Another 2 pence. Nik is clearly hijacking my thoughts. I had the same thoughts on fluoro - include a flag that would allow/disallow counting fluorine at all, and reduce it to aromatic fluorine only. I opted to consider that I would modify the definition myself, but on further consideration that might be problematic if any of my code (or someone else's) becomes available for public consumption. Differing definitions might create problems with performance or interpretation.
-Kirk On Wed, Oct 29, 2008 at 3:30 AM, <[email protected]> wrote: > > Hi, > > maybe I have to rephrase a little. > > With respect to fluoro - the best way to put it would be: > > ... if at all I would reduce it to aromatic fluoro only ... > > Hence, personally I would leave th fluoro out of the general acceptor > definition. I know there is cases where you find them but the frequency is > really not comparable to things like carbonyls or similar (i.e. the rest of > your query). Maybe something like a "useFluoro" flag which is by default set > to false? > > Hope that clarifies things a little. > > Nik > > > > *"Greg Landrum" <[email protected]>* > > 29.10.2008 06:20 > To > [email protected] cc > Subject > Re: [Rdkit-discuss] H-bond Acceptor problem > > > > > On Tue, Oct 28, 2008 at 5:38 PM, Robert DeLisle <[email protected]> > wrote: > > I agree with Nik an additional 2 pence. In fact, while reading Greg's > > original note, my thoughts were essentially identical to Nik's comments. > > Excellent. Here's an altered proposal based on Nik's comments. > > The definition of NumHAcceptors will be modified (modifications > discussed below). I won't make any changes to the NOCount or NHOHCount > descriptors or introduce new names for them. The new names would > conceivably break existing code and wouldn't really contribute to > clarity of future code, so the change doesn't seem worth making. > > For the purposes of fixing the more complex HAcceptor descriptor I > propose the following SMARTS: > HAcceptorSmarts = Chem.MolFromSmarts('[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),\ > $([O,S;H0;v2]),$([O,S;-]),\ > $([N;v3;!$(n-...@[o,N,P,S])]),\ > $([nH0,o,s;+0]),\ > $(F-a)]') > > There are two changes here relative to the current definition: the > third line and the last one. > The third line includes nitrogens that have three neighbors and that > are not connected to another atom that has a non-ring double bond to > O, N, P, or S. The last line includes Fs that are connected to an > aromatic atom. > > Comments? > -greg > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > _________________________ > > CONFIDENTIALITY NOTICE > > The information contained in this e-mail message is intended only for the > exclusive use of the individual or entity named above and may contain > information that is privileged, confidential or exempt from disclosure under > applicable law. If the reader of this message is not the intended recipient, > or the employee or agent responsible for delivery of the message to the > intended recipient, you are hereby notified that any dissemination, > distribution or copying of this communication is strictly prohibited. If you > have received this communication in error, please notify the sender > immediately by e-mail and delete the material from any computer. Thank you. > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
