Mercurial > repos > bgruening > sucos_max_score
view utils.py @ 3:bf99565cec1f draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 8542cbcae3ebed4cb9a6c20b1fabd418a6efb7e8"
author | bgruening |
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date | Sat, 28 Mar 2020 05:16:25 -0400 |
parents | bb5365381c8f |
children | 9b48456a96fe |
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#!/usr/bin/env python """ Utility functions for SuCOS and other RDKit modules """ from __future__ import print_function import sys, gzip from rdkit import Chem def log(*args, **kwargs): """Log output to STDERR """ print(*args, file=sys.stderr, **kwargs) def open_file_for_reading(filename): """Open the file gunzipping it if it ends with .gz.""" if filename.lower().endswith('.gz'): return gzip.open(filename, 'rb') else: return open(filename, 'rb') def open_file_for_writing(filename): if filename.lower().endswith('.gz'): return gzip.open(filename, 'at') else: return open(filename, 'w+') def read_single_molecule(filename, index=1, format=None): """Read a single molecule as a RDKit Mol object. This can come from a file in molfile or SDF format. If SDF then you can also specify an index of the molecule that is read (default is the first) """ mol = None if format == 'mol' or filename.lower().endswith('.mol') or filename.lower().endswith('.mol.gz'): file = open_file_for_reading(filename) mol = Chem.MolFromMolBlock(file.read()) file.close() elif format == 'sdf' or filename.lower().endswith('.sdf') or filename.lower().endswith('.sdf.gz'): file = open_file_for_reading(filename) supplier = Chem.ForwardSDMolSupplier(file) for i in range(0,index): if supplier.atEnd(): break mol = next(supplier) file.close() if not mol: raise ValueError("Unable to read molecule") return mol