 'YKR', '15L', 'WZ1', 'BTG', 'GPK', '5MM', '26O', 'AMN', 'DEL', 'CTT', '83Y', 'GMT', 'CTO', 'MBE', '1SD', 
+           '6ZC', 'AXP', 'OX2', '5LT', 'MRH', '6BG', 'MDA', 'SG7', '045', 'GC4', 'LDY', 'YYJ', '07Y', 'KDO', 'GP1', 'BHG', 
+           'DPC', 'BM3', 'GU4', 'ISX', 'P6P', 'GPQ', '1S4', '475', 'GYE', 'CBK', 'CEZ', 'SGD', 'TH1', 'V3M', 'RWI', 'RM4', 
+           'U9M', 'U2A', '7GP', '05L', 'Z0F', 'GLO', 'LXB', 'TGA', '61J', 'GYG', 'GCU', 'GE1', 'F1P', 'GLP', 'CTR', 'AHR', 
+           '3LJ', 'FUY', 'JVA', 'LAT', 'NHF', 'RB5', 'XYS', 'LXC', 'SLT', 'U8V', 'GMH', 'EAG', 'GCV', 'B6D', 'IDU', 'KG1', 
+           'BDF', 'NTP', 'IXD', 'RZM', 'PH5', 'SHB', 'X6Y', 'B16', 'Z9E', '9VP', 'LAH', 'H2P', 'TNX', '5GO', 'TGY', '5SP', 
+           'RHA', '5KV', 'GTK', 'SUS', 'DAF', '6DM', '8S0', '6MN', 'G4D', 'NT1', 'XYF', '5TJ', '46Z', '9AM', '7K2', '6C2', 
+           'WIA', '9YW', 'G4S', '46D', 'Z9W', 'ABL', 'XYZ', 'G3I', 'S7P', 'GC9', 'GQ1', 'GCO', 'M6P', 'WUN', 'U63', 'ZB2', 
+           'GLD', 'T6P', 'ZEL', '145', '2OS', 'BGP', 'C4W', 'IDX', 'MUR', '3SA', 'CR1', '34V', 'DEG', 'F55', 'L0W', 'TYV', 
+           'CJB', 'TW7', 'DDL', '5L3', 'NGC', 'ACX', 'JVS', 'NA1', 'GAD', '7JZ', 'BOG', 'GCW', 'BDG', 'Z15', '0LP', 'ABE', 
+           'RG1', 'DGU', 'N1L', 'NGE', 'PUF', 'B9D', '49S', '5LS', '4N2', '23V', 'RUU', 'B0D', 'RTV', '42D', 'M1P', 'MAB', 
+           '2F8', 'TQY', 'L6S', 'V71', '2H5', 'M8C', 'NTF', 'H3S', 'LM2', 'MN0', 'JV4', '9WN', 'U9G', 'LZ0', 'X0X', 'TXB', 
+           '3DO', 'SG4', 'IDR', '8B9', 'TOA', 'CRA', 'HSJ', '0HX', 'FDQ', 'FUC', 'ABF', 'ALL', 'G20', 'GL9', 'IDC', 'LOX', 
+           'Z2T', 'RP6', '2HA', 'AHM', 'DRI', 'EMZ', 'GMZ', 'HD4', 'GU9', 'L1L', 'PNW', 'PPC', 'MMA', 'CE6', '5KS', 'MGC', 
+           'XLF', 'KO2', 'RUG', 'HSG', 'SF6', 'IPT', 'TF0', 'GCD', 'B8D', '0YT', 'GRX', 'HNV', 'FVQ', 'RV7', 'J5B', 'ERE', 
+           'DFR', 'LVO', '4GP', 'BQY', 'BMA', 'KDA', 'ARA', 'KDN', 'ZCD', 'A5C', 'T68', 'XYL', 'YJM', 'NM6', '9CD', 'CNP', 
+           'U97', '9T1', 'C5X', 'R1X', 'BW3', '09X', 'GNX', 'PDX', 'Z9D', 'DGO', 'SLM', '66O', '4CQ', 'X6X', 'RTG', 'HSY', 
+           '20X', 'GCB', 'EUS', 'FNG', '1S3', 'EGA', 'MQT', 'NXD', '5TK', 'Z9K', 'TGR', '9MR', 'M7P', 'PA1', 'MFU', 'UBH', 
+           'CBI', 'TMX', 'T6D', '32O', 'JHM', 'X2F', '4SG', '3DY', 'SGC', 'PAV', 'A2G', 'LAI', '0UB', 'BXF', '3J3', '9T7', 
+           'T6T', 'OI7', 'ANA', '9QG', 'K5B', 'KOT', 'GIV', 'MGL', 'GL4', '9SP', 'FDP', 'GPV', '6KS', 'GXV', 'NFG', 'M7B', 
+           'DG0', '57S', 'GUZ', '96O', 'GCS', 'MAN', 'YYB', 'TWD', 'MGS', 'TT7', 'PNJ', 'GXL', 'TRE', 'G28', '7NU', '8PK', 
+           'LKA', 'ASG', 'SF9', '2M8', '1GL', '5KT', 'BWG', 'OTG', 'VJ1', 'ZGE', '40J', 'Z4K', 'F58', 'KME', 'SR1', 'ZB0', 
+           'UDC', '6KL', '6LW', '8EX', 'D1M', '62I', 'H6Q', 'RAE', 'SHD', 'AGL', 'DGS', 'VKN', 'TWJ', 'MRP', 'TGK', 'HSQ', 
+           'ASC', 'F8X', '6GB', '0XY', 'BMX', 'SN5', 'Z5J', 'ZD0', 'DJB', 'KDE', 'TEU', 'M55', 'YYQ', 'DK4', 'D6G', 'KD5', 
+           'AH2', '4AM', 'RER', '16O', 'C3B', 'G1P', 'NG6', 'MBG', 'Z4W', 'MAW', '147', 'NGK', 'CKP', 'DJE', 'GL5', 'TVG', 
+           'PKM', 'L6T', 'XS2', '2GS', 'BTU', 'G16', 'PSV', 'AQA', 'MCU', 'SNG', '2M5', 'SLB', 'BM7', 'H53', 'MA8', 'OAK', 
+           'GRF', 'BGS', 'NTO', 'YYK', 'EPG', '6GP', 'MYG', 'FCT', 'Z9H', 'GL7', '48Z', '4UZ', '7CV', 'DYM', 'GLF', 'GU0', 
+           'CGF', 'STZ', '44S', 'LB2', 'TU4', 'Z8H', '5QP', 'A6P', 'XYP', 'B2G', 'U9A', 'SWE', 'NGZ', 'SGN', 'B7G', 'MAL', 
+           '291', 'FSI', 'R1P', 'ACR', 'PZU', 'X2Y', 'Z9L', 'STW', 'U9D', 'X1P', 'TTV', 'GS9', 'QKH', 'SHG', 'N9S', 'NNG', 
+           'RP3', 'G3F', 'YX1', 'EMP', 'XIL', '08U', 'WOO', 'FCB', 'NG1', 'TRV', '20S', 'RAF', 'GZL', 'C4B', '9SG', 'GAC'}  # fmt: skip
+
+
+# AlphaFold3 SI Tabel 12
+IONS = {'XGP', 'Z4K', '147', 'B0D', 'G6D', 'RIB', 'AXR', 'SOG', 'NTF', 'SHB', 'RG1', 'G6S', 'GPO', 'BTG', '5LT', 'CEG', 'KG1', 
+        'TDG', 'TRV', 'WZ1', 'ARI', 'HVC', 'TM6', '2DG', '6K3', 'ARA', 'ASO', '6GB', 'NBX', 'OTG', 'ASG', 'YO5', 'MRH', 'GYP', 
+        'C4B', 'GDA', 'MUB', 'XXM', 'M6D', 'OPM', 'GYV', 'DKX', '9SG', 'LOG', 'TRE', 'DLG', 'FNG', 'BBK', 'ABF', 'AQA', '3BU', 
+        'SIA', 'CGF', 'LBS', 'QV4', 'NAA', 'GLC', 'BHG', 'MSX', 'ZB1', 'YYJ', 'TUP', '6ZC', '0WK', 'RY7', 'L1L', 'RRY', 'M55', 
+        '9PG', '5GF', '4V5', 'FMO', 'SWE', 'KDA', 'P8E', '14T', 'DL6', 'CKB', '2M8', 'AHR', 'NGY', '8GP', 'YYQ', 'LVO', 'CRA', 
+        'GU9', 'PPC', '6GP', 'CR1', 'G20', 'T6P', 'EMZ', 'RHA', 'GC4', 'AH2', 'FCT', 'QDK', 'DDA', 'RTV', '8S0', 'TVG', 'HNV', 
+        'FYJ', 'BDP', 'GYE', 'TS8', 'CEZ', '42D', 'NHF', 'NT1', 'WOO', '0LP', 'HBZ', 'SG5', 'NM9', 'CJB', 'DLF', 'EUS', 'IDY', 
+        '2GL', 'NTO', 'PNG', 'B2G', '7NU', '4UZ', '5LS', '475', 'DJE', 'Z9E', 'GC9', 'QPS', '0NZ', 'F1X', 'G8Z', '2F8', '3SA', 
+        '46D', '3DO', '6PZ', 'OI7', 'SLM', 'A0K', '9SJ', 'TWD', 'AOG', 'TW7', '2WS', 'GU5', 'NSQ', 'FUD', 'GLO', 'TNX', 'XYP', 
+        'JFZ', '2HA', 'G16', 'V3M', 'RTG', 'C4W', 'R2G', 'HD4', '66O', 'MFB', 'GXL', '8YV', 'NFG', 'FFC', '3YW', 'XYZ', '445', 
+        'IXD', 'GUL', 'CTO', '05L', 'Z3L', 'RBL', 'DR5', 'S81', 'CTR', '15L', 'GLP', '7K3', 'LDY', 'Z4S', 'H2P', '4GP', '5SP', 
+        '18O', 'DGS', 'OX2', 'DFR', 'GN1', 'BGL', 'Z9K', 'GU4', '0V4', 'MA2', 'U2A', 'MXZ', 'PA1', '9YW', 'GS9', '3MK', 'AAL', 
+        'NBY', 'XXX', 'ISD', 'SEJ', 'DKZ', 'GL9', '23V', 'AMN', 'AHG', '25E', 'DJB', '7K2', 'GDL', '08U', 'TT7', 'DRI', 'HSY', 
+        'LB2', 'GCV', 'X1P', 'MN0', 'BW3', 'U9J', 'FFX', 'Z3U', 'LOX', 'MQG', 'HSG', 'GCO', 'GPQ', 'IDR', '2GS', 'AGL', 'RUU', 
+        '5KV', 'R1X', 'LZ0', 'P6P', '0H0', '32O', 'LAG', 'YYK', '07E', '6KS', 'KOT', '17T', 'TQY', 'RM4', 'LNV', 'BGN', 'STW', 
+        'NGC', 'GLF', '2WP', 'GL5', 'KHP', '9SP', 'LAI', 'KDB', 'JVA', 'OTN', 'NA1', 'RR7', 'B16', 'PSV', 'NXD', 'C5X', 'G1P', 
+        'RRJ', 'DAF', '5N6', 'SG4', 'KDN', '95Z', 'FDQ', 'K5B', 'MDP', 'GTK', '4SG', 'ALL', 'LXC', 'TM5', 'NGA', '98U', '7JZ', 
+        'A6P', 'UBH', '293', '9T7', 'PUF', '5TM', 'VTB', 'BGP', 'JV4', 'SN5', 'FSA', 'LAK', 'G7P', 'BGC', 'ZCD', '7GP', '79J', 
+        'FKD', 'TWY', 'ZGE', 'OAK', 'FMF', 'ZCZ', 'GL2', 'MAV', 'ZB3', 'SA0', '3LR', 'SHD', 'XLS', 'DOM', 'Z4R', 'GP0', '5KS', 
+        'KO1', 'FCB', 'LFC', 'AC1', 'NPF', 'X6Y', 'IDF', '20X', '6KL', '6LW', '49S', '0YT', 'BDR', 'GBH', 'LAH', 'KO2', '40J', 
+        '4CQ', 'D5E', 'T6D', 'SUP', 'TGR', 'Z57', 'SDY', '4NN', 'MNA', 'Z5J', '20S', 'CT3', 'DQR', '5MM', '83Y', '49T', 'BDG', 
+        'GL1', 'TOC', '6UD', 'GM0', 'GU3', '18D', 'ADA', '4AM', '9WZ', 'HSX', 'QIF', '6DM', '4RS', 'KDF', 'GAL', 'ISL', 'Z9H', 
+        'GC1', 'Z9W', 'NBG', 'MAL', 'BGS', 'W9T', 'U9A', '62I', 'M6P', 'AFO', 'C3G', 'M2F', 'RUG', 'ARW', 'LEC', 'B8D', '61J', 
+        'GL7', 'F58', 'GP4', 'GFP', 'TVY', 'ZB0', 'FSM', 'BDF', 'TCB', 'ZEL', 'IDG', '9CD', 'PNA', 'SF9', 'DSR', 'MG5', 'E5G', 
+        'PNW', 'TH1', '1S4', 'PTQ', 'KDD', 'SSH', 'F55', 'V71', 'VG1', '9T1', '145', 'GU2', '2M5', '8I4', 'H1S', 'YYB', '1LL', 
+        '4N2', 'BG6', 'R2B', 'MAT', 'LMO', 'OSU', 'PSG', 'RCD', '26O', 'DGO', 'SID', 'FUB', '2FL', '3HD', '34V', 'FK9', 'AMG', 
+        'G4D', 'EPG', 'BWG', 'KTU', '491', 'JHM', 'NG1', 'DLD', 'MCU', 'MQT', 'EQV', 'CBF', '4GL', 'GS1', 'DEG', 'DDL', 'SGA', 
+        '16O', 'X6X', 'H53', 'FUC', 'IDS', 'LTG', 'TMX', '9SM', '045', 'DAN', 'FRU', 'Z5L', 'AHM', 'BNG', 'AFP', 'MAF', 'UBO', 
+        'BOG', '2H5', 'NG6', '10M', 'NM6', 'RST', 'C3X', '9S7', '49A', 'AXP', 'PH5', 'ISX', 'B6D', 'GU6', 'TWG', '6GR', 'H3S', 
+        'Z61', '9WJ', 'BMA', 'U63', 'LKA', 'GRF', 'VJ1', 'RZM', 'MA3', '0XY', 'GAF', 'GAD', '1FT', '149', 'DPC', 'LFR', 'B9D', 
+        'CE5', 'SOR', '6KU', 'SFU', 'BEM', 'YKR', '38J', 'N3U', 'ARB', 'CBK', 'SGD', '8EX', 'WZ2', '8B9', 'TF0', 'X2Y', 'PKM', 
+        'RF5', 'D1M', 'AF1', 'DR2', 'EQP', 'AMV', 'PRP', 'VJ4', 'BCD', '1GN', 'SMD', '9QG', 'GCW', 'A5C', 'M3N', 'SZZ', 'B1H', 
+        'GPH', 'NDG', '5KT', 'TYV', 'KDM', 'A2G', 'CE6', 'H1M', 'JVS', 'ABL', 'LAO', 'P53', 'GCN', 'QKH', 'U2D', 'YYH', '6S2', 
+        'L0W', 'DEL', 'G2F', 'LER', 'MGC', 'RI2', '5KQ', 'DT6', 'U97', 'BG8', '1X4', 'GYG', 'U9D', 'SG7', '8B7', 'FCA', 'RWI', 
+        '8GG', 'TAG', 'ERE', '46Z', '5QP', 'UDC', '51N', 'SGN', 'NLC', '8LR', 'L6T', 'WIA', 'TMR', 'IDC', 'GLT', 'FDP', 'GCT', 
+        'FSW', 'XYS', 'GAA', 'N9S', 'DO8', 'UAP', 'TUG', 'F1P', '2FG', '12E', '56N', 'IAB', 'LAT', 'X1X', 'MBE', 'GP1', 'X34', 
+        '6MJ', '6KH', 'G3F', '3DY', 'XYF', 'GE1', 'MAB', 'Z9L', '289', 'GIV', 'F8X', '9WN', 'KDO', 'GLA', 'SIZ', 'G0S', 'EGA', 
+        'MJJ', 'B7G', 'BND', 'JRV', '1S3', 'DAG', 'GL0', 'GPV', 'HTM', '3R3', 'SHG', 'DR3', 'TTV', 'DK4', '22S', 'IDU', 'XIL', 
+        'RER', '6BG', 'GXV', 'BTU', 'GE3', 'H6Z', 'ZD0', 'SF6', 'VKN', 'GYU', '16F', 'K99', 'KGM', 'FX1', 'NGS', 'RVG', 'YX1', 
+        '4GC', 'EEQ', 'XDX', 'MVP', 'PNJ', 'BS7', 'M7B', '0BD', 'AIG', 'TVV', 'BXY', 'T68', 'SIO', '8OQ', '2OS', 'S7P', 'GNX', 
+        'TUR', 'YX0', 'DVC', 'NGK', 'M8C', 'RHC', 'GPM', 'LKS', '64K', 'GMT', 'JLT', 'XS2', 'LBT', 'TVM', '6MN', 'DYM', 'E3M', 
+        'NGR', 'G6P', 'RAO', 'SCR', 'YJM', 'MRP', 'YIO', 'ACR', '291', '3GR', 'M1F', 'L6S', 'XLF', 'GU1', 'LVZ', 'DNO', '22O', 
+        'SOL', 'GPW', 'KD5', 'GCU', 'ERI', 'YZ0', 'TXB', 'ABD', 'YYM', 'BFN', 'G4S', 'GAC', 'PAV', 'MMA', 'RV7', 'MBG', '16G', 
+        'MA8', 'GU8', '4JA', 'NTP', 'FNY', '07Y', '1CF', 'KDE', 'Z16', 'CBI', '50A', 'Z4W', 'U9G', 'D6G', 'JSV', 'YDR', 'DGU', 
+        'Z15', 'G3I', 'XKJ', 'IEM', 'CDR', 'GLG', '0HX', 'TA6', '57S', 'LGU', '27C', 'BO1', 'EEN', 'HSJ', 'GLD', 'RP3', 'FSI', 
+        'LRH', '8PK', 'GTR', 'B1N', 'XXR', 'TFU', 'RAF', 'ETT', 'AY9', '3FM', 'G28', '2DR', 'FUL', 'CE8', 'GQ1', 'TGA', '6C2', 
+        'NGZ', '6LS', 'SOE', 'BQY', 'HSH', 'XYL', '5TH', 'A1Q', 'HTG', 'Z3K', '3MG', 'GMH', 'M1P', 'ASC', '73E', 'Z8T', 'STZ', 
+        'RAE', 'GL6', '7CV', 'GPU', '5L3', '7D1', 'CKP', 'BXP', 'M7P', 'RVM', 'TWA', '4R1', 'N1L', 'X2F', 'TVD', '3J3', 'TOA', 
+        'B4G', 'WUN', '0MK', '6YR', 'H6Q', 'CNP', 'TEU', 'MBF', '44S', 'Z9N', 'BM7', 'NGE', 'U9M', 'GMB', 'MTT', '9GP', 'DG0', 
+        'RP5', 'KBA', 'ALX', 'FVQ', 'TGY', 'EBG', 'BXF', '9C1', 'BBV', 'AFD', '4QY', 'GCD', 'FBP', '96O', 'GNS', 'OTU', 'ACX', 
+        'RP6', 'UEA', 'SGC', 'Z4V', 'RAM', 'AZC', 'J5B', '1GL', 'TGK', 'HSQ', 'LM2', 'MYG', 'PDX', 'Z6W', 'ZDC', '09X', 'IDX', 
+        '9MR', 'MFU', 'CR6', 'Z8H', 'SUS', 'PZU', '89Y', '5TK', 'KME', 'U1Y', 'Z4U', 'LCN', 'GPK', 'MUR', '5TJ', 'NYT', '24S', 
+        'SR1', '0UB', '48Z', 'MGL', 'Z6J', 'BMX', 'C3B', 'TVS', 'SLB', 'IPT', 'MLB', 'SLT', 'Z9D', 'GRX', 'AH8', 'F6P', 'BNX', 
+        'JZR', 'LXB', 'M3M', 'XYT', 'MA1', 'GTM', 'SCG', 'Z3Q', 'KFN', 'LGC', 'ZB2', 'FIF', 'GLS', 'SSG', 'Z4Y', 'T6T', 'GCS', 
+        'GZL', 'U8V', 'V3P', 'ABE', 'MGS', '6KW', '8GA', 'BZD', 'FUF', 'GMZ', 'FUY', 'HNW', 'LXZ', 'IN1', 'SNG', 'GAT', 'Z9M', 
+        'BM3', 'ZDO', '9AM', '3LJ', 'X0X', 'MAN', '5GO', 'AMU', 'GUF', 'XMM', 'EAG', 'SUC', 'BXX', 'Z0F', '9OK', 'CTT', 'MLR', 
+        '49V', 'ZMR', 'TWJ', 'MAW', '5II', 'ZEE', 'KBG', 'EMP', 'GUZ', 'TUJ', 'RB5', 'GCB', '9KJ', 'MAG', 'Z2D', '6LA', '2M4', 
+        'GN4', 'MDA', 'TU4', 'Z2T', 'GL4', 'EBQ', 'NNG', '1SD', 'ANA', 'MXY', 'Z6H', 'GU0', 'GUP', 'SG6', 'NAG', '9VP', 'RIP', 
+        '3S6', 'KDR', 'R1P', '3J4', 'DFX', 'RGG'}  # fmt: skip
+
+
+# AlphaFold3 SI Tabel 15
+PBV2_COMMON_NATURAL_LIGANDS = {'UPG', 'CDP', 'DSG', 'APC', 'GSP', 'FAD', 'IPE', 'NAI', '2BA', 'PGA', 'A3P', 'PRP', 'NAD', 'PLG', 
+                               'SFG', 'MFU', 'APR', 'GTP', 'PLP', 'UDP', 'SAH', 'ACP', 'GSH', 'CTP', 'AKG', 'F15', '5AD', 'BCN', 
+                               'BDP', 'H4B', 'PHO', 'FMN', 'MTA', 'NGA', 'OGA', 'SLB', 'SIN', 'C5P', 'TPP', 'BGC', 'NCA', 'UD1', 
+                               'ANP', 'DGL', 'FDA', 'URI', 'ADP', 'MTE', 'PJ8', 'ATP'}  # fmt: skip

model/Protenix-pxd/protenix/data/data_pipeline.py

@@ -0,0 +1,373 @@
+# Copyright 2024 ByteDance and/or its affiliates.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import logging
+import os
+from collections import defaultdict
+from pathlib import Path
+from typing import Any, Optional, Union
+
+import biotite.structure.io as strucio
+import numpy as np
+import pandas as pd
+import torch
+from biotite.structure import AtomArray
+
+from protenix.data.msa_featurizer import MSAFeaturizer
+from protenix.data.parser import DistillationMMCIFParser, MMCIFParser
+from protenix.data.tokenizer import AtomArrayTokenizer, TokenArray
+from protenix.utils.cropping import CropData
+from protenix.utils.file_io import load_gzip_pickle
+
+torch.multiprocessing.set_sharing_strategy("file_system")
+
+
+class DataPipeline(object):
+    """
+    DataPipeline class provides static methods to handle various data processing tasks related to bioassembly structures.
+    """
+
+    @staticmethod
+    def get_data_from_mmcif(
+        mmcif: Union[str, Path],
+        pdb_cluster_file: Union[str, Path, None] = None,
+        dataset: str = "WeightedPDB",
+        interface_radius: float = 5,
+    ) -> tuple[list[dict[str, Any]], dict[str, Any]]:
+        """
+        Get raw data from mmcif with tokenizer and a list of chains and interfaces for sampling.
+
+        Args:
+            mmcif (Union[str, Path]): The raw mmcif file.
+            pdb_cluster_file (Union[str, Path, None], optional): Cluster info txt file. Defaults to None.
+            dataset (str, optional): The dataset type, either "WeightedPDB" or "Distillation". Defaults to "WeightedPDB".
+            interface_radius (float, optional): The radius of the interface. Defaults to 5.
+        Returns:
+            tuple[list[dict[str, Any]], dict[str, Any]]:
+                sample_indices_list (list[dict[str, Any]]): The sample indices list (each one is a chain or an interface).
+                bioassembly_dict (dict[str, Any]): The bioassembly dict with sequence, atom_array, and token_array.
+        """
+        try:
+            if dataset == "WeightedPDB":
+                parser = MMCIFParser(mmcif_file=mmcif)
+                bioassembly_dict = parser.get_bioassembly()
+            elif dataset == "Distillation":
+                parser = DistillationMMCIFParser(mmcif_file=mmcif)
+                bioassembly_dict = parser.get_structure_dict()
+            else:
+                raise NotImplementedError(
+                    'Unsupported "dataset", please input either "WeightedPDB" or "Distillation".'
+                )
+
+            sample_indices_list = parser.make_indices(
+                bioassembly_dict=bioassembly_dict,
+                pdb_cluster_file=pdb_cluster_file,
+                interface_radius=interface_radius,
+            )
+            if len(sample_indices_list) == 0:
+                # empty indices and AtomArray
+                return [], bioassembly_dict
+
+            atom_array = bioassembly_dict["atom_array"]
+            atom_array.set_annotation(
+                "resolution", [parser.resolution] * len(atom_array)
+            )
+
+            tokenizer = AtomArrayTokenizer(atom_array)
+            token_array = tokenizer.get_token_array()
+            bioassembly_dict["msa_features"] = None
+            bioassembly_dict["template_features"] = None
+
+            bioassembly_dict["token_array"] = token_array
+            return sample_indices_list, bioassembly_dict
+
+        except Exception as e:
+            logging.warning("Gen data failed for %s due to %s", mmcif, e)
+            return [], {}
+
+    @staticmethod
+    def get_label_entity_id_to_asym_id_int(atom_array: AtomArray) -> dict[str, int]:
+        """
+        Get a dictionary that associates each label_entity_id with its corresponding asym_id_int.
+
+        Args:
+            atom_array (AtomArray): AtomArray object
+
+        Returns:
+            dict[str, int]: label_entity_id to its asym_id_int
+        """
+        entity_to_asym_id = defaultdict(set)
+        for atom in atom_array:
+            entity_id = atom.label_entity_id
+            entity_to_asym_id[entity_id].add(atom.asym_id_int)
+        return entity_to_asym_id
+
+    @staticmethod
+    def get_data_bioassembly(
+        bioassembly_dict_fpath: Union[str, Path],
+    ) -> dict[str, Any]:
+        """
+        Get the bioassembly dict.
+
+        Args:
+            bioassembly_dict_fpath (Union[str, Path]): The path to the bioassembly dictionary file.
+
+        Returns:
+            dict[str, Any]: The bioassembly dict with sequence, atom_array and token_array.
+
+        Raises:
+            AssertionError: If the bioassembly dictionary file does not exist.
+        """
+        assert os.path.exists(
+            bioassembly_dict_fpath
+        ), f"File not exists {bioassembly_dict_fpath}"
+        bioassembly_dict = load_gzip_pickle(bioassembly_dict_fpath)
+
+        return bioassembly_dict
+
+    @staticmethod
+    def _map_ref_chain(
+        one_sample: pd.Series, bioassembly_dict: dict[str, Any]
+    ) -> list[int]:
+        """
+        Map the chain or interface chain_x_id to the reference chain asym_id.
+
+        Args:
+            one_sample (pd.Series): A dict of one chain or interface from indices list.
+            bioassembly_dict (dict[str, Any]): The bioassembly dict with sequence, atom_array and token_array.
+
+        Returns:
+            list[int]: A list of asym_id_lnt of the chosen chain or interface, length 1 or 2.
+        """
+        atom_array = bioassembly_dict["atom_array"]
+        ref_chain_indices = []
+        for chain_id_field in ["chain_1_id", "chain_2_id"]:
+            chain_id = one_sample[chain_id_field]
+            assert np.isin(
+                chain_id, np.unique(atom_array.chain_id)
+            ), f"PDB {bioassembly_dict['pdb_id']} {chain_id_field}:{chain_id} not in atom_array"
+            chain_asym_id = atom_array[atom_array.chain_id == chain_id].asym_id_int[0]
+            ref_chain_indices.append(chain_asym_id)
+            if one_sample["type"] == "chain":
+                break
+        return ref_chain_indices
+
+    @staticmethod
+    def get_msa_raw_features(
+        bioassembly_dict: dict[str, Any],
+        selected_indices: np.ndarray,
+        msa_featurizer: Optional[MSAFeaturizer],
+    ) -> Optional[dict[str, np.ndarray]]:
+        """
+        Get tokenized MSA features of the bioassembly
+
+        Args:
+            bioassembly_dict (Mapping[str, Any]): The bioassembly dict with sequence, atom_array and token_array.
+            selected_indices (torch.Tensor): Cropped token indices.
+            msa_featurizer (MSAFeaturizer): MSAFeaturizer instance.
+
+        Returns:
+            Optional[dict[str, np.ndarray]]: The tokenized MSA features of the bioassembly.
+        """
+        if msa_featurizer is None:
+            return None
+
+        entity_to_asym_id_int = dict(
+            DataPipeline.get_label_entity_id_to_asym_id_int(
+                bioassembly_dict["atom_array"]
+            )
+        )
+
+        msa_feats = msa_featurizer(
+            bioassembly_dict=bioassembly_dict,
+            selected_indices=selected_indices,
+            entity_to_asym_id_int=entity_to_asym_id_int,
+        )
+
+        return msa_feats
+
+    @staticmethod
+    def get_template_raw_features(
+        bioassembly_dict: dict[str, Any],
+        selected_indices: np.ndarray,
+        template_featurizer: None,
+    ) -> Optional[dict[str, np.ndarray]]:
+        """
+        Get tokenized template features of the bioassembly.
+
+        Args:
+            bioassembly_dict (dict[str, Any]): The bioassembly dict with sequence, atom_array and token_array.
+            selected_indices (np.ndarray): Cropped token indices.
+            template_featurizer (None): Placeholder for the template featurizer.
+
+        Returns:
+            Optional[dict[str, np.ndarray]]: The tokenized template features of the bioassembly,
+                or None if the template featurizer is not provided.
+        """
+        if template_featurizer is None:
+            return None
+
+        entity_to_asym_id_int = dict(
+            DataPipeline.get_label_entity_id_to_asym_id_int(
+                bioassembly_dict["atom_array"]
+            )
+        )
+
+        template_feats = template_featurizer(
+            bioassembly_dict=bioassembly_dict,
+            selected_indices=selected_indices,
+            entity_to_asym_id_int=entity_to_asym_id_int,
+        )
+        return template_feats
+
+    @staticmethod
+    def crop(
+        one_sample: pd.Series,
+        bioassembly_dict: dict[str, Any],
+        crop_size: int,
+        msa_featurizer: Optional[MSAFeaturizer],
+        template_featurizer: None,
+        method_weights: list[float] = [0.2, 0.4, 0.4],
+        contiguous_crop_complete_lig: bool = False,
+        spatial_crop_complete_lig: bool = False,
+        drop_last: bool = False,
+        remove_metal: bool = False,
+    ) -> tuple[str, TokenArray, AtomArray, dict[str, Any], dict[str, Any]]:
+        """
+        Crop data based on the crop size and reference chain indices.
+
+        Args:
+            one_sample (pd.Series): A dict of one chain or interface from indices list.
+            bioassembly_dict (dict[str, Any]): A dict of bioassembly dict with sequence, atom_array and token_array.
+            crop_size (int): the crop size.
+            msa_featurizer (MSAFeaturizer): Default to an empty replacement for msa featurizer.
+            template_featurizer (None): Placeholder for the template featurizer.
+            method_weights (list[float]): The weights corresponding to these three cropping methods:
+                                          ["ContiguousCropping", "SpatialCropping", "SpatialInterfaceCropping"].
+            contiguous_crop_complete_lig (bool): Whether to crop the complete ligand in ContiguousCropping method.
+            spatial_crop_complete_lig (bool): Whether to crop the complete ligand in SpatialCropping method.
+            drop_last (bool): Whether to drop the last fragment in ContiguousCropping.
+            remove_metal (bool): Whether to remove metal atoms from the crop.
+
+        Returns:
+            tuple[str, TokenArray, AtomArray, dict[str, Any], dict[str, Any]]:
+                crop_method (str): The crop method.
+                cropped_token_array (TokenArray): TokenArray after cropping.
+                cropped_atom_array (AtomArray): AtomArray after cropping.
+                cropped_msa_features (dict[str, Any]): The cropped msa features.
+                cropped_template_features (dict[str, Any]): The cropped template features.
+        """
+        if crop_size <= 0:
+            selected_indices = None
+            # Prepare msa
+            msa_features = DataPipeline.get_msa_raw_features(
+                bioassembly_dict=bioassembly_dict,
+                selected_indices=selected_indices,
+                msa_featurizer=msa_featurizer,
+            )
+            # Prepare template
+            template_features = DataPipeline.get_template_raw_features(
+                bioassembly_dict=bioassembly_dict,
+                selected_indices=selected_indices,
+                template_featurizer=template_featurizer,
+            )
+            return (
+                "no_crop",
+                bioassembly_dict["token_array"],
+                bioassembly_dict["atom_array"],
+                msa_features or {},
+                template_features or {},
+                -1,
+            )
+
+        ref_chain_indices = DataPipeline._map_ref_chain(
+            one_sample=one_sample, bioassembly_dict=bioassembly_dict
+        )
+
+        crop = CropData(
+            crop_size=crop_size,
+            ref_chain_indices=ref_chain_indices,
+            token_array=bioassembly_dict["token_array"],
+            atom_array=bioassembly_dict["atom_array"],
+            method_weights=method_weights,
+            contiguous_crop_complete_lig=contiguous_crop_complete_lig,
+            spatial_crop_complete_lig=spatial_crop_complete_lig,
+            drop_last=drop_last,
+            remove_metal=remove_metal,
+        )
+        # Get crop method
+        crop_method = crop.random_crop_method()
+        # Get crop indices based crop method
+        selected_indices, reference_token_index = crop.get_crop_indices(
+            crop_method=crop_method
+        )
+        # Prepare msa
+        msa_features = DataPipeline.get_msa_raw_features(
+            bioassembly_dict=bioassembly_dict,
+            selected_indices=selected_indices,
+            msa_featurizer=msa_featurizer,
+        )
+        # Prepare template
+        template_features = DataPipeline.get_template_raw_features(
+            bioassembly_dict=bioassembly_dict,
+            selected_indices=selected_indices,
+            template_featurizer=template_featurizer,
+        )
+
+        (
+            cropped_token_array,
+            cropped_atom_array,
+            cropped_msa_features,
+            cropped_template_features,
+        ) = crop.crop_by_indices(
+            selected_token_indices=selected_indices,
+            msa_features=msa_features,
+            template_features=template_features,
+        )
+
+        if crop_method == "ContiguousCropping":
+            resovled_atom_num = cropped_atom_array.is_resolved.sum()
+            # The criterion of “more than 4 atoms” is chosen arbitrarily.
+            assert (
+                resovled_atom_num > 4
+            ), f"{resovled_atom_num=} <= 4 after ContiguousCropping"
+
+        return (
+            crop_method,
+            cropped_token_array,
+            cropped_atom_array,
+            cropped_msa_features,
+            cropped_template_features,
+            reference_token_index,
+        )
+
+    @staticmethod
+    def save_atoms_to_cif(
+        output_cif_file: str, atom_array: AtomArray, include_bonds: bool = False
+    ) -> None:
+        """
+        Save atom array data to a CIF file.
+
+        Args:
+            output_cif_file (str): The output path for saving atom array in cif
+            atom_array (AtomArray): The atom array to be saved
+            include_bonds (bool): Whether to include bond information in the CIF file. Default is False.
+
+        """
+        strucio.save_structure(
+            file_path=output_cif_file,
+            array=atom_array,
+            data_block=os.path.basename(output_cif_file).replace(".cif", ""),
+            include_bonds=include_bonds,
+        )