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# 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"),
}
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"),
}
DATA_ROOT_DIR = "./release_data/ccd_cache"
# 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"
# )
# 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"
)
# This is a patch in inference stage for users that do not have root permission.
# If you run
# ```
# bash inference_demo.sh
# ```
# or
# ```
# protenix predict --input examples/example.json --out_dir ./output
# ````
# The checkpoint and the data cache will be downloaded to the current code directory.
if (not os.path.exists(CCD_COMPONENTS_FILE_PATH)) or (
not os.path.exists(CCD_COMPONENTS_RDKIT_MOL_FILE_PATH)
):
print("Try to find the ccd cache data in the code directory for inference.")
current_file_path = os.path.abspath(__file__)
current_directory = os.path.dirname(current_file_path)
code_directory = os.path.dirname(current_directory)
data_cache_dir = os.path.join(code_directory, "release_data/ccd_cache")
CCD_COMPONENTS_FILE_PATH = os.path.join(data_cache_dir, "components.cif")
CCD_COMPONENTS_RDKIT_MOL_FILE_PATH = os.path.join(
data_cache_dir, "components.cif.rdkit_mol.pkl"
)
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_cache_dir, "components.v20240608.cif"
)
CCD_COMPONENTS_RDKIT_MOL_FILE_PATH = os.path.join(
data_cache_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": 2048,
},
"max_size": {
"train": 16384,
"test": 16384,
},
"sample_cutoff": {
"train": 2048,
"test": 2048,
},
},
"template": {
"enable": False,
},
"ccd_components_file": CCD_COMPONENTS_FILE_PATH,
"ccd_components_rdkit_mol_file": CCD_COMPONENTS_RDKIT_MOL_FILE_PATH,
}
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