Dear RDKitters,
I have the following test code:
std::string smiles="Clc1ccccc1";
RDKit::ROMol *m_local = RDKit::SmilesToMol(smiles);
RDDepict::compute2DCoords(*m_local);
RDKit::Conformer conf = m_local->getConformer();
WedgeMolBonds(*m_local, &conf);
bool includeStereo = true;
bool kekulize = false;
std::string mol_file_name = "testmol.mol";
RDKit::MolToMolFile(*m_local, mol_file_name, includeStereo, confId,
kekulize);
std::string png_file_name = "image-test.png";
{
RDKit::MolDraw2DCairo drawer(200, 200);
drawer.drawMolecule(*m_local);
drawer.finishDrawing();
drawer.writeDrawingText(png_file_name.c_str());
}
The mol file seems sane (attached) but the png has strangely positioned
atoms (the Cl in this case) (attached).
What am I doing wrong?
(Using RDKit-2015-03-01)
Thanks,
Paul.
RDKit 2D
7 7 0 0 0 0 0 0 0 0999 V2000
3.0000 0.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 4 0
3 4 4 0
4 5 4 0
5 6 4 0
6 7 4 0
7 2 4 0
M END
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