| |
| |
|
|
| """ |
| Parse PDB files to extract the coordinates of the 4 key atoms from AAs to |
| generate json records compatible to the LM-GVP model. |
| |
| This script is intended for Fluorescence and Protease datasets from TAPE. |
| """ |
|
|
| import json |
| import os |
| import argparse |
| from collections import defaultdict |
| import pandas as pd |
| import numpy as np |
|
|
| from tqdm import tqdm |
| from joblib import Parallel, delayed |
| from Bio.PDB import PDBParser |
| from Bio.PDB.Polypeptide import three_to_one |
|
|
| import xpdb |
| from contact_map_utils import parse_pdb_structure |
|
|
|
|
| def parse_args(): |
| """Prepare argument parser. |
| |
| Args: |
| |
| Return: |
| |
| """ |
| parser = argparse.ArgumentParser( |
| description="Generate json records for GVP from pdb files" |
| ) |
| parser.add_argument( |
| "--data_file", |
| help="Path to csv file containing pdbpaths", |
| required=True, |
| ) |
| parser.add_argument( |
| "--target_col", |
| help="target column in data", |
| required=True, |
| ) |
| parser.add_argument( |
| "--smiles_col", |
| help="smiles column in data", |
| required=True, |
| ) |
| parser.add_argument("--out_prefix", help="output prefix for json records") |
|
|
| args = parser.parse_args() |
| return args |
|
|
|
|
| def get_atom_coords(residue, target_atoms=["N", "CA", "C", "O"]): |
| """Extract the coordinates of the target_atoms from an AA residue. |
| |
| Args: |
| residue: a Bio.PDB.Residue object representing the residue. |
| target_atoms: Target atoms which residues will be returned. |
| |
| Retruns: |
| Array of residue's target atoms (in the same order as target atoms). |
| """ |
| return np.asarray([residue[atom].coord for atom in target_atoms]) |
|
|
|
|
| def structure_to_coords(struct, target_atoms=["N", "CA", "C", "O"], name=""): |
| """Convert a PDB structure in to coordinates of target atoms from all AAs |
| |
| Args: |
| struct: a Bio.PDB.Structure object representing the protein structure |
| target_atoms: Target atoms which residues will be returned. |
| name: String. Name of the structure |
| |
| Return: |
| Dictionary with the pdb sequence, atom 3D coordinates and name. |
| """ |
| output = {} |
| |
| pdb_seq = "".join( |
| [three_to_one(res.get_resname()) for res in struct.get_residues()] |
| ) |
| output["seq"] = pdb_seq |
| |
| coords = np.asarray( |
| [ |
| get_atom_coords(res, target_atoms=target_atoms) |
| for res in struct.get_residues() |
| ] |
| ) |
| output["coords"] = coords.tolist() |
| output["name"] = name |
| return output |
|
|
|
|
| def parse_pdb_gz_to_json_record(parser, sequence, pdb_file_path, name=""): |
| """ |
| Reads and reformats a pdb strcuture into a dictionary. |
| |
| Args: |
| parser: a Bio.PDB.PDBParser or Bio.PDB.MMCIFParser instance. |
| sequence: String. Sequence of the structure. |
| pdb_file_path: String. Path to the pdb file. |
| name: String. Name of the protein. |
| |
| Return: |
| Dictionary with the pdb sequence, atom 3D coordinates and name. |
| """ |
| struct = parse_pdb_structure(parser, sequence, pdb_file_path) |
| record = structure_to_coords(struct, name=name) |
| return record |
|
|
| if __name__=='__main__': |
| args = parse_args() |
| df = pd.read_csv(args.data_file) |
|
|
| |
| sloppyparser = PDBParser( |
| QUIET=True, |
| PERMISSIVE=True, |
| structure_builder=xpdb.SloppyStructureBuilder(), |
| ) |
|
|
| |
| records = Parallel(n_jobs=-1)( |
| delayed(parse_pdb_gz_to_json_record)( |
| sloppyparser, |
| df.iloc[i]["sequence"], |
| df.iloc[i]["pdbpath"], |
| df.iloc[i]["pdbpath"].split("/")[-1], |
| ) |
| for i in tqdm(range(df.shape[0])) |
| ) |
| |
| target_col = args.target_col |
| smiles_col = args.smiles_col |
| |
| for i, rec in enumerate(records): |
| row = df.iloc[i] |
| target = row[target_col] |
| smiles = row[smiles_col] |
| rec["target"] = target |
| rec["ec"] = row["ec"] |
| rec["taxonomy_id"] = row["taxonomy_id"] |
|
|
| outprefix = args.out_prefix |
| |
| print("number of records:", len(records)) |
| outfile = os.path.join(f"{outprefix}_pdbrecords.json") |
| json.dump(records, open(outfile, "w")) |
| print('Success!') |
