Hi RDKitters,
I would like to consider parts of a conformation rigid (fixed dihedral
angles) during minimization
My end goal would be to generate only ring conformations starting with
valid 3D molecules.
I can already consider a specific dihedral angle as rigid:
from rdkit import Chem
from rdkit.Chem import AllChem, rdMolTransforms
# create test mol
s = 'COCCN1CCOCC1'
m = Chem.MolFromSmiles(s)
m = Chem.AddHs(m)
# add 3D coordinates
AllChem.EmbedMolecule(m)
# freeze one dihedral angle (composed of atoms 0-3)
MMFFs_MP = AllChem.MMFFGetMoleculeProperties(m, mmffVariant='MMFF94s')
MMFFs_FF = AllChem.MMFFGetMoleculeForceField(m, MMFFs_MP)
MMFFs_FF.MMFFAddTorsionConstraint(0, 1, 2, 3, relative=True,
minDihedralDeg=0.0, maxDihedralDeg=0.0,forceConstant=99999999999999.0)
c = m.GetConformer()
print "before min", rdMolTransforms.GetDihedralDeg(c, 0,1,2,3) #
-53.0873064656
# minimize molecule with constrained dihedral angle
MMFFs_FF.Minimize(maxIts=10)
print "after first min", rdMolTransforms.GetDihedralDeg(c,0,1,2,3) #
-53.0873064656
MMFFs_FF.Minimize(maxIts=10)
print "after second min", rdMolTransforms.GetDihedralDeg(c,0,1,2,3) #
-53.0873064656
However, I have difficulties to find all dihedral angles to consider
rigid...
I would like to detect dihedral angles with 4 atoms where:
- none is hydrogen
- no more than 2 atoms are in different rings
First I looked for a function to return me the list of dihedral angles
and iterate over it, but could not find any.
My other alternative would be to iterate over atoms to get their
neighbors, and then get their neighbor' neighbors, but that looks very
very slow.
Any other way to do this?
Thank you!
Jose Manuel
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