Hi Paul,
On Fri, Sep 10, 2010 at 7:29 PM, Paul Emsley <paul.ems...@bioch.ox.ac.uk> wrote:
>
> I've been tinkering a bit more with RDKit and having fun.
Glad to hear it.
> I have hit a problem though. I am trying to reproduce Greg's "Generating
> 3D coordinates" in RDKit-overview.pdf in C++:
>
> This is what I have (mostly via cut 'n paste):
>
>
>
> int
> main(int argc, char **argv) {
>
> std::string smiles_string = "C1CCC1";
>
> RDKit::RWMol *mol=new RDKit::RWMol();
> mol = RDKit::SmilesToMol(smiles_string);
> RDDepict::compute2DCoords(*mol);
>
> double vdwThresh=10.0;
> int confId = -1;
> bool ignoreInterfragInteractions=true;
> int maxIters = 200;
>
> ForceFields::ForceField *ff =
> RDKit::UFF::constructForceField(*mol,
> vdwThresh, confId,
> ignoreInterfragInteractions);
> ff->initialize();
> int res=ff->minimize(maxIters);
> delete ff;
>
> std::cout << RDKit::MolToMolBlock(*mol, true, -1) << std::endl;
>
> return 0;
> }
>
>
> But I get 2D coordinates:
>
>
> RDKit 2D
>
> 5 5 0 0 0 0 0 0 0 0999 V2000
> 1.2879 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.3980 1.2249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.0419 0.7570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.0419 -0.7570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.3980 -1.2249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> 2 3 1 0
> 3 4 1 0
> 4 5 1 0
> 5 1 1 0
> M END
>
It's kind of interesting (and encouraging) that the optimizer doesn't
completely freak out when you hand it a 2D conformer. :-)
> What makes 3D coordinates? (I'm guessing it's a one-liner somewhere...)
It is indeed a one-liner (two lines with a bit of error checking). To
get a 3D conformer, you need to include
<GraphMol/DistGeomHelpers/Embedder.h> and do the following:
int cid = DGeomHelpers::EmbedMolecule(*m);
if(cid<0) // embedding failed, do something
There are a bunch of optional arguments to EmbedMolecule, but the
defaults normally work reasonably well.
Best Regards,
-greg
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