Looks like something's up. I'll look into it. In the meanwhile, as a
workaround, try adding a bond between the two dimers.
- Noel
On 6 January 2014 08:51, Igor Leontyev <ileont...@ucdavis.edu> wrote:
> Dear OB community,
>
> I'm faced with a problem of computing RMSD with symmetry correction. My
> code (given bellow) uses RMSD for detection of duplicates in ensemble of
> configurations of molecular dimers. The problem is that computed RMSDs are
> not always equal to zero (e.g. 0.5 or 2.0) for the same Reference and Target
> configuration, i.e. when j==i. The problem disappears once I turn off
> symmetry but the symmetry in necessary for my goal. Watching variables at
> run time showed that RMSD for "0" permutation has unphysically high value
> ~10^66 instead of 0.
>
> Note, order of atoms is the same for all configurations. I am attaching
> input files with canonical and noncanonical order of atoms. Canonical order
> provides more correct RMSDs but not always. I use openbabel-2.3.2 compiled
> with Eigen3.2.0.
>
>
> Any suggestions?
>
> Thank you,
> Igor
>
>
> RMSD CODE
> ////////////////////////////////////////////////////////
> std::vector<OBMol> Conf;
> OBMol mol;
>
> //Read DIMER configurations
> for (;;)
> {
> mol.Clear();
> conv.Read(&mol,&ifs); // Read molecule
> if (mol.Empty())
> break;
> Conf.push_back(mol);
> }
> // Compute RMSD
> OBAlign MyAlign(true,true);
> for (int i = 0; i<Conf.size(); i++) {
> MyAlign.SetRefMol(Conf[i]);
> for (int j=i; j<Conf.size(); j++) {
> MyAlign.SetTargetMol(Conf[j]);
> MyAlign.Align();
> rmsd = MyAlign.GetRMSD(); // Get rmsd with symmetry
> printf("%d %d RMSD =%14.8f\n",i,j,rmsd);
> }
> }
> ////////////////////////////////////////////////////////
>
>
>
>
>
>
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