Daniel, thanx for your detailed analysis of this corner of the CDK!
On Thu, Apr 5, 2012 at 12:18 PM, Szisz Daniel <[email protected]> wrote: > I got 2-3 messages on ModelBuilder 3D and I do think it would be > good to designate the package as deprecated as it fails in many > cases. In your opinion, is it beyond repair? If so, we should probably remove it. > I would also like to share a bug : in many drug-size molecules the > builder assigns bad MMFF94 atom types to the amide Ns, which results > in bad 3D geometry, namely neglecting the amide plane. It works well > in cases when the amide in like NC=OR, where R is alkyl group, but fails > when the first R atom is not C. Therefore in cases like urea, hydroxyurea > the result is bad. This code base too is from before we introduced the CDK atom types... I have mapping for Sybyl atom types, but have had on my agenda for a long time mappings to MMFF94 too... That way, we remove yet another custom atom typer. > The problem was in MMFF94BasedAtomTypePattern where you have to change the > N atom HOSECODE pattern > > N-[1-3];[CH]{1,3}.{1}+[A-Z]{0,3}+[,]?+=OC.*+ > > to > > N-[1-3];[CH]{1,3}.{1}+[A-Z]{0,3}+[,]?+=O[CNX].*+ > > to handle other types of amides. > > How can I report this bug ? Copy paste what you just write into the bug tacker :) But what about doing those mapping from CDK atom types to MMFF94 atom types? It will likely mean we have to define some subtypes, but I have done that for the Sybyl atom types too... If you think this is useful (considering the builder is going to be deprecated or even removed), then we can set up a Google Doc with two columns: the first the MMFF94 atom types, in the second the matching CDK atom types. Then I (or someone else) can make a like just like the SybylAtomTypeMatcher class. Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
