Hi JP,
When you generate a mol from a smiles I don't think a conformer is added by
default.
So you have to do this yourself:
molecule = Chem.MolFromSmiles('CCCC')
mol_h = AllChem.AddHs(molecule)
mol_h.AddConformer(Chem.Conformer(mol_h.GetNumAtoms()))
ff = AllChem.UFFGetMoleculeForceField(mol_h)
energy_value = str(ff.CalcEnergy())
print energy_value
Should at least get rid of the error ... not that the above code is tested ...
plus it obviously doesn't make any sense since all coordinates will be 0.0 :(
Ciao
Nik
From: JP [mailto:[email protected]]
Sent: Friday, January 13, 2012 1:07 PM
To: [email protected]
Subject: [Rdkit-discuss] UFF energy question(s)...
Hi there, (using RDKit 2011.09.01)
Any ideas why
molecule = Chem.MolFromSmiles('CCCC')
mol_h = AllChem.AddHs(molecule)
ff = AllChem.UFFGetMoleculeForceField(mol_h)
energy_value = str(ff.CalcEnergy())
print energy_value
Gives me:
Traceback (most recent call last):
File "./energy_test.py", line 8, in <module>
ff = AllChem.UFFGetMoleculeForceField(mol_h)
ValueError: Bad Conformer Id
There are no conformers in the molecule - so the default (implicit) confId -1
should do the work no?
This code somehow works when I use suppliers...
Also, any ideas what the energy units returned from ff.CalcEnergy() are? They
must be in calories (not K/cal) as they are massive. Correct?
-
Jean-Paul Ebejer
Early Stage Researcher
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