Author: bugman Date: Thu Dec 11 11:20:03 2014 New Revision: 27082 URL: http://svn.gna.org/viewcvs/relax?rev=27082&view=rev Log: Converted the structure.rmsd user function to the new pipes/models/molecules/atom_id design. This allows the RMSD calculation to work on atomic coordinates from different data pipes, different structural models, and different molecules. The user function backend uses the new pipe_control.structure.main.assemble_coordinates() function. The Structure.test_rmsd_molecules system test has been updated for the user function argument changes. Modified: trunk/pipe_control/structure/main.py trunk/test_suite/system_tests/structure.py trunk/user_functions/structure.py Modified: trunk/pipe_control/structure/main.py URL: http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27082&r1=27081&r2=27082&view=diff ============================================================================== --- trunk/pipe_control/structure/main.py (original) +++ trunk/pipe_control/structure/main.py Thu Dec 11 11:20:03 2014 @@ -998,15 +998,17 @@ cdp.structure.load_xyz(file_path, read_mol=read_mol, set_mol_name=set_mol_name, read_model=read_model, set_model_num=set_model_num, verbosity=verbosity) -def rmsd(atom_id=None, models=None, molecules=None): +def rmsd(pipes=None, models=None, molecules=None, atom_id=None): """Calculate the RMSD between the loaded models. - @keyword atom_id: The molecule, residue, and atom identifier string. Only atoms matching this selection will be used. + @keyword pipes: The data pipes to determine the RMSD for. + @type pipes: None or list of str + @keyword models: The list of models to determine the RMSD for. The number of elements must match the pipes argument. If set to None, then all models will be used. + @type models: None or list of lists of int + @keyword molecules: The list of molecules to determine the RMSD for. The number of elements must match the pipes argument. + @type molecules: None or list of lists of str + @keyword atom_id: The atom identification string of the coordinates of interest. This matches the spin ID string format. @type atom_id: str or None - @keyword models: The list of models to calculate the RMSD of. If set to None, then all models will be used. - @type models: list of int or None - @keyword molecules: The list of molecules to calculate the RMSD between. This overrides the models. - @type molecules: None or list of str @return: The RMSD value. @rtype: float """ @@ -1014,53 +1016,8 @@ # Test if the current data pipe exists. check_pipe() - # The selection object. - selection = cdp.structure.selection(atom_id=atom_id) - - # RMSD between models. - if molecules == None: - # Create a list of all models. - if models == None: - models = [] - for model in cdp.structure.model_loop(): - models.append(model.num) - - # Assemble the atomic coordinates of all models. - coord = [] - for model in models: - coord.append([]) - for pos in cdp.structure.atom_loop(selection=selection, model_num=model, pos_flag=True): - coord[-1].append(pos[0]) - coord[-1] = array(coord[-1]) - - # RMSD between structures. - else: - # No models allowed. - if cdp.structure.num_models() > 1: - raise RelaxError("When calculating the RMSD between different molecules, no models are allowed to be present.") - - # Assemble the atomic coordinates of all molecules. - coord = [] - current_mol = '' - for mol_name, pos in cdp.structure.atom_loop(selection=selection, mol_name_flag=True, pos_flag=True): - # No molecule match, so skip. - if mol_name not in molecules: - continue - - # A new molecule. - if mol_name != current_mol: - # Change the current molecule name. - current_mol = mol_name - - # Extend the coordinates. - coord.append([]) - - # Append the coordinate. - coord[-1].append(pos[0]) - - # Numpy conversion. - for i in range(len(coord)): - coord[i] = array(coord[i]) + # Assemble the atomic coordinates. + coord, ids = assemble_coordinates(pipes=pipes, molecules=molecules, models=models, atom_id=atom_id) # Calculate the RMSD. cdp.structure.rmsd = atomic_rmsd(coord, verbosity=1) Modified: trunk/test_suite/system_tests/structure.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=27082&r1=27081&r2=27082&view=diff ============================================================================== --- trunk/test_suite/system_tests/structure.py (original) +++ trunk/test_suite/system_tests/structure.py Thu Dec 11 11:20:03 2014 @@ -4262,7 +4262,7 @@ self.interpreter.structure.add_atom(atom_name='A', res_name='UNK', res_num=3, mol_name='Z', pos=[-1., 20., 1.], element='S') # Calculate the RMSD. - self.interpreter.structure.rmsd(molecules=['X', 'Y', 'Z']) + self.interpreter.structure.rmsd(molecules=[['X', 'Y', 'Z']]) # Checks. self.assert_(hasattr(cdp.structure, 'rmsd')) Modified: trunk/user_functions/structure.py URL: http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=27082&r1=27081&r2=27082&view=diff ============================================================================== --- trunk/user_functions/structure.py (original) +++ trunk/user_functions/structure.py Thu Dec 11 11:20:03 2014 @@ -1052,30 +1052,46 @@ # The structure.rmsd user function. uf = uf_info.add_uf('structure.rmsd') -uf.title = "Determine the RMSD between the models." +uf.title = "Determine the RMSD between structures." uf.title_short = "Structural RMSD." uf.add_keyarg( + name = "pipes", + py_type = "str_list", + desc_short = "data pipes", + desc = "The data pipes to determine the RMSD for.", + wiz_combo_iter = pipe_names, + wiz_read_only = False, + can_be_none = True +) +uf.add_keyarg( + name = "models", + py_type = "int_list_of_lists", + desc_short = "model list for each data pipe", + desc = "The list of models for each data pipe to determine the RMSD for. The number of elements must match the pipes argument. If no models are given, then all will be used.", + can_be_none = True +) +uf.add_keyarg( + name = "molecules", + py_type = "str_list_of_lists", + desc_short = "molecule list for each data pipe", + desc = "The list of molecules for each data pipe to determine the RMSD for. The RMSD will only be calculated for atoms with identical residue name and number and atom name. The number of elements must match the pipes argument. If no molecules are given, then all will be used.", + can_be_none = True +) +uf.add_keyarg( name = "atom_id", py_type = "str", desc_short = "atom identification string", - desc = "The atom identification string.", - can_be_none = True -) -uf.add_keyarg( - name = "molecules", - py_type = "str_list", - desc_short = "molecule list", - desc = "The optional molecule list to perform the RMSD calculation on rather than the models. The RMSD will only be calculated for atoms with identical residue name and number and atom name.", + desc = "The atom identification string of the coordinates of interest.", can_be_none = True ) # Description. uf.desc.append(Desc_container()) uf.desc[-1].add_paragraph("This allows the root mean squared deviation (RMSD) between all models to be calculated.") uf.desc[-1].add_paragraph("The atom ID, which uses the same notation as the spin ID strings, can be used to restrict the RMSD calculation to certain molecules, residues, or atoms.") -uf.desc[-1].add_paragraph("If the optional molecules list is supplied, then the RMSD calculation will be between the molecules in the list rather than the models. Therefore no models are allowed to be present in the current data pipe.") +uf.desc[-1].add_paragraph("If the optional molecules list is supplied, then the RMSD calculation will be between the molecules in the list.") # Prompt examples. uf.desc.append(Desc_container("Prompt examples")) -uf.desc[-1].add_paragraph("To determine the RMSD, simply type:") +uf.desc[-1].add_paragraph("To determine the RMSD of all models in the current data pipe, simply type:") uf.desc[-1].add_prompt("relax> structure.rmsd()") uf.backend = pipe_control.structure.main.rmsd uf.menu_text = "&rmsd"