Re: [Rdkit-discuss] Sanitizing SD file

On Thu, Dec 14, 2017 at 6:35 AM, Francois BERENGER < beren...@bioreg.kyushu-u.ac.jp> wrote: > On 12/14/2017 02:10 PM, Greg Landrum wrote: > > > > On Thu, Dec 14, 2017 at 4:22 AM, Francois BERENGER > > mailto:beren...@bioreg.kyushu-u.ac.jp>> > > wrote: > > > > On 12/14/2017 05:15 AM, Sundar wro

Re: [Rdkit-discuss] Sanitizing SD file

On 12/14/2017 02:10 PM, Greg Landrum wrote: > > On Thu, Dec 14, 2017 at 4:22 AM, Francois BERENGER > mailto:beren...@bioreg.kyushu-u.ac.jp>> > wrote: > > On 12/14/2017 05:15 AM, Sundar wrote: > > Hi RDkit users, > > > > I encounter following sanitize issue while I was trying to lo

Re: [Rdkit-discuss] SanitizeMol changing drawing

Hi Jason, This is a nice one. Here's what's going on: The depiction code (the piece that generates 2D coordinates) attempts to generate "canonical" coordinates : it tries to generate the same coordinates for a molecule no matter what the input atom ordering is. In order to do that it needs a cano

Re: [Rdkit-discuss] Sanitizing SD file

On Thu, Dec 14, 2017 at 4:22 AM, Francois BERENGER < beren...@bioreg.kyushu-u.ac.jp> wrote: > On 12/14/2017 05:15 AM, Sundar wrote: > > Hi RDkit users, > > > > I encounter following sanitize issue while I was trying to load an SD > > file using > > Chem.SDMolSupplier('lig.sdf') > > > > Explicit va

Re: [Rdkit-discuss] Sanitizing SD file

On 12/14/2017 05:15 AM, Sundar wrote: > Hi RDkit users, > > I encounter following sanitize issue while I was trying to load an SD > file using > Chem.SDMolSupplier('lig.sdf') > > Explicit valence for atom # 16 N, 4, is greater than permitted > ERROR: Could not sanitize molecule ending on line 314

Re: [Rdkit-discuss] Sanitizing SD file

Hello Sundar, Without access to your sd file I cannot be sure. But it is likely that you have a nitrogen with a valence exceeding 4. You may need to, e.g., change the N=O form into [N+][O-]. You may take a look at some of the following threads. https://www.mail-archive.com/rdkit-discuss@lists.sou

[Rdkit-discuss] SanitizeMol changing drawing

using the recent release, m = Chem.MolFromSmiles("N[C@@H](C)C(=O)O") m2 = Chem.MolFromSmiles("N[C@@H](C)C(=O)O") Chem.rdmolops.SanitizeMol(m2) The two molecules above seem identical - MolFromSmiles already performs a sanitization so why wouldn't they be? They produce the same pickle, pickle.

[Rdkit-discuss] Sanitizing SD file

Hi RDkit users, I encounter following sanitize issue while I was trying to load an SD file using Chem.SDMolSupplier('lig.sdf') Explicit valence for atom # 16 N, 4, is greater than permitted ERROR: Could not sanitize molecule ending on line 3145 The molecule RDkit complains about has a charged N

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()

Re: [Rdkit-discuss] ?==?utf-8?q? Similarity maps using machine learning

Hi, Getting the similarity maps for multiple structures should be straightforward, just add the function call in your loop. Concerning the export of the generated images to a web service, I did the following: (assuming the figure returned by the SimilarityMaps.GetSimilarityMapForModel() functi