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Andrew Dalke committed 353b44b

Changed the incorrect "OpenBabel" to the correct "Open Babel".

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  • Parent commits 270a4c6

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Files changed (4)

File BindingDB_exact/README

   o OEChem from OpenEye. Used via:
       python bindingdb_cleanup.py --oechem --quiet raw/exact.dat.bz2 > BindingDB_exact.oechem.dat
 
-  o OpenBabel. Used via:
+  o Open Babel. Used via:
       python bindingdb_cleanup.py --openbabel --quiet raw/exact.dat.bz2 > BindingDB_exact.openbabel.dat
 
   o RDKit. Used via:

File BindingDB_exact/bindingdb_cleanup.py

 parser.add_argument('--rdkit', action="store_true", default=None,
                     help="Validate SMILES using the RDKit toolkit")
 parser.add_argument('--openbabel', action="store_true", default=None,
-                    help="Validate SMILES using the OpenBabel toolkit")
+                    help="Validate SMILES using the Open Babel toolkit")
 parser.add_argument("--output", default=None,
                     help="output filename (default is stdout)")
 parser.add_argument("--failed", action="store_true",
     return bool(Chem.MolFromSmiles(smiles))
 
 
-############## Check that OpenBabel accepts the SMILES
+############## Check that Open Babel accepts the SMILES
 
 def is_valid_openbabel(smiles):
     return True
         #  Fc1ccccc1COC(C(=O)NC3c2ccccc2CC3O)C(O)C( O)C(OCc4ccccc4F)C(=O)NC6c5ccccc5CC6O
         # This gets converted to:
         #  Fc1ccccc1COC(C(=O)NC3c2ccccc2CC3O)C(O)C(
-        # which isn't a valid SMILES, but OpenBabel accepts it.
+        # which isn't a valid SMILES, but Open Babel accepts it.
         # There are many SMILES in similar.dat.bz2 which are broken by this strange space.
         if smiles[-1:] in "(=/#-":
             return False
         ## if strict_is_valid_oechem(smiles):
         ##     raise AssertionError("OEChem/strict says %r is real" % (smiles,))
 
-        ## # Verified that OpenSMILES-Ragel rejects molecules that OpenBabel doesn't support.
-        ## # (I hand-checked the failed SMILES which OpenBabel does support, and
+        ## # Verified that OpenSMILES-Ragel rejects molecules that Open Babel doesn't support.
+        ## # (I hand-checked the failed SMILES which Open Babel does support, and
         ## # verified that they should be ignored.)
         ## 
         ## if real_is_valid_openbabel(smiles):
-        ##     raise AssertionError("OpenBabel says %r is real\n" % (smiles,))
+        ##     raise AssertionError("Open Babel says %r is real\n" % (smiles,))
         
         return False, "opensmiles"
     

File BindingDB_substructure/README

             |  rdkit - oechem              |       1
 ------------+------------------------------------------
 
-The OpenBabel and OEChem toolkits are the most similar. Most of the
+The Open Babel and OEChem toolkits are the most similar. Most of the
 RDKit-specific rejections come from "Explicit valence for atom ... is
 greater than permitted" messages. I decided to stick with RDKit for
 (perhaps needless) consistency with the other BindingDB results.

File RDMACCS/README

 ===============
 
 Greg Landrum wrote the patterns for RDKit's MACCS 166
-implementation. CDK and OpenBabel use the same SMARTS patterns for
+implementation. CDK and Open Babel use the same SMARTS patterns for
 their respected MACCS implementations.
 
 Andrew Dalke (that's me!) converted the SMARTS definitions into a form