Hi,
Based on src/conformer.cpp:
OBMol mol; // read a molecule...
OBRototList rotorList
rotorList.Setup(mol);
if (!rotorList.Size()) { // only one conformer
return;
}
// create some random rotor keys
RotorKey rotorKey(rotorList.Size() + 1, 0); // indexed from 1
rotorKeys.push_back(rotorKey);
OBRandom generator;
generator.TimeSeed();
int tries = 0;
while (rotorKeys.size() < numConformers && tries < numConformers * 1000) {
tries++;
// perform random mutation(s)
OBRotorIterator ri;
OBRotor *rotor = rotorList.BeginRotor(ri);
for (int i = 1; i < rotorList.Size() + 1; ++i, rotor =
rotorList.NextRotor(ri)) {
rotorKey[i] = generator.NextInt() % rotor->GetResolution().size();
}
// add the key
rotorKeys.push_back(rotorKey);
}
OBRotamerList rotamers;
rotamers.SetBaseCoordinateSets(mol);
rotamers.Setup(mol, m_rotorList);
// Add all rotor keys
for (unsigned int i = 0; i < m_rotorKeys.size(); ++i)
rotamers.AddRotamer(m_rotorKeys[i]);
// Get conformers for the rotor keys
std::vector<double*> conformers;
rotamers.ExpandConformerList(mol, conformers);
if (conformers.size())
mol.SetConformers(conformers);
Most of the code is populating the rotorKeys variable but it outlines
how to go from the start to real conformers. Documentation on this is
not that clear as you mentioned.
Tim
On Wed, Jul 25, 2012 at 10:01 PM, Kasper Thofte <kasper.tho...@gmail.com> wrote:
> Hello
>
> I am trying to go from a set of rotorKeys (lists of integers, conforming to
> the rotor rules) to a set of conformers attached to the OBMol object, given
> a base coordinate set (which I take to mean bond angles and lengths and
> dihedrals including non-heavy atoms).
>
> The example given in the OBRotamerList docs page,
> http://openbabel.org/api/current/classOpenBabel_1_1OBRotamerList.shtml#_details,
> seems to me to be doing this. However, when I try it and call
> mol.NumConformers, I get zero conformers.
>
> I apologize if this question is answered by looking at the docs, but I'm
> kinda stuck here. I just want to go from rotorkeys to multiple conformers in
> an OBMol object, given the base coordinates.
>
> Thanks
>
> Kasper
>
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