Author: bugman
Date: Thu Dec 11 10:50:16 2014
New Revision: 27078
URL: http://svn.gna.org/viewcvs/relax?rev=27078&view=rev
Log:
Converted the structure.displacement user function to the new
pipes/models/molecules/atom_id design.
This allows the displacements to be calculated between atomic coordinates
from different data pipes,
different structural models, and different molecules. The user function
backend has been hugely
simplified as it now uses the new
pipe_control.structure.main.assemble_coordinates() function.
The Structure.test_displacement 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=27078&r1=27077&r2=27078&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Thu Dec 11 10:50:16 2014
@@ -427,106 +427,35 @@
del interatom.vector
-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.
- @type model_from: int or None
- @keyword model_to: The optional model number for the ending
position of the displacement.
- @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
+def displacement(pipes=None, models=None, molecules=None, atom_id=None,
centroid=None):
+ """Calculate the rotational and translational displacement between
structures or models.
+
+ @keyword pipes: The data pipes to determine the displacements for.
+ @type pipes: None or list of str
+ @keyword models: The list of models to determine the displacements
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 displacements
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 centroid: An alternative position of the centroid, used for
studying pivoted systems.
+ @type centroid: list of float or numpy rank-1, 3D array
"""
# Test if the current data pipe exists.
check_pipe()
- # 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_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)
+ # Assemble the atomic coordinates.
+ coord, ids = assemble_coordinates(pipes=pipes, molecules=molecules,
models=models, atom_id=atom_id)
+
+ # Initialise the data structure.
+ if not hasattr(cdp.structure, 'displacments'):
+ cdp.structure.displacements = Displacements()
+
+ # Double loop over all structures, sending the data to the base
container for the calculations.
+ for i in range(len(ids)):
+ for j in range(len(ids)):
+ cdp.structure.displacements._calculate(id_from=ids[i],
id_to=ids[j], coord_from=coord[i], coord_to=coord[j], centroid=centroid)
def find_pivot(pipes=None, models=None, molecules=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=27078&r1=27077&r2=27078&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Thu Dec 11 10:50:16 2014
@@ -2973,7 +2973,7 @@
self.interpreter.structure.rotate(R, model=3)
# The data to check.
- models = [1, 2]
+ ids = ['model 1, Ap4Aase_res1-12_mol1', 'model 2,
Ap4Aase_res1-12_mol1']
trans_vect = [
[[0.0, 0.0, 0.0],
[ 2.270857972754659, -1.811667138656451,
1.878400649688508]],
@@ -2997,18 +2997,18 @@
# Test the results.
self.assert_(hasattr(cdp.structure, 'displacements'))
- for i in range(len(models)):
- for j in range(len(models)):
+ for i in range(len(ids)):
+ for j in range(len(ids)):
# Check the translation.
-
self.assertAlmostEqual(cdp.structure.displacements._translation_distance[models[i]][models[j]],
dist[i][j])
+
self.assertAlmostEqual(cdp.structure.displacements._translation_distance[ids[i]][ids[j]],
dist[i][j])
for k in range(3):
-
self.assertAlmostEqual(cdp.structure.displacements._translation_vector[models[i]][models[j]][k],
trans_vect[i][j][k])
+
self.assertAlmostEqual(cdp.structure.displacements._translation_vector[ids[i]][ids[j]][k],
trans_vect[i][j][k])
# Check the rotation.
-
self.assertAlmostEqual(cdp.structure.displacements._rotation_angle[models[i]][models[j]],
angle[i][j])
+
self.assertAlmostEqual(cdp.structure.displacements._rotation_angle[ids[i]][ids[j]],
angle[i][j])
if rot_axis[i][j] != None:
for k in range(3):
-
self.assertAlmostEqual(cdp.structure.displacements._rotation_axis[models[i]][models[j]][k],
rot_axis[i][j][k])
+
self.assertAlmostEqual(cdp.structure.displacements._rotation_axis[ids[i]][ids[j]][k],
rot_axis[i][j][k])
# Save the results.
self.tmpfile = mktemp()
@@ -3022,18 +3022,18 @@
# Test the re-loaded data.
self.assert_(hasattr(cdp.structure, 'displacements'))
- for i in range(len(models)):
- for j in range(len(models)):
+ for i in range(len(ids)):
+ for j in range(len(ids)):
# Check the translation.
-
self.assertAlmostEqual(cdp.structure.displacements._translation_distance[models[i]][models[j]],
dist[i][j])
+
self.assertAlmostEqual(cdp.structure.displacements._translation_distance[ids[i]][ids[j]],
dist[i][j])
for k in range(3):
-
self.assertAlmostEqual(cdp.structure.displacements._translation_vector[models[i]][models[j]][k],
trans_vect[i][j][k])
+
self.assertAlmostEqual(cdp.structure.displacements._translation_vector[ids[i]][ids[j]][k],
trans_vect[i][j][k])
# Check the rotation.
-
self.assertAlmostEqual(cdp.structure.displacements._rotation_angle[models[i]][models[j]],
angle[i][j])
+
self.assertAlmostEqual(cdp.structure.displacements._rotation_angle[ids[i]][ids[j]],
angle[i][j])
if rot_axis[i][j] != None:
for k in range(3):
-
self.assertAlmostEqual(cdp.structure.displacements._rotation_axis[models[i]][models[j]][k],
rot_axis[i][j][k])
+
self.assertAlmostEqual(cdp.structure.displacements._rotation_axis[ids[i]][ids[j]][k],
rot_axis[i][j][k])
def test_displacement_molecules(self):
Modified: trunk/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=27078&r1=27077&r2=27078&view=diff
==============================================================================
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Thu Dec 11 10:50:16 2014
@@ -599,34 +599,36 @@
# The structure.displacement user function.
uf = uf_info.add_uf('structure.displacement')
-uf.title = "Determine the rotational and translational displacement between
a set of models."
+uf.title = "Determine the rotational and translational displacement between
a set of models or molecules."
uf.title_short = "Rotational and translational displacement."
uf.add_keyarg(
- name = "model_from",
- py_type = "int",
- desc_short = "model from",
- desc = "The optional model number for the starting position of the
displacement.",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "model_to",
- py_type = "int",
- desc_short = "model to",
- desc = "The optional model number for the ending position of the
displacement.",
+ name = "pipes",
+ py_type = "str_list",
+ desc_short = "data pipes",
+ desc = "The data pipes to determine the displacements 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
displacements 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
displacements for. This allows differently named molecules in the same or
different data pipes to be superimposed. 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 displacement
calculation on rather than the models. The displacements 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
)
uf.add_keyarg(
@@ -638,7 +640,7 @@
)
# Description.
uf.desc.append(Desc_container())
-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("This user function allows the rotational and
translational displacement between different models or molecules 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. Therefore the displacements in all
directions between all models and molecules 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.")
@@ -646,13 +648,6 @@
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:")
uf.desc[-1].add_prompt("relax> structure.displacement()")
-uf.desc[-1].add_paragraph("To determine the displacement from model 5 to all
other models, type:")
-uf.desc[-1].add_prompt("relax> structure.displacement(model_from=5)")
-uf.desc[-1].add_paragraph("To determine the displacement of all models to
model 5, type:")
-uf.desc[-1].add_prompt("relax> structure.displacement(model_to=5)")
-uf.desc[-1].add_paragraph("To determine the displacement of model 2 to model
3, type one of:")
-uf.desc[-1].add_prompt("relax> structure.displacement(2, 3)")
-uf.desc[-1].add_prompt("relax> structure.displacement(model_from=2,
model_to=3)")
uf.backend = pipe_control.structure.main.displacement
uf.menu_text = "displace&ment"
uf.wizard_height_desc = 400
r27078 - in /trunk: pipe_control/structure/main.py test_suite/system_tests/structure.py user_functions/structure.py