# Copyright 2025 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 ListValue eval_configs = { "save_dir": "", "monomer": { "eval_diversity": False, "num_seqs": 8, "tools": { "mpnn": { "model_type": "ca", # [ca, bb, soluble] "model_name": "v_48_020", "temperature": "0.1", } }, }, "binder": { "eval_diversity": False, "eval_binder_monomer": True, "eval_complex": True, "eval_protenix_mini": True, "eval_protenix": False, "num_seqs": 1, "use_gt_seq": False, "use_binder_seq_list": False, "is_cyclic": False, "tools": { "mpnn": { "weights": "original", # [original, soluble] "rm_aa": "C", "temperature": "0.0001", "fix_interface": False, # whether fixing interface restype or not }, "af2": { "use_multimer": False, "model_ids": ListValue([0]), "use_initial_guess": True, "use_initial_atom_pos": False, "use_binder_template": True, "is_cyclic": False, }, "ptx_mini": { "model_name": "protenix_mini_default_v0.5.0", "load_checkpoint_dir": "", "dtype": "bf16", "use_deepspeed_evo_attention": True, "N_cycle": 4, "N_sample": 1, "N_step": 2, "step_scale_eta": 1.0, "gamma0": 0, "use_template": False, "use_msa": True, }, "ptx": { "model_name": "protenix_base_default_v0.5.0", "load_checkpoint_dir": "", "dtype": "bf16", "use_deepspeed_evo_attention": True, "N_cycle": 4, "N_sample": 1, "N_step": 2, "step_scale_eta": 1.0, "gamma0": 0, "use_template": False, "use_msa": True, }, }, "filters": { "af2_easy": { "pLDDT": (">", 0.8), "i_pTM": (">", 0.5), "i_pAE": ("<", 0.35), "bound_unbound_RMSD": ("<", 3.5), }, "af2_opt": { "pLDDT": (">", 0.9), "unscaled_i_pAE": ("<", 7.0), "af2_binder_pred_design_rmsd": ("<", 1.5), }, "ptx_mini": { "ptx_mini_iptm_binder": (">", 0.85), "ptx_mini_ptm_binder": (">", 0.88), "ptx_mini_pred_design_rmsd": ("<", 2.5), }, "ptx": { "ptx_iptm_binder": (">", 0.85), "ptx_ptm_binder": (">", 0.88), "ptx_pred_design_rmsd": ("<", 2.5), }, "ptx_basic": { "ptx_iptm_binder": (">", 0.8), "ptx_ptm_binder": (">", 0.8), "ptx_pred_design_rmsd": ("<", 2.5), }, }, }, }