Yes, exactly, thank you very much! On Fri, Jan 24, 2014 at 12:08 PM, sereina riniker <[email protected]> wrote: > Hi Michael, > > You can get the atom positions via the conformer: > > m = Chem.MolFromSmiles('c1ccccc1') > AllChem.Compute2DCoords() > pos = m.GetConformer().GetAtomPosition(0) # position of atom 0 > > This gives you a rdGeometry.Point3D - e.g. the x coordinates you get with: > > x = pos.x > > I hope this is what you were looking for. > > Best, > Sereina > > > > > 2014/1/24 Michał Nowotka <[email protected]> >> >> Hi, >> >> Let's say I loaded a molfile containing coordinates to RDKit mol >> object or loaded it from smiles but called >> AllChem.Compute2DCoords(mol). >> Now I would like to get coordinates for each atom. Unfortunately Atom >> class doesn't have any GetCoords method but this is understandable >> since position is optional. I tried to look into properties but it >> seems that they are stored in some stage container exported from C++: >> >> for atom in mol.GetAtoms(): >> print atom.GetPropNames() >> ....: >> <rdkit.rdBase._vectSs object at 0xa455aec> >> <rdkit.rdBase._vectSs object at 0xa455aec> >> ... >> >> >> Some blind guesses such as: atom.GetProp('x'), atom.GetProp('X') >> failed. Mol object itself doesn't provide any method that would >> suggest that it can return coordinates.... >> >> So is there any way to get this data without parsing original molfile? >> >> >> Regards, >> >> Michal Nowotka >> >> >> ------------------------------------------------------------------------------ >> CenturyLink Cloud: The Leader in Enterprise Cloud Services. >> Learn Why More Businesses Are Choosing CenturyLink Cloud For >> Critical Workloads, Development Environments & Everything In Between. >> Get a Quote or Start a Free Trial Today. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk >> _______________________________________________ >> Rdkit-discuss mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
------------------------------------------------------------------------------ CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
