• RE: Problem with atomic coordinates

    Hi,

    I've got some problems. For for example molecule HIZWAQ I've got an error. Could you tell me what does this mean?

     

    TypeError('The symmetry operator %s is not applicable to this crystal' % symmop)
    TypeError: The symmetry operator 1/3+y,2/3-x+y,1.66667-z is not applicable to this crystal
  • RE: Problem with atomic coordinates

    Thank you. It was very helpful.

    Kindest regards

    Anna

  • Problem with atomic coordinates

    Hi,

    I've got a problem with my script for Python API. I'm searching for Bromine atom with distance 3.1-3.5 A from Oxygen atom. Search tool finds some results and the distance in constranints is ok (for first hit 3.1A) and result is compatible with the serch parameters. But when I acces atoms in single hits results and try to manually calculate the distance between them using MolecularDescriptors.atom_distance its different (9.9A). I've chcecked the atom coordinates in my hits results and in Mercury  for oxygen atom and they are different. I used the Python API 2017 and there were no such problem. How can I get good atom coordinates to calculate the distance in my script? Can you help me?

    import ccdc.search
    hal = ccdc.search.SMARTSSubstructure('Br[C,c]')
    acc = ccdc.search.SMARTSSubstructure('C(=O)')
    halogen_bond_search = ccdc.search.SubstructureSearch()
    hal_id = halogen_bond_search.add_substructure(hal)
    acc_id = halogen_bond_search.add_substructure(acc)
    halogen_bond_search.add_distance_constraint('DIST',hal_id, 0,acc_id, 1,(3.1, 3.5),'Intermolecular')
    hits = halogen_bond_search.search(max_hits_per_structure=1)
    dist=[h.constraints['DIST']for h in hits]
    print "Distance from Br to O for the first hit"
    print dist[0]
    X=hits[0].match_atoms()[0]
    Y=hits[0].match_atoms()[3]
    print "Coordinates of Br and O for the first hit"
    print "Br"
    print X.coordinates
    print "O"
    print Y.coordinates
    print "Calculated distance from Br to O for the first hit"
    print ccdc.descriptors.MolecularDescriptors.atom_distance (X,Y)