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