To make it clear, the current implementation of RMSD with symmetry does
not support objects that consist of several molecules such as dimers or
multimers.
Thank you Noel for your advice. I may try it.
Igor
On 1/9/2014 1:33 AM, Noel O'Boyle wrote:
> Sorry - my suggestion was dumb. That's not going to work.
>
> The only workaround I can think of is to do the alignment (using
> OBAlign) using the coordinates (rather than the molecule), and juggle
> around the coordinates of the Target yourself based on the 12 * 12
> automorphisms. In other words, get the automorphisms for a benzene
> with the atoms in the same order as in your dimer, and use that
> information to switch around the coordinates.
>
> for automorphA in automorphsA:
> # move coordinates for first benzene
> for automorphB in automorphsB:
> #move coordinates for second benzene
> SetTarget()
> Align()
> GetRMSD()
>
> - Noel
>
> On 8 January 2014 22:15, Noel O'Boyle <baoille...@gmail.com> wrote:
>> 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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