Hi Greg,
I'm writing a piece of script that identifies the hydrophobic parts of
compounds using the pharmacophore features and then fragment the compounds
around the hydrophobic regions.
While I was doing this I noticed that some compounds were raising
ValueError exceptions during the fragmentation process.
I've created a sample IPython Notebook that shows this.
http://nbviewer.ipython.org/gist/CKannas/10255625/Fragmentation%20Bug%20Maybe.ipynb
Check cell 6, you will notice the ValueError print out.
For example for the first compound :
COc1cc(C=CC(=O)OC2OC[C@@H](O)[C@H](O)[C@H]2O)ccc1O
the hydrophobe region is:
CC=Cc
but when the compound is broken up in sidechains and core(hydrophobe
region) the SMILES are:
SideChains: [1*]:cc(OC)c(O)cc:[4*].[2*]=O.[3*]OC1OC[C@@H](O)[C@H](O)[C@H]1O
Hydrophobe: [1*]c([2*])C=CC(=[3*])[4*]
which I think is has some errors in the attachment points in hydrophobe
region core.
Is this the normal behaviour, or a bug?
Also if I merge the two families of Hydrophobe features then I do not get
the error.
Regards,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Christos Kannas's profile on
LinkedIn]<http://cy.linkedin.com/in/christoskannas>
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