Author: bugman
Date: Wed Dec 10 17:34:55 2014
New Revision: 27062
URL: http://svn.gna.org/viewcvs/relax?rev=27062&view=rev
Log:
Implemented the molecules argument for the structure.displacement user
function.
This allows the displacements (translations and rotations) to be calculated
between different
molecules rather than different models. This information is stored in the
dictionaries of the
cdp.structure.displacement object with the keys set to the molecule list
indices.
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=27062&r1=27061&r2=27062&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Wed Dec 10 17:34:55 2014
@@ -489,7 +489,7 @@
del interatom.vector
-def displacement(model_from=None, model_to=None, atom_id=None,
centroid=None):
+def displacement(model_from=None, model_to=None, atom_id=None,
molecules=None, centroid=None):
"""Calculate the rotational and translational displacement between two
structural models.
@keyword model_from: The optional model number for the starting
position of the displacement.
@@ -498,6 +498,8 @@
@type model_to: int or None
@keyword atom_id: The molecule, residue, and atom identifier
string. This matches the spin ID string format.
@type atom_id: str or None
+ @keyword molecules: The list of molecules to calculate the
displacements between. This overrides the models.
+ @type molecules: None or list of str
@keyword centroid: An alternative position of the centroid,
used for studying pivoted systems.
@type centroid: list of float or numpy rank-1, 3D array
"""
@@ -505,46 +507,88 @@
# Test if the current data pipe exists.
check_pipe()
- # Convert the model_from and model_to args to lists, is supplied.
- if model_from != None:
- model_from = [model_from]
- if model_to != None:
- model_to = [model_to]
-
- # Create a list of all models.
- models = []
- for model in cdp.structure.model_loop():
- models.append(model.num)
-
- # Set model_from or model_to to all models if None.
- if model_from == None:
- model_from = models
- if model_to == None:
- model_to = models
-
- # Initialise the data structure.
- if not hasattr(cdp.structure, 'displacements'):
- cdp.structure.displacements = Displacements()
-
- # The selection object.
- selection = cdp.structure.selection(atom_id=atom_id)
-
- # Loop over the starting models.
- for i in range(len(model_from)):
- # Assemble the atomic coordinates.
- coord_from = []
- for pos in cdp.structure.atom_loop(selection=selection,
model_num=model_from[i], pos_flag=True):
- coord_from.append(pos[0])
-
- # Loop over the ending models.
- for j in range(len(model_to)):
+ # Displacements between models.
+ if molecules == None:
+ # Convert the model_from and model_to args to lists, is supplied.
+ if model_from != None:
+ model_from = [model_from]
+ if model_to != None:
+ model_to = [model_to]
+
+ # Create a list of all models.
+ models = []
+ for model in cdp.structure.model_loop():
+ models.append(model.num)
+
+ # Set model_from or model_to to all models if None.
+ if model_from == None:
+ model_from = models
+ if model_to == None:
+ model_to = models
+
+ # Initialise the data structure.
+ if not hasattr(cdp.structure, 'displacements'):
+ cdp.structure.displacements = Displacements()
+
+ # The selection object.
+ selection = cdp.structure.selection(atom_id=atom_id)
+
+ # Loop over the starting models.
+ for i in range(len(model_from)):
# Assemble the atomic coordinates.
- coord_to = []
- for pos in cdp.structure.atom_loop(selection=selection,
model_num=model_to[j], pos_flag=True):
- coord_to.append(pos[0])
-
- # Send to the base container for the calculations.
- cdp.structure.displacements._calculate(model_from=model_from[i],
model_to=model_to[j], coord_from=array(coord_from), coord_to=array(coord_to),
centroid=centroid)
+ coord_from = []
+ for pos in cdp.structure.atom_loop(selection=selection,
model_num=model_from[i], pos_flag=True):
+ coord_from.append(pos[0])
+
+ # Loop over the ending models.
+ for j in range(len(model_to)):
+ # Assemble the atomic coordinates.
+ coord_to = []
+ for pos in cdp.structure.atom_loop(selection=selection,
model_num=model_to[j], pos_flag=True):
+ coord_to.append(pos[0])
+
+ # Send to the base container for the calculations.
+
cdp.structure.displacements._calculate(model_from=model_from[i],
model_to=model_to[j], coord_from=array(coord_from), coord_to=array(coord_to),
centroid=centroid)
+
+ # Displacements between molecules.
+ 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.")
+
+ # Initialise the data structure.
+ if not hasattr(cdp.structure, 'displacements'):
+ cdp.structure.displacements = Displacements()
+
+ # The selection object.
+ selection = cdp.structure.selection(atom_id=atom_id)
+
+ # Loop over the starting molecules.
+ for i in range(len(molecules)):
+ # Assemble the atomic coordinates.
+ coord_from = []
+ 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 != molecules[i]:
+ continue
+
+ # Add the coordinate.
+ coord_from.append(pos[0])
+
+ # Loop over the ending molecules.
+ for j in range(len(molecules)):
+ # Assemble the atomic coordinates.
+ coord_to = []
+ 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 != molecules[j]:
+ continue
+
+ # Add the coordinate.
+ coord_to.append(pos[0])
+
+ # Send to the base container for the calculations.
+ cdp.structure.displacements._calculate(model_from=i,
model_to=j, coord_from=array(coord_from), coord_to=array(coord_to),
centroid=centroid)
def find_pivot(models=None, atom_id=None, init_pos=None, func_tol=1e-5,
box_limit=200):
Modified: trunk/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=27062&r1=27061&r2=27062&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Wed Dec 10 17:34:55 2014
@@ -3091,15 +3091,15 @@
for i in range(len(molecules)):
for j in range(len(molecules)):
# Check the translation.
-
self.assertAlmostEqual(cdp.structure.displacements._translation_distance[molecules[i]][molecules[j]],
dist[i][j])
+
self.assertAlmostEqual(cdp.structure.displacements._translation_distance[i][j],
dist[i][j])
for k in range(3):
-
self.assertAlmostEqual(cdp.structure.displacements._translation_vector[molecules[i]][molecules[j]][k],
trans_vect[i][j][k])
+
self.assertAlmostEqual(cdp.structure.displacements._translation_vector[i][j][k],
trans_vect[i][j][k])
# Check the rotation.
-
self.assertAlmostEqual(cdp.structure.displacements._rotation_angle[molecules[i]][molecules[j]],
angle[i][j])
+
self.assertAlmostEqual(cdp.structure.displacements._rotation_angle[i][j],
angle[i][j])
if rot_axis[i][j] != None:
for k in range(3):
-
self.assertAlmostEqual(cdp.structure.displacements._rotation_axis[molecules[i]][molecules[j]][k],
rot_axis[i][j][k])
+
self.assertAlmostEqual(cdp.structure.displacements._rotation_axis[i][j][k],
rot_axis[i][j][k])
# Save the results.
self.tmpfile = mktemp()
@@ -3116,15 +3116,15 @@
for i in range(len(molecules)):
for j in range(len(molecules)):
# Check the translation.
-
self.assertAlmostEqual(cdp.structure.displacements._translation_distance[molecules[i]][molecules[j]],
dist[i][j])
+
self.assertAlmostEqual(cdp.structure.displacements._translation_distance[i][j],
dist[i][j])
for k in range(3):
-
self.assertAlmostEqual(cdp.structure.displacements._translation_vector[molecules[i]][molecules[j]][k],
trans_vect[i][j][k])
+
self.assertAlmostEqual(cdp.structure.displacements._translation_vector[i][j][k],
trans_vect[i][j][k])
# Check the rotation.
-
self.assertAlmostEqual(cdp.structure.displacements._rotation_angle[molecules[i]][molecules[j]],
angle[i][j])
+
self.assertAlmostEqual(cdp.structure.displacements._rotation_angle[i][j],
angle[i][j])
if rot_axis[i][j] != None:
for k in range(3):
-
self.assertAlmostEqual(cdp.structure.displacements._rotation_axis[molecules[i]][molecules[j]][k],
rot_axis[i][j][k])
+
self.assertAlmostEqual(cdp.structure.displacements._rotation_axis[i][j][k],
rot_axis[i][j][k])
def test_get_model(self):
Modified: trunk/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=27062&r1=27061&r2=27062&view=diff
==============================================================================
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Wed Dec 10 17:34:55 2014
@@ -623,6 +623,13 @@
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 displacement
calculation on rather than the models. The displacements will only be
calculated for atoms with identical residue name and number and atom name.",
+ can_be_none = True
+)
+uf.add_keyarg(
name = "centroid",
py_type = "float_array",
desc_short = "centroid position",
@@ -634,6 +641,7 @@
uf.desc[-1].add_paragraph("This user function allows the rotational and
translational displacement between two models of the same structure to be
calculated. The information will be printed out in various formats and held
in the relax data store. This is directional, so there is a starting and
ending position for each displacement. If the starting and ending models are
not specified, then the displacements in all directions between all models
will 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 displacement calculation to
certain molecules, residues, or atoms. This is useful if studying domain
motions, secondary structure rearrangements, amino acid side chain rotations,
etc.")
uf.desc[-1].add_paragraph("By supplying the position of the centroid, an
alternative position than the standard rigid body centre is used as the focal
point of the motion. The allows, for example, a pivot of a rotational domain
motion to be specified. This is not a formally correct algorithm, all
translations will be zero, but does give an indication to the amplitude of
the pivoting angle.")
+uf.desc[-1].add_paragraph("If the optional molecules list is supplied, then
the displacements will be calculated 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 rotational and translational
displacements between all sets of models, type:")
r27062 - in /trunk: pipe_control/structure/main.py test_suite/system_tests/structure.py user_functions/structure.py