Author: bugman
Date: Wed Dec 10 17:03:24 2014
New Revision: 27059
URL: http://svn.gna.org/viewcvs/relax?rev=27059&view=rev
Log:
Implemented the new molecules argument for the structure.rmsd user function.
This allows the RMSD between different molecules rather than different models
to be calculated,
extending the functionality of this user function.
Modified:
trunk/pipe_control/structure/main.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=27059&r1=27058&r2=27059&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Wed Dec 10 17:03:24 2014
@@ -1108,13 +1108,15 @@
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):
+def rmsd(atom_id=None, models=None, molecules=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.
@type atom_id: str or None
- @keyword models: The list of models to calculate the RMDS of. If set
to None, then all models will be used.
+ @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
"""
@@ -1122,22 +1124,53 @@
# Test if the current data pipe exists.
check_pipe()
- # Create a list of all models.
- if models == None:
- models = []
- for model in cdp.structure.model_loop():
- models.append(model.num)
-
# The selection object.
selection = cdp.structure.selection(atom_id=atom_id)
- # 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):
+ # 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])
- coord[-1] = array(coord[-1])
+
+ # Numpy conversion.
+ for i in range(len(coord)):
+ coord[i] = array(coord[i])
# Calculate the RMSD.
cdp.structure.rmsd = atomic_rmsd(coord, verbosity=1)
Modified: trunk/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=27059&r1=27058&r2=27059&view=diff
==============================================================================
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Wed Dec 10 17:03:24 2014
@@ -1041,17 +1041,25 @@
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.",
+ 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.")
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To determine the RMSD, simply type:")
uf.desc[-1].add_prompt("relax> structure.rmsd()")
uf.backend = pipe_control.structure.main.rmsd
uf.menu_text = "&rmsd"
-uf.wizard_size = (700, 500)
+uf.wizard_size = (800, 600)
uf.wizard_image = WIZARD_IMAGE_PATH + 'structure' + sep + '2JK4.png'
r27059 - in /trunk: pipe_control/structure/main.py user_functions/structure.py