Yes, as Igor suggests, calling DGeomHelpers::EmbedMolecule will
generate a set of 3D coordinates for the molecule.
The conformations that one gets from EmbedMolecule aren't particularly
nice looking, so if you'd like the 3D coordinates to be a little
nicer, try cleaning them up:
ForceFields::ForceField *ff=UFF::constructForceField(*mol);
ff->initialize();
int res=1;
while res {
res=ff->minimize();
}
delete ff;
If you'd rather have 2D coordinates for the molecules, do this instead:
RDDepict::compute2DCoords(*mol)
Best Regards,
-greg
On Fri, Aug 8, 2008 at 2:10 PM, Igor Filippov <[email protected]> wrote:
> Add this on top:
> DGeomHelpers::EmbedMolecule(*mol);
>
> Igor
>
> On Fri, 2008-08-08 at 13:07 +0100, Evgueni Kolossov wrote:
>> Thanks - this is kind of works.
>> Unfortunately there is no atomic coordinates generated - how we can do
>> this? Otherwise it will display just single dot.
>>
>> Regards,
>> Evgueni
