On Wed, Oct 21, 2009 at 12:08 PM, Evgueni Kolossov <ekolos...@gmail.com> wrote: > Sorry Greg, > > Actually I found the problem - in this case to pass structure into the > viewer I been using MolToMolBlock(*mol, true, -1, false) instead of SDWriter > function write(*mol) and this is what making the difference - write(*mol) > doing it OK but MolToMolBlock producing an effect I described to you. > I have moved into write(*mol) now and everything is OK. > I can only suggest you take a look at MolToMolBlock function.
MolToMolBlock is fine, in fact it's what the SDWriter is using (look at line 75 of SDWriter.cpp). The problem that you are having is maybe the last argument you provide to MolToMolBlock, which tells it that the molecule should *not* be kekulized on output. The default value for this (which is what the SDWriter uses) is true. None of this explains why you are getting double bonds in the output. Are you *sure* that there are double bonds? The bond type flag in the output mol blocks is really equal to "2"? Could it be that your viewer is seeing aromatic bonds in the output (bond type "4") and drawing them as double bonds? -greg ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
