|
Hi Nick,
would you mind sending me the SD file which is triggering the
infinite loop? Then I'll come back to you as soon as I find out
something.
Best,
p.
On 10/08/2013 11:36 AM, Nicholas Firth wrote:
Hi RDKitters,
I'm having an issue using the MMFF to minimise a CORINA
conformation. I've written a little script which adds hydrogens
to a molecule then tries to use the MMFF forcefield to minimise
the conformer. The problem is that the script hangs on the
minimise step.
This error only occurs when I add hydrogens to the
conformation, I assume the reason for this is because the
hydrogens are all added at the origin. Is there a way of getting
round this (in RDKit, as I want to keep the AddHs function)?
I've included the script below, it will work like this
however if you switch wrong the commented lines in the first for
loop then the it no longer works.
from
rdkit import Chem
from
rdkit.Chem import
AllChem
from
rdkit.Chem import
ChemicalForceFields
from
sys import argv
suppl = Chem.SDMolSupplier(argv[1])
molList = []
for
mol in suppl:
#molList.append(Chem.AddHs(mol))
molList.append(mol)
del
suppl
#w =
Chem.SDWriter(argv[1])
w = Chem.SDWriter('test.sdf')
for
mol in molList:
mp =
ChemicalForceFields.MMFFGetMoleculeProperties(mol)
field =
AllChem.MMFFGetMoleculeForceField(mol, mp)
field.Minimize()
w.write(mol)
w.close()
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