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#!/usr/bin/env python
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"""
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utils.py
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Simple tools for use with the quanformer package
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Version: Mar 29 2019
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By: Victoria T. Lim
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"""
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import openeye.oechem as oechem
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import quanformer.reader as reader
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def convert_extension(infile, outfile, canonical=False):
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"""
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Convert one molecule file format into another using OpenEye tools.
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The user may also assign canonical smiles as name before writing output.
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"""
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# open input file
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mols = reader.read_mols(infile)
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# open output file
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ofs = oechem.oemolostream()
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if not ofs.open(outfile):
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oechem.OEThrow.Fatal("Unable to open %s for writing" % outfile)
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# write to output
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for mol in mols:
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if canonical:
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smi = oechem.OEMolToSmiles(mol)
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for conf in mol.GetConfs():
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if canonical:
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conf.SetTitle(smi)
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oechem.OEWriteConstMolecule(ofs, conf)
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# close filestreams
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ofs.close()
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def convert_extension_separate(infile, presuffix, canonical=False, separate='mol'):
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"""
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Convert one molecule file format into another using OpenEye tools.
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The user may also assign canonical smiles as name before writing output.
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Separate output into (each mol with all confs) or (each conf).
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presuffix : list
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first item contains prefix of output name, last item contains extension
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ex. ['alkyl', '.xyz']
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separate : string
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'mol' or 'conf'
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"""
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# open input file
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mols = reader.read_mols(infile)
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# write to output
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for i, mol in enumerate(mols):
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# open output file
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if separate=='mol':
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ofs = oechem.oemolostream()
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if not ofs.open('{}_{}{}'.format(presuffix[0], str(i), presuffix[1])):
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oechem.OEThrow.Fatal("Unable to open %s for writing" % outfile)
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if canonical:
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smi = oechem.OEMolToSmiles(mol)
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for j, conf in enumerate(mol.GetConfs()):
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# open output file
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if separate=='conf':
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ofs = oechem.oemolostream()
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if not ofs.open('{}_{}_{}{}'.format(presuffix[0], str(i), str(j), presuffix[1])):
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oechem.OEThrow.Fatal("Unable to open %s for writing" % outfile)
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if canonical:
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conf.SetTitle(smi)
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oechem.OEWriteConstMolecule(ofs, conf)
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# close filestreams
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ofs.close()
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vtlim