Re: [Rdkit-discuss] regarding hydrogens from SMILES

Hi Jorgen, Which version of RDKit are you using? The ETKDG conformer generator (which will keep sp2 centers flat) has become only recently the default. If you are using an older RDKit version, the following code should give you a flat aromatic system for the SMILES you provided in your

[Rdkit-discuss] regarding hydrogens from SMILES

Hi all, I am trying to built 3D structures from SMILES which for most of the molecules works fine - I get the SMILES from pubchem ('canonical_smiles' and 'isomeric_smiles') but some of the molecules they hydrogens are not added correctly and are out of plane - e.g. amide group in ATP ( see below

Re: [Rdkit-discuss] regarding hydrogens from SMILES

Cheers Paolo, It looks like that it keeps sp3 as the optimal geometry and not sp2. The optimization did converge : AllChem.MMFFOptimizeMolecule(m2,) #returned 1 I think it is getting the types wrong or I have to specify the types? On Tue, Oct 8, 2019 at 10:10 AM Paolo Tosco wrote: > Hi

Re: [Rdkit-discuss] regarding hydrogens from SMILES

Dear Sereina and Paolo, Thank you for your replies and they both seemed to correct the problem. I really like to do it during the embedding of the molecule. cheers! On Tue, Oct 8, 2019 at 12:34 PM Sereina wrote: > Hi Jorgen, > > Which version of RDKit are you using? The ETKDG conformer

Re: [Rdkit-discuss] regarding hydrogens from SMILES

Hi Jorgen, use the MMFF94s variant of the forcefield if you wish to force trigonal nitrogens to be planar: AllChem.MMFFOptimizeMolecule(m2, mmffVariant="MMFF94s") More information here: https://doi.org/10.1002/(SICI)1096-987X(199905)20:7%3C720::AID-JCC7%3E3.0.CO;2-X Cheers, p. On 10/08/19

[Rdkit-discuss] Inchi which flavour??

Dear RdKit users,I was reading the inchi module docs and I couldn't find methods to call the InChI API.  Are these exposed in RDKit?  It says the default is the standard Inchi.  What happens when this conversion fails? Thanks,Mike___ Rdkit-discuss

Re: [Rdkit-discuss] regarding hydrogens from SMILES

Hi Jorgen, optimizing your molecule geometry with UFF or MMFF should fix the problem: AllChem.UFFOptimizeMolecule(m2) or AllChem.MMOptimizeMolecule(m2) see rdkit.Chem.rdForceFieldHelpers.UFFOptimizeMolecule

[Rdkit-discuss] change SMILES based on charge state of molecule

Hi all, I am try to change my SMILES of a bunch of small molecules that I have downloaded from pubchem. The problem is that the charge in the physiological state of the molecule differs from string from pubchem e.g. ATP charge 0: SMILES =

Re: [Rdkit-discuss] Inchi which flavour??

Hi Mike, The InChI API itself is not exposed. The contents of the module are in the documentation along with some explanations of how to call it: http://rdkit.org/docs/source/rdkit.Chem.rdinchi.html If something is missing there, please let us know. -greg On Tue, Oct 8, 2019 at 5:20 PM wrote: