Re: [Rdkit-discuss] How can I escape to this error
Dear Christian, 2010/6/28 Christian de Bouillé : > > How can I escape to this error ? > as I cannot change the smiles > To review for the mailing list. The molecule in question is: CC[NH+](CC)CC.O1c2c2O[P-]1123Oc4c4O1.O2c1c1O3 What I said before: > I'm not sure what your question is. The error message is pretty clear: > the P in your molecule has a valence of 7. The RDKit expects P to have > a valence of either 3 or 5. The anion in this compound, trisphat, is > an example of a hypervalent phosphorous, which the RDKit does not > currently accept. > > If enough people think it's important, we can discuss how to molecules > like this can be supported by the RDKit. To continue and try to answer Christian's question: it is currently impossible to really work with this hypervalent molecule in the RDKit. The only real solution is to tell the RDKit that P is allowed to have 7 substituents. If you really want to do this you can edit the file $RDBASE/Code/GraphMol/atomic_data.cpp and change the allowed valence list for P from "3 5" to "3 5 7". After you do this, you will need to rebuild the code. Best Regards, -greg -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] How can I escape to this error
Hi Greg, Apologies for resurrecting a rather old thread, but I have been investigating the Q32010_1beta1 release on a set of commercial amines (from ACD) and came across the 'hypervalent P' issue as well. Greg wrote: > To continue and try to answer Christian's question: it is currently > impossible to really work with this hypervalent molecule in the RDKit. > The only real solution is to tell the RDKit that P is allowed to have > 7 substituents. If you really want to do this you can edit the file > $RDBASE/Code/GraphMol/atomic_data.cpp and change the allowed valence > list for P from "3 5" to "3 5 7". After you do this, you will need to > rebuild the code. With the new release currently in beta, I wondered whether this would be a good time to consider if the change you suggest above for P should make it into the release code(?) Having said that, I am expecting that your comment "it is currently impossible to really work with this hypervalent molecule in the RDKit" suggests that a robust solution is not as simple as just changing the allowed valence list... Anyway, what I was finding from my list of amines was that the hexafluorophosphate counterion [PF6]- was triggering the error. Not a particularly common counterion - so I can certainly live without(!) - but not particularly esoteric either :-) Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. __ -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] How can I escape to this error
Dear all, On Wed, Sep 29, 2010 at 10:51 AM, James Davidson wrote: > > Apologies for resurrecting a rather old thread, but I have been > investigating the Q32010_1beta1 release on a set of commercial amines > (from ACD) and came across the 'hypervalent P' issue as well. > > Greg wrote: >> To continue and try to answer Christian's question: it is currently >> impossible to really work with this hypervalent molecule in the RDKit. >> The only real solution is to tell the RDKit that P is allowed to have >> 7 substituents. If you really want to do this you can edit the file >> $RDBASE/Code/GraphMol/atomic_data.cpp and change the allowed valence >> list for P from "3 5" to "3 5 7". After you do this, you will need to >> rebuild the code. > > With the new release currently in beta, I wondered whether this would be > a good time to consider if the change you suggest above for P should > make it into the release code(?) Having said that, I am expecting that > your comment "it is currently impossible to really work with this > hypervalent molecule in the RDKit" suggests that a robust solution is > not as simple as just changing the allowed valence list... That comment really meant "without changing the allowed valence list it is currently impossible..." > > Anyway, what I was finding from my list of amines was that the > hexafluorophosphate counterion [PF6]- was triggering the error. Not a > particularly common counterion - so I can certainly live without(!) - > but not particularly esoteric either :-) It's easy enough to add the extra valence state so that PF6- (and trisphat, and the like) can be read in. They aren't going to behave optimally (for example the 3D coordinate generation won't necessarily generate nice results), but they also shouldn't lead to too many problems. If there are no objections, I will go ahead and add the extra allowed valence state to P for the next release. Best, -greg -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
