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| """
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| References:
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| - TM-align:
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| Zhang, Y., & Skolnick, J. (2005). TM-align: A protein structure alignment algorithm based on TM-score.
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| Nucleic Acids Research, 33(7), 2302-2309. [https://zhanggroup.org/TM-align/]
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| """
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| import os
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| import re
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| import subprocess
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| from pathlib import Path
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| from Bio import PDB
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| from pxdbench.globals import TMALIGN_PATH
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| def extract_chain(input_pdb: str, chain_id: str, output_pdb: str):
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| """
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| Extract a specific chain from a PDB file.
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| Args:
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| input_pdb (str): Path to the input PDB file.
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| chain_id (str): The chain ID to extract.
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| output_pdb (str): Path to the output PDB file.
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| """
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| parser = PDB.PDBParser(QUIET=True)
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| io = PDB.PDBIO()
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| structure = parser.get_structure("structure", input_pdb)
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| class ChainSelect(PDB.Select):
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| def accept_chain(self, chain):
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| return chain.id == chain_id
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| io.set_structure(structure)
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| io.save(output_pdb, select=ChainSelect())
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| def run_tmalign(file1: str, file2: str):
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| """
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| Run TM-align between two PDB files.
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| Args:
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| file1 (str): Path to the first PDB file.
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| file2 (str): Path to the second PDB file.
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| Returns:
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| float or None: The TM-score between the two structures.
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| Returns None if the TM-align command fails.
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| """
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| try:
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| result = subprocess.run(
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| [TMALIGN_PATH, file1, file2],
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| capture_output=True,
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| text=True,
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| check=True,
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| )
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| for line in result.stdout.splitlines():
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| if "TM-score=" in line and "Chain_1" in line:
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| match = re.search(r"TM-score=\s*([0-9.]+)", line)
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| if match:
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| return float(match.group(1))
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| except subprocess.CalledProcessError as e:
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| print(f"Error running TMalign on {file1} and {file2}: {e}")
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| return None
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| def get_pdb_basename(pdb_path: str):
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| assert pdb_path.endswith(".pdb")
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| basename = os.path.basename(pdb_path)
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| return basename[:-4]
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| def get_tm_score(
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| pdb1: str, pdb2: str, chain1=None, chain2=None, keep_temp=False, temp_dir="tmp"
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| ):
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| """
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| Calculate the TM-score between two PDB structures, optionally using specific chains.
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| If specific chains are provided, extracts those chains into temporary files, runs TM-align,
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| and optionally cleans up temporary files. If no chains are specified, runs TM-align directly
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| on the input PDB files.
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| Args:
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| pdb1 (str): Path to the first PDB file.
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| pdb2 (str): Path to the second PDB file.
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| chain1 (str, optional): Chain ID to extract from the first PDB file. Defaults to None.
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| chain2 (str, optional): Chain ID to extract from the second PDB file. Defaults to None.
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| keep_temp (bool, optional): Whether to keep temporary chain files. Defaults to False.
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| temp_dir (str, optional): Directory to store temporary chain files. Defaults to "tmp".
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| Returns:
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| float or None: The TM-score between the specified structures/chains.
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| Returns None if TM-align execution fails or no valid TM-score is found.
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| """
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| if chain1 is None or chain2 is None:
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| tm_score = run_tmalign(pdb1, pdb2)
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| else:
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| Path(temp_dir).mkdir(parents=True, exist_ok=True)
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| pdb1_chain = os.path.join(
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| temp_dir, f"{get_pdb_basename(pdb1)}_chain{chain1}.pdb"
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| )
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| pdb2_chain = os.path.join(
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| temp_dir, f"{get_pdb_basename(pdb2)}_chain{chain2}.pdb"
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| )
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| extract_chain(pdb1, chain1, pdb1_chain)
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| extract_chain(pdb2, chain2, pdb2_chain)
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| tm_score = run_tmalign(pdb1_chain, pdb2_chain)
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| if not keep_temp:
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| os.remove(pdb1_chain)
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| os.remove(pdb2_chain)
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| return tm_score
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|
|
