File size: 3,908 Bytes
d766458 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 | # 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),
},
},
},
}
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