Dear Michal,
I have the impression that you wanted to select atoms 5,6,7,8, which do
indicate the bond between the two rings, but the RDKit counts atoms
starting from 0, so the tuple
atoms=(5,6,7,8)
should probably read
atoms=(4,5,6,7)
and this actually works; instead, the first tuple indicates a bond
inside a ring.
I hope that I understood the problem correctly; if this is not the case
please let me know.
Kind regards,
Paolo
On 10/22/2013 02:42 PM, Michal Krompiec wrote:
> Hello, I am trying to use the new functionality for manipulation of
> dihedral angles in a function similar to OpenBabel's obrotate tool.
> But it doesn't work: I get a ValueError exception. Here is an example
> that replicates the error:
>
> from rdkit import Chem
> from rdkit.Chem import AllChem
> from rdkit.Chem import rdMolTransforms
>
> mol=Chem.MolFromSmiles('c2ccsc2c1sccc1') #2,2'-bithiophene
> mol=Chem.AddHs(mol)
> AllChem.EmbedMolecule(mol)
> sp=Chem.MolFromSmarts("c2([H])ccsc2c1sccc1")
> atoms=(5,6,7,8)
> newangle=180.0
> maplist = mol.GetSubstructMatches(sp)
> if (len(maplist)>0):
> for match in maplist :
> a=[]
> for i in range (0,4) :
> a.append(match[atoms[i]])
> angle=rdMolTransforms.GetDihedralDeg(mol.GetConformer(), a[0],
> a[1], a[2], a[3])
> print("angle between atoms {}".format(a)+" is
> {}".format(angle))
> print("trying to set to the same angle")
> rdMolTransforms.SetDihedralDeg(mol.GetConformer(), a[0], a[1],
> a[2], a[3], angle) #if you comment this line out
> print("trying to set to another angle")
> rdMolTransforms.SetDihedralDeg(mol.GetConformer(), a[0], a[1],
> a[2], a[3], newangle) #this one will crash as well
> angle=rdMolTransforms.GetDihedralDeg(mol.GetConformer(), a[0],
> a[1], a[2], a[3])
> print("angle between atoms {}".format(a)+" is
> {}".format(angle))
>
> Best wishes,
> Michal Krompiec
>
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--
==========================================================
Paolo Tosco, Ph.D.
Department of Drug Science and Technology
Via Pietro Giuria, 9 - 10125 Torino (Italy)
Tel: +39 011 670 7680 | Mob: +39 348 5537206
Fax: +39 011 670 7687 | E-mail: paolo.to...@unito.it
http://open3dqsar.org | http://open3dalign.org
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