diff utils.py @ 0:1f19b95adc5c draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utils.py	Wed Oct 02 13:00:36 2019 -0400
@@ -0,0 +1,49 @@
+#!/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
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