Dear Greg,
Now I have found that Compute2DCoords(m) failing in Atom::getNumImplicitHs()
on
PRECONDITION(d_implicitValence>-1, "getNumImplicitHs() called without
preceding call to calcImplicitValence()")
mol it trying to process: [*]NC(=N)N[*]
>To have a chance at getting something reasonable for
>fragments, you probably ought to generate 2D coordinates for the full
>molecule, then manually set the positions of the atoms in the
>fragment's conformer.
And how I can do that?
Regards,
Evgueni
2009/7/6 Greg Landrum <greg.land...@gmail.com>
> Dear Evgueni,
>
>
> On Mon, Jul 6, 2009 at 8:03 PM, Evgueni Kolossov<ekolos...@gmail.com>
> wrote:
> >
> > To display structure I need to put string MDLMol into the control.
> >
> > If I call compute2DCoords - it raised an exception but if do not - all
> >
> > atoms in one dot and you cannot see it at all The same is if I try to
> >
> > read call sanitizeMol.
> >
> > Looking like problem in Kekilizer because some of my fragments can
> >
> > contain atoms and bonds taken from the aromatic ring (and it must be so).
> >
> > Simple fragments like chain fragments displayed Ok because they are
> >
> > not causing exception in compute2Dcoords.
>
> RDKit::MolToMolBlock (or MolToMolFile) each take an optional kekulize
> argument (the last one). If you set this to false, the mol file writer
> will not attempt to kekulize aromatic bonds. Here's an example of
> doing this from python:
> ------------
> [72]>>> m = Chem.MolFromSmiles('cccc',sanitize=False)
> [73]>>> AllChem.Compute2DCoords(m)
> Out[73] 0
> [74]>>> print Chem.MolToMolBlock(m,kekulize=False)
>
> RDKit 2D
>
> 4 3 0 0 0 0 0 0 0 0999 V2000
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.0000 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.0000 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 4 0
> 2 3 4 0
> 3 4 4 0
> M END
> ------------
>
> A note: as this example shows the coordinates generated by the
> depictor for unsanitized molecules are likely to be less than
> pleasing. To have a chance at getting something reasonable for
> fragments, you probably ought to generate 2D coordinates for the full
> molecule, then manually set the positions of the atoms in the
> fragment's conformer.
>
> Best Regards,
> -greg
>
