Mercurial > repos > bgruening > sdf_to_tab
view sdf_to_tab.py @ 0:06828e0cc8a7 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
author | bgruening |
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date | Wed, 16 Oct 2019 07:26:19 -0400 |
parents | |
children | 40ff81f67f5e |
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#!/usr/bin/env python3 import argparse import pandas as pd from rdkit import Chem def sdf_to_tab(vars): mols = Chem.SDMolSupplier(vars.inp, sanitize=False) df = pd.DataFrame() # for output for n in range(len(mols)): if mols[n]: d = mols[n].GetPropsAsDict() # filter dict for desired props if vars.props.strip() == '': # none specified, return all d = {prop: val for (prop, val) in d.items() if not any(x in str(val) for x in ['\n', '\t'])} # remove items containing newlines or tabs else: d = {prop: val for (prop, val) in d.items() if prop in vars.props.replace(' ', '').split(',')} # remove items not requested via CLI if vars.name: d['Name'] = mols[n].GetProp('_Name') if vars.smiles: d['SMILES'] = Chem.MolToSmiles(mols[n], isomericSmiles=False) d['Index'] = int(n) df = df.append(d, ignore_index=True) else: print("Molecule could not be read - skipped.") df = df.astype({'Index': int}).set_index('Index') df.to_csv(vars.out, sep='\t', header=vars.header) def main(): parser = argparse.ArgumentParser(description="Convert SDF to tabular") parser.add_argument('--inp', '-i', help="The input file", required=True) parser.add_argument('--out', '-o', help="The output file", required=True) parser.add_argument('--props', '-p', help="Properties to filter (leave blank for all)", required=True) parser.add_argument('--header', '-t', action='store_true', help="Write property name as the first row.") parser.add_argument('--smiles', '-s', action='store_true', help="Include SMILES in output.") parser.add_argument('--name', '-n', action='store_true', help="Include molecule name in output.") sdf_to_tab(parser.parse_args()) if __name__ == "__main__": main()