Author: bugman
Date: Thu Dec 11 09:25:06 2014
New Revision: 27069
URL: http://svn.gna.org/viewcvs/relax?rev=27069&view=rev
Log:
Converted the structure.find_pivot user function to the new
pipes/models/molecules/atom_id design.
This allows the motional pivot algorithm to work on atomic coordinates from
different data pipes,
different structural models, and different molecules. The change allows the
Structure.test_find_pivot_molecules system test to now pass, as missing
atomic data is now correctly
handled. The user function backend uses the new
pipe_control.structure.main.assemble_coordinates()
function.
The Structure.test_find_pivot and Structure.test_find_pivot_molecules system
tests have 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=27069&r1=27068&r2=27069&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Thu Dec 11 09:25:06 2014
@@ -112,7 +112,7 @@
@type pipes: None or list of str
@keyword models: The list of models to for each data pipe
superimpose. The number of elements must match the pipes argument. If set
to None, then all models will be used.
@type models: list of lists of int or None
- @keyword molecules: The molecule names to include in the alignment
and superimposition.
+ @keyword molecules: The molecule names to include in the alignment
and superimposition. The number of elements must match the pipes argument.
@type molecules: None or list of str
@keyword atom_id: The molecule, residue, and atom identifier
string. This matches the spin ID string format.
@type atom_id: str or None
@@ -616,13 +616,15 @@
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, molecules=None, atom_id=None, init_pos=None,
func_tol=1e-5, box_limit=200):
+def find_pivot(pipes=None, models=None, molecules=None, atom_id=None,
init_pos=None, func_tol=1e-5, box_limit=200):
"""Find the pivoted motion of a set of structural models or structures.
- @keyword models: The list of models to use. If set to None, then all
models will be used.
- @type models: list of int or None
- @keyword molecules: The list of molecules to find the pivoted motion
for. This overrides the models.
- @type molecules: None or list of str
+ @keyword pipes: The data pipes to use in the motional pivot
algorithm.
+ @type pipes: None or list of str
+ @keyword models: The list of models to use. 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 find the pivoted motion
for. The number of elements must match the pipes argument.
+ @type molecules: None or list of lists of str
@keyword atom_id: The molecule, residue, and atom identifier string.
This matches the spin ID string format.
@type atom_id: str or None
@keyword init_pos: The starting pivot position for the pivot point
optimisation.
@@ -641,60 +643,8 @@
init_pos = zeros(3, float64)
init_pos = array(init_pos)
- # The selection object.
- selection = cdp.structure.selection(atom_id=atom_id)
-
- # Motional pivot between models.
- if molecules == None:
- # Validate the models.
- cdp.structure.validate_models()
-
- # 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])
- coord = array(coord)
-
- # Motional pivot 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.")
-
- # Assemble the atomic coordinates of all models.
- 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])
-
- # The models list.
- models = list(range(len(molecules)))
+ # Assemble the atomic coordinates and obtain the corresponding element
information.
+ coord = assemble_coordinates(pipes=pipes, molecules=molecules,
models=models, atom_id=atom_id)
# Linear constraints for the pivot position (between -1000 and 1000
Angstrom).
A = zeros((6, 3), float64)
@@ -706,7 +656,7 @@
b[2*i+1] = -box_limit
# The target function.
- finder = Pivot_finder(models, coord)
+ finder = Pivot_finder(list(range(len(coord))), coord)
results = generic_minimise(func=finder.func, x0=init_pos, min_algor='Log
barrier', min_options=('simplex',), A=A, b=b, func_tol=func_tol, print_flag=1)
# No result.
Modified: trunk/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=27069&r1=27068&r2=27069&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Thu Dec 11 09:25:06 2014
@@ -3187,7 +3187,7 @@
self.interpreter.structure.rotate(R=R, atom_id='#Z', origin=pivot)
# Find the pivot.
- self.interpreter.structure.find_pivot(molecules=['X', 'Y', 'Z'],
init_pos=[0.95, 2.05, 3.02], func_tol=1e-7)
+ self.interpreter.structure.find_pivot(molecules=[['X', 'Y', 'Z']],
init_pos=[0.95, 2.05, 3.02], func_tol=1e-7)
# Check the pivot.
self.assertAlmostEqual(cdp.structure.pivot[0], pivot[0], 3)
Modified: trunk/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=27069&r1=27068&r2=27069&view=diff
==============================================================================
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Thu Dec 11 09:25:06 2014
@@ -665,17 +665,26 @@
uf.title = "Find the pivot point of the motion of a set of structures."
uf.title_short = "Pivot search."
uf.add_keyarg(
+ name = "pipes",
+ py_type = "str_list",
+ desc_short = "data pipes",
+ desc = "The data pipes to use in the motional pivot algorithm.",
+ wiz_combo_iter = pipe_names,
+ wiz_read_only = False,
+ can_be_none = True
+)
+uf.add_keyarg(
name = "models",
- py_type = "int_list",
- desc_short = "model list",
- desc = "The list of models to use.",
+ py_type = "int_list_of_lists",
+ desc_short = "model list for each data pipe",
+ desc = "The list of models for each data pipe to use in the motional
pivot algorithm. 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",
- desc_short = "molecule list",
- desc = "The optional molecule list to perform the optimisation on rather
than the models. Only atoms with identical residue name and number and atom
name will be used.",
+ py_type = "str_list_of_lists",
+ desc_short = "molecule list for each data pipe",
+ desc = "The list of molecules for each data pipe to use in the motional
pivot algorithm. This allows differently named molecules in the same or
different data pipes to be used. 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(
r27069 - in /trunk: pipe_control/structure/main.py test_suite/system_tests/structure.py user_functions/structure.py