diff rdkit_descriptors.py @ 0:0f3e5c69251e draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rdkit_descriptors.py	Tue Mar 10 12:57:24 2020 -0400
@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+
+from rdkit.Chem import Descriptors
+from rdkit import Chem
+import sys, os, re
+import argparse
+import inspect
+
+def get_supplier( infile, format = 'smiles' ):
+    """
+    Returns a generator over a SMILES or InChI file. Every element is of RDKit 
+    molecule and has its original string as _Name property.
+    """
+    with open(infile) as handle:
+        for line in handle:
+            line = line.strip()
+            if format == 'smiles':
+                mol = Chem.MolFromSmiles( line, sanitize=True )
+            elif format == 'inchi':
+                mol = Chem.inchi.MolFromInchi( line, sanitize=True, removeHs=True, logLevel=None, treatWarningAsError=False )
+            if mol is None:
+                yield False
+            else:
+                mol.SetProp( '_Name', line.split('\t')[0] )
+                yield mol
+
+def get_rdkit_descriptor_functions():
+    """
+    Returns all descriptor functions under the Chem.Descriptors Module as tuple of (name, function)
+    """
+    ret = [ (name, f) for name, f in inspect.getmembers( Descriptors ) if inspect.isfunction( f ) and not name.startswith( '_' ) ]
+    ret.sort()
+    return ret
+
+
+def descriptors( mol, functions ):
+    """
+    Calculates the descriptors of a given molecule.
+    """
+    for name, function in functions:
+        yield (name, function( mol ))
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-i', '--infile', required=True, help='Path to the input file.')
+    parser.add_argument("--iformat", help="Specify the input file format.")
+
+    parser.add_argument('-o', '--outfile', type=argparse.FileType('w+'), 
+        default=sys.stdout, help="path to the result file, default it sdtout")
+
+    parser.add_argument("--header", dest="header", action="store_true",
+                    default=False,
+                    help="Write header line.")
+
+    args = parser.parse_args()
+
+    if args.iformat == 'sdf':
+        supplier = Chem.SDMolSupplier( args.infile )
+    elif args.iformat =='smi':
+        supplier = get_supplier( args.infile, format = 'smiles' )
+    elif args.iformat == 'inchi':
+        supplier = get_supplier( args.infile, format = 'inchi' )
+
+    functions = get_rdkit_descriptor_functions()
+
+    if args.header:
+        args.outfile.write( '%s\n' % '\t'.join( ['MoleculeID'] + [name for name, f in functions] ) )
+
+    for mol in supplier:
+        if not mol:
+            continue
+        descs = descriptors( mol, functions )
+        molecule_id = mol.GetProp("_Name")
+        args.outfile.write( "%s\n" % '\t'.join( [molecule_id]+ [str(round(res, 6)) for name, res in descs] ) )
+