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 <paolo.tosco.m...@gmail.com> wrote: > Hi Jorgen, > > optimizing your molecule geometry with UFF or MMFF should fix the problem: > > AllChem.UFFOptimizeMolecule(m2) > > or > > AllChem.MMFFFFOptimizeMolecule(m2) > > see rdkit.Chem.rdForceFieldHelpers.UFFOptimizeMolecule > <https://www.rdkit.org/docs/source/rdkit.Chem.rdForceFieldHelpers.html?highlight=optimize#rdkit.Chem.rdForceFieldHelpers.UFFOptimizeMolecule> > or rdkit.Chem.rdForceFieldHelpers.MMFFOptimizeMolecule > <https://www.rdkit.org/docs/source/rdkit.Chem.rdForceFieldHelpers.html?highlight=optimize#rdkit.Chem.rdForceFieldHelpers.MMFFOptimizeMolecule> > . > > Cheers, > p. > > On 10/08/19 14:41, Jorgen Simonsen wrote: > > 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 > for an example or arginine in a peptide). > > I use the following code to generate the 3D structure : > > from rdkit import Chem > from rdkit.Chem import AllChem > m1 = > Chem.MolFromSmiles('C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N') > > m2 = Chem.AddHs(m1) > AllChem.EmbedMolecule(m2) > > w = Chem.SDWriter('foo.sdf') > w.write(m2) > > # or to mol file > > print(Chem.MolToMolBlock(m2),file=open('foo.mol','w+')) > > How to insure that the atomtype are correct ? > > Thanks in advance > > Best > Jorgen > > > > > > > > > > > > _______________________________________________ > Rdkit-discuss mailing > listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > >
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