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
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