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use_pymol_align_merge args add

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lingyuzeng
2024-03-06 18:05:57 +08:00
parent eaa1c6dd2b
commit ef30cc9908
1 changed files with 15 additions and 13 deletions
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28
modelbuilder.py
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@@ -11,7 +11,6 @@
import argparse import argparse
from dataclasses import dataclass, field from dataclasses import dataclass, field
from pathlib import Path from pathlib import Path
import os
import logging import logging
from analysis_pdb import PDBAnalyzer from analysis_pdb import PDBAnalyzer
from build_modeller import PDBModeler from build_modeller import PDBModeler
@@ -19,13 +18,11 @@ from modeller import ModellerError
import pymol import pymol
from typing import Dict from typing import Dict
from Bio.SeqRecord import SeqRecord from Bio.SeqRecord import SeqRecord
from concurrent.futures import ProcessPoolExecutor
from functools import partial
@dataclass @dataclass
class PDBAlign: class PDBAlign:
template_file: Path template_file: Path
target_file: Path target_file: Path
pymol_instance: object = field(init=False) pymol_instance: object = field(init=False)
out_file: Path = field(default=None) # 输出文件路径 out_file: Path = field(default=None) # 输出文件路径
@@ -58,6 +55,7 @@ class LoopModelBuilder:
pymol_instance: object = field(init=False) pymol_instance: object = field(init=False)
analyzer_instance: PDBAnalyzer = field(init=False) analyzer_instance: PDBAnalyzer = field(init=False)
pdb_id: str = field(init=False) pdb_id: str = field(init=False)
use_pymol_align_merge: bool = False # 控制是否使用 PyMOL 进行对齐和合并的标志
def __post_init__(self): def __post_init__(self):
self.pdb_id = self.pdb_file.stem self.pdb_id = self.pdb_file.stem
@@ -158,14 +156,17 @@ class LoopModelBuilder:
# change id to original # change id to original
for i in modeller_results: for i in modeller_results:
self.change_chain_identifier(i, 'A', mc, split=False) self.change_chain_identifier(i, 'A', mc, split=False)
# use pymol to align and merge # Use PyMOL to align and merge, controlled by use_pymol_align_merge flag
if len(modeller_results) == 1: if self.use_pymol_align_merge:
# use pymol to align self.logger.warning("PyMOL alignment and merging is disabled or multiple model files exist. "
aligner = PDBAlign(self.pdb_file, modeller_results[0]) "This may result in clashes between multiple protein chains, leading to failures in MD simulations. "
pdbstr = aligner.align() "Please ensure the structures are compatible for simulations.")
mc_dict.update({mc: pdbstr}) if len(modeller_results) == 1:
else: aligner = PDBAlign(self.pdb_file, modeller_results[0])
self.logger.warning('more than one model file, please set num_loop to 1') pdbstr = aligner.align()
mc_dict.update({mc: pdbstr})
else:
self.logger.warning('more than one model file, please set num_loop to 1')
return mc_dict return mc_dict
@staticmethod @staticmethod
@@ -200,6 +201,7 @@ def main():
help="Model refinement type (default: refine.very_fast)") help="Model refinement type (default: refine.very_fast)")
parser.add_argument("--output_dir", type=str, default=None, parser.add_argument("--output_dir", type=str, default=None,
help="Output directory (default: same as PDB file directory)") help="Output directory (default: same as PDB file directory)")
parser.add_argument("--use_pymol_align_merge", action='store_true', help="Use PyMOL for alignment and merging. Note: This may result in clashes between multiple protein chains, leading to failures in MD simulations.")
# 解析参数 # 解析参数
args = parser.parse_args() args = parser.parse_args()
@@ -208,7 +210,7 @@ def main():
pdb_path = Path(args.pdb_file).absolute() pdb_path = Path(args.pdb_file).absolute()
output_dir = Path(args.output_dir).absolute() if args.output_dir else None output_dir = Path(args.output_dir).absolute() if args.output_dir else None
model_builder = LoopModelBuilder(pdb_file=pdb_path, output_dir=output_dir) model_builder = LoopModelBuilder(pdb_file=pdb_path, output_dir=output_dir, use_pymol_align_merge=args.use_pymol_align_merge)
result_path = model_builder.run(typestr=args.typestr) result_path = model_builder.run(typestr=args.typestr)
print(f"Modeling completed. Output file: {result_path}") print(f"Modeling completed. Output file: {result_path}")