On Thursday, April 24, 2014, Stephen O'hagan <[email protected]>
wrote:
> OK,
>
>
>
> Adding:
>
>
>
> AllChem.EmbedMolecule(m1)
>
> AllChem.UFFOptimizeMolecule(m1)
>
>
>
> Fixed the problem. Now to work out what it all means!
>
>
That part is left as an exercise for the reader. ;-)
>
>
> *From:* Greg Landrum
> [mailto:[email protected]<javascript:_e(%7B%7D,'cvml','[email protected]');>]
>
> *Sent:* 24 April 2014 04:39
> *To:* Stephen O'hagan
> *Cc:*
> [email protected]<javascript:_e(%7B%7D,'cvml','[email protected]');>
> *Subject:* Re: [Rdkit-discuss] RDKit pharmacophore features
>
>
>
> Hi Steve,
>
>
>
> On Wed, Apr 23, 2014 at 5:41 PM, Stephen O'hagan
> <[email protected]<javascript:_e(%7B%7D,'cvml','[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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