Mercurial > repos > bgruening > sucos_docking_scoring

annotate utils.py @ 5:fe318c648502 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:48:35 -0400
parents f8f53668d5a2
children 4f1896782f7c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
1 #!/usr/bin/env python
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
2 """
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
3 Utility functions for SuCOS and other RDKit modules
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
4 """
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
5
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
6 from __future__ import print_function
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
7 import sys, gzip
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
8 from rdkit import Chem
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
9
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
10 def log(*args, **kwargs):
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
11 """Log output to STDERR
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
12 """
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
13 print(*args, file=sys.stderr, **kwargs)
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
14
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
15 def open_file_for_reading(filename):
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
16 """Open the file gunzipping it if it ends with .gz."""
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
17 if filename.lower().endswith('.gz'):
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
18 return gzip.open(filename, 'rb')
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
19 else:
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
20 return open(filename, 'rb')
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
21
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
22 def open_file_for_writing(filename):
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
23 if filename.lower().endswith('.gz'):
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
24 return gzip.open(filename, 'at')
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
25 else:
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
26 return open(filename, 'w+')
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
27
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
28 def read_single_molecule(filename, index=1, format=None):
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
29 """Read a single molecule as a RDKit Mol object. This can come from a file in molfile or SDF format.
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
30 If SDF then you can also specify an index of the molecule that is read (default is the first)
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
31 """
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
32 mol = None
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
33 if format == 'mol' or filename.lower().endswith('.mol') or filename.lower().endswith('.mol.gz'):
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
34 file = open_file_for_reading(filename)
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
35 mol = Chem.MolFromMolBlock(file.read())
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
36 file.close()
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
37 elif format == 'sdf' or filename.lower().endswith('.sdf') or filename.lower().endswith('.sdf.gz'):
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
38 file = open_file_for_reading(filename)
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
39 supplier = Chem.ForwardSDMolSupplier(file)
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
40 for i in range(0,index):
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
41 if supplier.atEnd():
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
42 break
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
43 mol = next(supplier)
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
44 file.close()
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
45
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
46 if not mol:
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
47 raise ValueError("Unable to read molecule")
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
48
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
49 return mol