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

2017-12-13 Thread gregori
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()

Re: [Rdkit-discuss] Stereo information lost

2017-12-13 Thread Paolo Tosco
Hi Marina, I assume you are using this SDF file: http://zinc11.docking.org/fget.pl?l=0=57393683=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] Stereo information lost

2017-12-13 Thread Paolo Tosco
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";    

Re: [Rdkit-discuss] Stereo information lost

2017-12-13 Thread Marina Garcia de Lomana
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 > > wrote: > Thanks for your answer Paolo! > But I

Re: [Rdkit-discuss] Sanitizing SD file

2017-12-13 Thread Greg Landrum
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

Re: [Rdkit-discuss] SanitizeMol changing drawing

2017-12-13 Thread Greg Landrum
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

Re: [Rdkit-discuss] Sanitizing SD file

2017-12-13 Thread Francois BERENGER
On 12/14/2017 02:10 PM, Greg Landrum wrote: > > On Thu, Dec 14, 2017 at 4:22 AM, Francois BERENGER > > > wrote: > > On 12/14/2017 05:15 AM, Sundar wrote: > > Hi RDkit users, > > > > I encounter following

Re: [Rdkit-discuss] Sanitizing SD file

2017-12-13 Thread Greg Landrum
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 > > > > > wrote: > > > >

Re: [Rdkit-discuss] Sanitizing SD file

2017-12-13 Thread Francois BERENGER
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

Re: [Rdkit-discuss] Sanitizing SD file

2017-12-13 Thread Ling Chan
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.

[Rdkit-discuss] SanitizeMol changing drawing

2017-12-13 Thread Jason Biggs
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,