Mercurial > repos > bgruening > enumerate_charges

comparison sdf_to_tab.py @ 0:759010d2e9cd draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
author bgruening
date Tue, 10 Mar 2020 16:55:50 +0000
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children d84dc786ccb9
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-1:000000000000 0:759010d2e9cd
1 #!/usr/bin/env python3
2 import argparse
3 import pandas as pd
4 from rdkit import Chem
5
6 def sdf_to_tab(vars):
7 mols = Chem.SDMolSupplier(vars.inp, sanitize=False)
8 df = pd.DataFrame() # for output
9
10 for n in range(len(mols)):
11 if mols[n]:
12 d = mols[n].GetPropsAsDict()
13 # filter dict for desired props
14 if vars.props.strip() == '': # none specified, return all
15 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
16 else:
17 d = {prop: val for (prop, val) in d.items() if prop in vars.props.replace(' ', '').split(',')} # remove items not requested via CLI
18 if vars.name:
19 d['Name'] = mols[n].GetProp('_Name')
20 if vars.smiles:
21 d['SMILES'] = Chem.MolToSmiles(mols[n], isomericSmiles=False)
22 d['Index'] = int(n)
23
24 df = df.append(d, ignore_index=True)
25 else:
26 print("Molecule could not be read - skipped.")
27
28 df = df.astype({'Index': int}).set_index('Index')
29 df.to_csv(vars.out, sep='\t', header=vars.header)
30
31 def main():
32 parser = argparse.ArgumentParser(description="Convert SDF to tabular")
33 parser.add_argument('--inp', '-i', help="The input file", required=True)
34 parser.add_argument('--out', '-o', help="The output file", required=True)
35 parser.add_argument('--props', '-p', help="Properties to filter (leave blank for all)", required=True)
36 parser.add_argument('--header', '-t', action='store_true',
37 help="Write property name as the first row.")
38 parser.add_argument('--smiles', '-s', action='store_true',
39 help="Include SMILES in output.")
40 parser.add_argument('--name', '-n', action='store_true',
41 help="Include molecule name in output.")
42 sdf_to_tab(parser.parse_args())
43
44
45 if __name__ == "__main__":
46 main()