Hi All,
I've been tinkering a bit more with RDKit and having fun.
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
What makes 3D coordinates? (I'm guessing it's a one-liner somewhere...)
Cheers,
Paul.
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