Hi Steve,
On Wed, Apr 23, 2014 at 5:41 PM, Stephen O'hagan
<[email protected]>wrote:
> I’m trying to understand how the RDKit pharmacophore features work;
> tried this fragment from a previous post:
>
>
>
>
>
> import os
>
> from rdkit import Chem
>
> from rdkit.Chem import ChemicalFeatures
>
> from rdkit import *Geometry*
>
> from rdkit import RDConfig
>
> from rdkit.Chem import *AllChem*
>
> from rdkit.Chem.Pharm3D import Pharmacophore, EmbedLib
>
>
>
> m1 = Chem.MolFromSmiles(*'Cc1ccccc1'*)
>
>
>
>
>
> FEATURE_DEF_FILE = os.path.join(RDConfig.RDDataDir,*'BaseFeatures.fdef'*)
>
> feat_factory = ChemicalFeatures.BuildFeatureFactory(FEATURE_DEF_FILE)
>
> feats = feat_factory.GetFeaturesForMol(m1)
>
> pcophore = Pharmacophore.Pharmacophore(feats)
>
>
>
> I get an immediate CTD on the call to *Pharmacophore.Pharmacophore(feats)*
>
There are two bugs here:
1) in your code the molecule has no conformations generated, so trying to
create a pharmacophore from the features associated with that molecule
should not work
2) instead of an error message or exception you get a crash (seg fault on
linux or the mac). The RDKit should never do that...
If you add coordinates (2D or 3D) to your molecule before constructing the
pharmacophore, your code should work.
Best,
-greg
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