Re: [OpenBabel-Devel] What's new in OB?

2013-03-27 Thread David van der Spoel
On 2013-03-27 22:04, Craig James wrote: > > > Reinis Danne mailto:rei4...@gmail.com>>wrote: > > > I think it was the thread where I mentioned I'm working on > > kekulization algorithm using graph theory (maximum matching). It > > has been quite some time when I last looked at that co

[OpenBabel-Devel] Fwd: MDL Molfile Extensions in Open Babel?

2013-03-27 Thread Geoffrey Hutchison
Speaking of potential v2.4 projects. Alex Clark implemented an extension to MDL Molfile with charge separation, etc. (http://pubs.acs.org/doi/abs/10.1021/ci200488k) http://sourceforge.net/projects/sketchel/files/SketchEl-1.56-src.tar.gz/download Sadly, I don’t see a source code repository for f

Re: [OpenBabel-Devel] What's new in OB?

2013-03-27 Thread Craig James
Reinis Danne wrote: > > I think it was the thread where I mentioned I'm working on > > kekulization algorithm using graph theory (maximum matching). It > > has been quite some time when I last looked at that code and it > > is not yet usable. > > I don't know if this overlaps with your work, but

Re: [OpenBabel-Devel] SMILES error on aromatic N?

2013-03-27 Thread Craig James
On Wed, Mar 27, 2013 at 10:35 AM, Geoffrey Hutchison < geoff.hutchi...@gmail.com> wrote: > > Maybe a proposed simplification of the valence system > > http://forums.openbabel.org/ImplicitH-failures-td2990439.html > > should be looked at again. > > > Copy/paste from Chris's earlier message: > > A s

Re: [OpenBabel-Devel] What's new in OB?

2013-03-27 Thread Geoffrey Hutchison
> I think it was the thread where I mentioned I'm working on > kekulization algorithm using graph theory (maximum matching). It > has been quite some time when I last looked at that code and it > is not yet usable. A maximal matching algorithm would be really great, since it would greatly improve

Re: [OpenBabel-Devel] SMILES error on aromatic N?

2013-03-27 Thread Geoffrey Hutchison
> Maybe a proposed simplification of the valence system > http://forums.openbabel.org/ImplicitH-failures-td2990439.html > should be looked at again. Copy/paste from Chris's earlier message: > A simpler and more obvious model for this purpose has essentially a > single IMPVAL for each charge sta