Source code for ssbio.databases.swissmodel


import json
import logging
import requests
import ssbio.utils
import os.path as op
from collections import defaultdict

log = logging.getLogger(__name__)

[docs]class SWISSMODEL(): """Methods to parse through a SWISS-MODEL metadata set. Download a particular organism's metadata from SWISS-MODEL here: Args: metadata_dir (str): Path to the extracted SWISS-MODEL_Repository folder """ def __init__(self, metadata_dir): self.metadata_dir = metadata_dir """str: Path to the extracted SWISS-MODEL_Repository folder""" self.all_models = None """dict: Dictionary of lists, UniProt ID as the keys""" # Parse the INDEX_JSON file and then store all the metadata in all_models self.parse_metadata() @property def metadata_index_json(self): """str: Path to the INDEX_JSON file.""" try: return op.join(self.metadata_dir, 'INDEX.json') except FileNotFoundError: return op.join(self.metadata_dir, 'INDEX_JSON') @property def uniprots_modeled(self): """list: Return all UniProt accession numbers with at least one model""" return list(self.all_models.keys())
[docs] def parse_metadata(self): """Parse the INDEX_JSON file and reorganize it as a dictionary of lists.""" all_models = defaultdict(list) with open(self.metadata_index_json) as f: loaded = json.load(f) for m in loaded['index']: all_models[m['uniprot_ac']].append(m)
self.all_models = dict(all_models)
[docs] def get_models(self, uniprot_acc): """Return all available models for a UniProt accession number. Args: uniprot_acc (str): UniProt ACC/ID Returns: dict: All available models in SWISS-MODEL for this UniProt entry """ if uniprot_acc in self.all_models: return self.all_models[uniprot_acc] else: log.error('{}: no SWISS-MODELs available'.format(uniprot_acc))
return None
[docs] def get_model_filepath(self, infodict): """Get the path to the homology model using information from the index dictionary for a single model. Example: use self.get_models(UNIPROT_ID) to get all the models, which returns a list of dictionaries. Use one of those dictionaries as input to this function to get the filepath to the model itself. Args: infodict (dict): Information about a model from get_models Returns: str: Path to homology model """ u = infodict['uniprot_ac'] original_filename = '{}_{}_{}_{}'.format(infodict['from'], infodict['to'], infodict['template'], infodict['coordinate_id']) file_path = op.join(self.metadata_dir, u[:2], u[2:4], u[4:6], 'swissmodel', '{}.pdb'.format(original_filename)) if op.exists(file_path): return file_path else: log.warning('{}: no file {} found for model'.format(u, file_path))
return None
[docs] def download_models(self, uniprot_acc, outdir='', force_rerun=False): """Download all models available for a UniProt accession number. Args: uniprot_acc (str): UniProt ACC/ID outdir (str): Path to output directory, uses working directory if not set force_rerun (bool): Force a redownload the models if they already exist Returns: list: Paths to the downloaded models """ downloaded = [] subset = self.get_models(uniprot_acc) for entry in subset: ident = '{}_{}_{}_{}'.format(uniprot_acc, entry['template'], entry['from'], entry['to']) outfile = op.join(outdir, ident + '.pdb') if ssbio.utils.force_rerun(flag=force_rerun, outfile=outfile): response = requests.get(entry['url']) if response.status_code == 404: log.error('{}: 404 returned, no model available.'.format(ident)) else: with open(outfile, 'w') as f: f.write(response.text) log.debug('{}: downloaded homology model'.format(ident)) downloaded.append(outfile) else: downloaded.append(outfile)
return downloaded
[docs] def organize_models(self, outdir, force_rerun=False): """Organize and rename SWISS-MODEL models to a single folder with a name containing template information. Args: outdir (str): New directory to copy renamed models to force_rerun (bool): If models should be copied again even if they already exist Returns: dict: Dictionary of lists, UniProt IDs as the keys and new file paths as the values """ for u, models in self.all_models: for m in models: original_filename = '{}_{}_{}_{}'.format(m['from'], m['to'], m['template'], m['coordinate_id']) file_path = op.join(self.metadata_dir, u[:2], u[2:4], u[4:], 'swissmodel', '{}.pdb'.format(original_filename)) if op.exists(file_path): uniprot_to_swissmodel[uni].append(file_path) else:
log.warning('{}: no file {} found for model'.format(u, ))
[docs]def get_oligomeric_state(swiss_model_path): """Parse the oligomeric prediction in a SWISS-MODEL repository file As of 2018-02-26, works on all E. coli models. Untested on other pre-made organism models. Args: swiss_model_path (str): Path to SWISS-MODEL PDB file Returns: dict: Information parsed about the oligomeric state """ oligo_info = {} with open(swiss_model_path, 'r') as f: for line in f: if line.startswith('REMARK 3 MODEL INFORMATION'): break for i in range(10): line = f.readline() if 'ENGIN' in line: oligo_info['ENGIN'] = line.rstrip().split(' ')[-1] elif 'OSTAT' in line: oligo_info['OSTAT'] = line.rstrip().split(' ')[-1] elif 'OSRSN' in line: oligo_info['OSRSN'] = line.rstrip().split(' ')[-1] elif 'QSPRD' in line: oligo_info['QSPRD'] = line.rstrip().split(' ')[-1] elif 'GMQE' in line: oligo_info['GMQE'] = line.rstrip().split(' ')[-1] elif 'QMN4' in line: oligo_info['QMN4'] = line.rstrip().split(' ')[-1] elif 'MODT' in line: oligo_info['MODT'] = line.rstrip().split(' ')[-1]
return oligo_info
[docs]def translate_ostat(ostat): """Translate the OSTAT field to an integer. As of 2018-02-26, works on all E. coli models. Untested on other pre-made organism models. Args: ostat (str): Predicted oligomeric state of the PDB file Returns: int: Translated string to integer """ ostat_lower = ostat.strip().lower() if ostat_lower == 'monomer': return 1 elif ostat_lower == 'homo-dimer': return 2 elif ostat_lower == 'homo-trimer': return 3 elif ostat_lower == 'homo-tetramer': return 4 elif ostat_lower == 'homo-pentamer': return 5 elif ostat_lower == 'homo-hexamer': return 6 elif ostat_lower == 'homo-heptamer': return 7 elif ostat_lower == 'homo-octamer': return 8 else: num = int(ostat_lower.split('-')[1])
return num