Hi Tim
Right you are =D
That fixed my problem!
Thanks a lot
Kasper
On Thu, Jul 26, 2012 at 1:27 AM, Tim Vandermeersch <
tim.vandermeer...@gmail.com> wrote:
> Hi,
>
> I could not run your example since I don't know what the repr_mols
> contains and don't have split(), is_any_of() and token_compress_on.
> However, I suspect that your rotorKey does not have the correct number
> of elements. The first element is ignored and adding an assert after
> this line:
>
> vector<int> rotorKey(split_vec.size());
>
> add
>
> assert(rotorKey.size() == rl.Size() + 1);
>
> If this assertion fails, change the line to:
>
> vector<int> rotorKey(split_vec.size() + 1);
>
> and
>
> rotorKey[i] = int_;
>
> to
>
> rotorKey[i+1] = int_;
>
> This should fix your problem.
>
> Tim
>
> On Thu, Jul 26, 2012 at 1:03 AM, Kasper Thofte <kasper.tho...@gmail.com>
> wrote:
> > Hi Tim
> >
> > Thanks for your answer. I am guessing that it is mostly the code
> starting at
> > OBRotamerList declaration I need to look at. I did more or less what it
> says
> > in the code snippet, and I still end up with 0 conformers. My code is
> here:
> >
> > OBConversion conv;
> > conv.SetInAndOutFormats("xyz", "mol");
> >
> > OBMol mol;
> > string xyz_file = "coords.xyz";
> > conv.ReadFile(&mol, xyz_file);
> >
> > OBRotamerList rotamers;
> > rotamers.SetBaseCoordinateSets(mol);
> >
> > OBRotorList rl;
> > rl.Setup(mol);
> >
> > rotamers.Setup(mol, rl);
> >
> > ifstream rm_file("repr_mols");
> > string line;
> > while (!rm_file.eof()) {
> > getline(rm_file, line);
> > vector<string> split_vec;
> > split(split_vec, line, is_any_of(" "),
> token_compress_on);
> > vector<int> rotorKey(split_vec.size());
> > for (int i = 0; i < split_vec.size(); i++) {
> > istringstream buffer(split_vec[i]);
> > int int_;
> > buffer >> int_;
> > rotorKey[i] = int_;
> > }
> > rotamers.AddRotamer(rotorKey);
> > }
> > rm_file.close();
> > vector<double*> conformers;
> > rotamers.ExpandConformerList(mol,
> > conformers);//mol.GetConformers());
> > mol.SetConformers(conformers);
> >
> > cout << mol.NumConformers() << endl;
> >
> > What am I doing wrong?
> >
> > Thanks
> >
> >
> > On Wed, Jul 25, 2012 at 10:16 PM, Tim Vandermeersch
> > <tim.vandermeer...@gmail.com> wrote:
> >>
> >> 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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>
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