NO_JIRA Adding two scripts from ccdc confidential for conformer analysis. Ori… #91
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| # Conformer Filter Density | ||
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| Filter conformers using a variety of metrics. See arguments in script for details. | ||
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| CCDC Python API Licence required, minimum version: 3.0.15 | ||
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| #!/usr/bin/env python3 | ||
| # | ||
| # This script can be used for any purpose without limitation subject to the | ||
| # conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx | ||
| # | ||
| # This permission notice and the following statement of attribution must be | ||
| # included in all copies or substantial portions of this script. | ||
| # | ||
| # 2026-02-03: created by the Cambridge Crystallographic Data Centre | ||
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| import argparse | ||
| import csv | ||
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| from ccdc import conformer, io | ||
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| def parse_args(): | ||
| """Parse command line arguments.""" | ||
| parser = argparse.ArgumentParser(description=__doc__) | ||
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| parser.add_argument('inmolfn', | ||
| metavar='<input molecule file>', | ||
| help='Input file (single- or multi-molecule file)') | ||
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| parser.add_argument('-m', '--mode', | ||
| choices=['absolute', 'relative'], | ||
| default='absolute', | ||
| help='Limit mode: absolute (fixed threshold) or relative ' | ||
| '(threshold based on molecule with fewest unusual torsions). ' | ||
| 'WARNING: Relative mode may behave unexpectedly with conformers ' | ||
| 'from multiple input molecules (default: %(default)s)') | ||
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| parser.add_argument('-l', '--limit', | ||
| dest='torsion_limit', | ||
| type=int, | ||
| default=0, | ||
| metavar='<limit>', | ||
| help='Maximum number of unusual torsions for a passing molecule ' | ||
| '(default: %(default)s)') | ||
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| parser.add_argument('-d', '--local-density', | ||
| dest='local_density_threshold', | ||
| type=float, | ||
| default=10.0, | ||
| metavar='<threshold>', | ||
| help='Local density threshold for classifying a torsion as unusual ' | ||
| '(default: %(default)s)') | ||
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| parser.add_argument('--incl-organometallics', | ||
| dest='incl_organometallics', | ||
| action='store_true', | ||
| help='Include organometallic compounds in the search ' | ||
| '(default: organic compounds only)') | ||
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| parser.add_argument('--generalisation', | ||
| action='store_true', | ||
| help='Turn on generalisation for searches') | ||
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| parser.add_argument('--successfn', | ||
| default='successes.mol', | ||
| metavar='<file>', | ||
| help='Output file for molecules that pass the filter ' | ||
| '(default: %(default)s)') | ||
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| parser.add_argument('--failurefn', | ||
| default='failures.mol', | ||
| metavar='<file>', | ||
| help='Output file for molecules that fail the filter ' | ||
| '(default: %(default)s)') | ||
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| parser.add_argument('-u', '--unusual-torsions', | ||
| dest='unusualtorsionfn', | ||
| default='unusual_torsions.csv', | ||
| metavar='<file>', | ||
| help='Output CSV file for unusual torsion details ' | ||
| '(default: %(default)s)') | ||
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| return parser.parse_args() | ||
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| def create_mogul_engine(local_density_threshold, incl_organometallics, generalisation): | ||
| """Create and configure a geometry analyser engine. | ||
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| Args: | ||
| local_density_threshold: Threshold for classifying torsions as unusual | ||
| incl_organometallics: Whether to include organometallic compounds | ||
| generalisation: Whether to enable generalisation for searches | ||
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| Returns: | ||
| Configured ccdc.conformer.GeometryAnalyser instance | ||
| """ | ||
| engine = conformer.GeometryAnalyser() | ||
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| engine.settings.bond.analyse = False | ||
| engine.settings.angle.analyse = False | ||
| engine.settings.ring.analyse = False | ||
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| engine.settings.torsion.local_density_threshold = local_density_threshold | ||
| engine.settings.generalisation = generalisation | ||
| engine.settings.organometallic_filter = 'all' if incl_organometallics else 'organics_only' | ||
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| return engine | ||
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| def analysis(torsion_limit, input_filename, mode, engine, success_file, failure_file, unusual_torsion_file): | ||
| """Analyze molecules for unusual torsions and filter based on criteria. | ||
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| Args: | ||
| torsion_limit: Maximum number of unusual torsions allowed | ||
| input_filename: Path to input molecule file | ||
| mode: 'absolute' or 'relative' filtering mode | ||
| engine: Configured GeometryAnalyser instance | ||
| success_file: Path to output file for passing molecules | ||
| failure_file: Path to output file for failing molecules | ||
| unusual_torsion_file: Path to CSV file for unusual torsion details | ||
| """ | ||
| # Analyze all molecules and collect unusual torsion data | ||
| molecules = [] | ||
| min_unusual_torsions = float('inf') | ||
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| with io.MoleculeReader(input_filename) as mol_reader: | ||
| for molecule in mol_reader: | ||
| molecule.standardise_aromatic_bonds() | ||
| molecule.standardise_delocalised_bonds() | ||
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| geometry_analysed_molecule = engine.analyse_molecule(molecule) | ||
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| molecule.unusual_torsions = [ | ||
| t for t in geometry_analysed_molecule.analysed_torsions | ||
| if t.unusual and t.enough_hits | ||
| ] | ||
| molecule.num_unusual_torsions = len(molecule.unusual_torsions) | ||
| molecules.append(molecule) | ||
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| min_unusual_torsions = min(min_unusual_torsions, molecule.num_unusual_torsions) | ||
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| # Write results | ||
| with io.MoleculeWriter(success_file) as passed_writer, \ | ||
| io.MoleculeWriter(failure_file) as failed_writer, \ | ||
| open(unusual_torsion_file, 'w', newline='') as csv_file: | ||
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| csv_writer = csv.writer(csv_file) | ||
| csv_writer.writerow(['MoleculeIndex', 'Value', 'Zscore', 'LocalDensity', 'NumHits', 'Atoms']) | ||
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| for idx, molecule in enumerate(molecules): | ||
| threshold = torsion_limit if mode == 'absolute' else min_unusual_torsions + torsion_limit | ||
| failed = molecule.num_unusual_torsions > threshold | ||
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| if failed: | ||
| failed_writer.write(molecule) | ||
| for torsion in molecule.unusual_torsions: | ||
| csv_writer.writerow([ | ||
| idx, | ||
| torsion.value, | ||
| torsion.z_score, | ||
| torsion.local_density, | ||
| torsion.nhits, | ||
| ' '.join(torsion.atom_labels) | ||
| ]) | ||
| else: | ||
| passed_writer.write(molecule) | ||
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| def run(): | ||
| """Main entry point for the script.""" | ||
| args = parse_args() | ||
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| if args.torsion_limit < 0: | ||
| raise ValueError('Torsion limit must be >= 0') | ||
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| engine = create_mogul_engine( | ||
| args.local_density_threshold, | ||
| args.incl_organometallics, | ||
| args.generalisation | ||
| ) | ||
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| analysis( | ||
| args.torsion_limit, | ||
| args.inmolfn, | ||
| args.mode, | ||
| engine, | ||
| args.successfn, | ||
| args.failurefn, | ||
| args.unusualtorsionsfn, | ||
| ) | ||
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| if __name__ == '__main__': | ||
| run() |
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| # Filter Poses | ||
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| This is a short script to filter molecular poses in a multi-molecule file based on the torsion probabilities. | ||
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| CCDC Python API Licence required, minimum version: 3.0.15 | ||
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Contributor
There was a problem hiding this comment. Same as previous comment please :) And can you add the scripts to the ReadMe in the script folder too please :) |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,189 @@ | ||
| #!/usr/bin/env python3 | ||
| # | ||
| # This script can be used for any purpose without limitation subject to the | ||
| # conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx | ||
| # | ||
| # This permission notice and the following statement of attribution must be | ||
| # included in all copies or substantial portions of this script. | ||
| # | ||
| # 2025-02-03: created by the Cambridge Crystallographic Data Centre | ||
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| import argparse | ||
| import copy | ||
| import csv | ||
| import math | ||
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| from ccdc import conformer, io | ||
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| def parse_args(): | ||
| """Parse command line arguments.""" | ||
| parser = argparse.ArgumentParser(description=__doc__) | ||
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| parser.add_argument('conformer_file', | ||
| metavar='<input file>', | ||
| help='Input file (multi-molecule file)') | ||
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| parser.add_argument('-csv', '--write-csv', | ||
| dest='write_csv', | ||
| action='store_true', | ||
| help='Write a csv file for all the analysed conformers.') | ||
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| return parser.parse_args() | ||
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| class ProbabilityScorer: | ||
| """ | ||
| Use the ConformerGenerator and GeometryAnalyser to score conformers based on their conformational | ||
| probabilities and unusual torsions. | ||
| """ | ||
| def __init__(self, user_conformer_generator_settings=None, skip_minimisation=True, | ||
| user_mogul_analysis_settings=None): | ||
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| self._generator = self._create_conformer_generator(user_conformer_generator_settings, skip_minimisation) | ||
| self._mogul_analysis_engine = self._create_analyser(user_mogul_analysis_settings) | ||
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| def _create_analyser(self, user_mogul_analyser_settings): | ||
| """Create a GeometryAnalyser engine to analyse the conformers.""" | ||
| engine = conformer.GeometryAnalyser() | ||
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| # Tweak the 'default defaults' | ||
| # By default, in this use case, we do not want to use generalisation. | ||
| engine.settings.generalisation = False | ||
| # By default, only the organic subset, i.e. exclude organometallic | ||
| engine.settings.organometallic_filter = 'Organic' | ||
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| # Ensure user settings are kept: | ||
| if user_mogul_analyser_settings is not None: | ||
| engine.settings = copy.copy(user_mogul_analyser_settings) | ||
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| # Only analyse torsions: | ||
| engine.settings.bond.analyse = False | ||
| engine.settings.angle.analyse = False | ||
| engine.settings.ring.analyse = False | ||
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| return engine | ||
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| def _create_conformer_generator(self, user_generator_settings, skip_minimisation=True): | ||
| """Create a ConformerGenerator engine to generate conformers for the molecules.""" | ||
| settings = conformer.ConformerSettings() | ||
| if user_generator_settings is not None: | ||
| settings = copy.copy(user_generator_settings) | ||
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| # Mandatory setting here: this must work in use_input_torsion_distributions mode. | ||
| settings.use_input_torsion_distributions = True | ||
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| engine = conformer.ConformerGenerator(settings, skip_minimisation) | ||
| return engine | ||
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| @staticmethod | ||
| def _combined_local_density(all_local_densities): | ||
| if all_local_densities: | ||
| return sum(all_local_densities) / len(all_local_densities) | ||
| return 100.0 | ||
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| def probability_analysis(self, molecule, bad_normalised_score=1.0, bad_probability_score=0.0, | ||
| bad_rmsd_score=9999.9): | ||
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| # Approximation excluding rings: | ||
| is_rigid = sum(bond.is_rotatable for bond in molecule.bonds) == 0 | ||
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| conformers = self._generator.generate(molecule) | ||
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| normalised_score = None | ||
| rmsd = None | ||
| ln_probability = None | ||
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| if conformers: | ||
| # First conformer is the most likely, so return its score. | ||
| normalised_score = conformers[0].normalised_score | ||
| rmsd = conformers[0].rmsd() | ||
| ln_probability = conformers[0].probability | ||
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| if is_rigid: | ||
| if ln_probability is None: | ||
| ln_probability = 0.0 | ||
| if normalised_score is None: | ||
| normalised_score = 0.0 | ||
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| if normalised_score is None: | ||
| normalised_score = bad_normalised_score | ||
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| if rmsd is None: | ||
| rmsd = bad_rmsd_score | ||
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| probability = bad_probability_score | ||
| if ln_probability is not None: | ||
| probability = math.exp(ln_probability) | ||
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| return normalised_score, probability, rmsd | ||
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| def unusual_torsions_analysis(self, molecule, max_hist_size=15): | ||
| checked_mol = self._mogul_analysis_engine.analyse_molecule(molecule) | ||
| unusual_count = 0 | ||
| local_densities = [] | ||
| unusual_local_densities = [] | ||
| no_data_torsions = 0 | ||
| for tor in checked_mol.analysed_torsions: | ||
| hist_size = sum(tor.histogram()) | ||
| if hist_size > max_hist_size: | ||
| local_densities.append(tor.local_density) | ||
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| if tor.unusual: | ||
| unusual_local_densities.append(tor.local_density) | ||
| unusual_count += 1 | ||
| else: | ||
| no_data_torsions += 1 | ||
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| # Expected number of torsions within 10 degrees assuming even distribution of observations. | ||
| # Number of Mogul bins would be strictly better than assuming 18. | ||
| uniform_torsion_dist = 100 / 18 | ||
| local_densities.append(uniform_torsion_dist) | ||
| return unusual_count, self._combined_local_density(local_densities), self._combined_local_density( | ||
| unusual_local_densities), no_data_torsions | ||
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| def process_molecule(self, molecule): | ||
| molecule.remove_unknown_atoms() | ||
| molecule.assign_bond_types() | ||
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| unusual_count, avg_local_density, avg_unusual_local_density, no_data_torsions = self.unusual_torsions_analysis( | ||
| molecule) | ||
| normalised_score, probability, rmsd = self.probability_analysis(molecule) | ||
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| return { | ||
| "identifier": molecule.identifier, | ||
| "number of unusual torsions": unusual_count, | ||
| "average local density": avg_local_density, | ||
| "average unusual local density": avg_unusual_local_density, | ||
| "number of torsions with no data": no_data_torsions, | ||
| "normalised probability score": normalised_score, | ||
| "probability score": probability, | ||
| "RMSD to input conformation": rmsd, | ||
| } | ||
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| def run(): | ||
| args = parse_args() | ||
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| p = ProbabilityScorer() | ||
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| all_data = [] | ||
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| with io.MoleculeReader(args.conformer_file) as reader: | ||
| for i, molecule in enumerate(reader): | ||
| data = p.process_molecule(molecule) | ||
| if i == 0: | ||
| print(", ".join(data.keys())) | ||
| print(", ".join(str(value) for value in data.values())) | ||
| all_data.append(data) | ||
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| if args.write_csv: | ||
| keys = all_data[0].keys() | ||
| with open('filtered_poses_analysis.csv', 'w', newline='') as output_file: | ||
| dict_writer = csv.DictWriter(output_file, keys) | ||
| dict_writer.writeheader() | ||
| dict_writer.writerows(all_data) | ||
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| if __name__ == "__main__": | ||
| run() |
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Can you please expan on this Readme to include the sections that is in the template https://github.com/ccdc-opensource/csd-python-api-scripts/tree/main/scripts/new_script_readme_template