Re: [Rdkit-discuss] Stereo information lost

Thanks! It works great! > El 13 dic 2017, a las 12:15, Paolo Tosco escribió: > > Hi Marina, > > If you wish to assign stereochemistry from the atom block parity flag rather > than from 3D coordinates you might try the following: > > #include > #include > #include > #include > #include >

Re: [Rdkit-discuss] Stereo information lost

Hi Marina, If you wish to assign stereochemistry from the atom block parity flag rather than from 3D coordinates you might try the following: #include #include #include #include #include int main(int argc, char **argv) {     std::string in_file_name = "zinc_3833800.sdf";     RDKit::SDMo

Re: [Rdkit-discuss] Stereo information lost

Ok thank you for the help! Marina > El 13 dic 2017, a las 11:22, Greg Landrum escribió: > > > On Wed, Dec 13, 2017 at 10:39 AM, Marina Garcia de Lomana > mailto:m.garciadelom...@gmail.com>> wrote: > Thanks for your answer Paolo! > But I would need to read in the stereochemistry information fr

Re: [Rdkit-discuss] Stereo information lost

On Wed, Dec 13, 2017 at 10:39 AM, Marina Garcia de Lomana < m.garciadelom...@gmail.com> wrote: > Thanks for your answer Paolo! > But I would need to read in the stereochemistry information from the SD > file (7th column in the atom block) and not calculate the chirality from > the coordinates, sin

Re: [Rdkit-discuss] Stereo information lost

Thanks for your answer Paolo! But I would need to read in the stereochemistry information from the SD file (7th column in the atom block) and not calculate the chirality from the coordinates, since this way the information about racemates would get lost. Is there a way to do that? > El 13 dic

Re: [Rdkit-discuss] Stereo information lost

Hi Marina, I assume you are using this SDF file: http://zinc11.docking.org/fget.pl?l=0&z=57393683&f=d which contains 3D coordinates and no wedge bond information. If this is the case, you will need to call MolOps::assignStereochemistryFrom3D()

[Rdkit-discuss] Stereo information lost

Hi, I am using the following C++ script to read a molecule from a SD file (with defined stereochemistry), but the information about the stereochemistry gets lost. The file I am using is from glucose (ZINC03833800; http://zinc.docking.org/substance/3833800