Author: bugman
Date: Thu Dec 11 12:25:03 2014
New Revision: 27088
URL: http://svn.gna.org/viewcvs/relax?rev=27088&view=rev
Log:
Code refactorisation for the structure.align user function backend.
The looping over data pipes, model numbers, and molecule names, skipping
those that don't match the
function arguments, has been shifted into the new structure_loop() generator
function of the
pipe_control.structure.main module. This function assembles the data from
the data store and then
calls the new loop_coord_structures() generator function of the
lib.structure.internal.coordinates
module which does all of the work.
Modified:
trunk/lib/structure/internal/coordinates.py
trunk/pipe_control/structure/main.py
Modified: trunk/lib/structure/internal/coordinates.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/coordinates.py?rev=27088&r1=27087&r2=27088&view=diff
==============================================================================
--- trunk/lib/structure/internal/coordinates.py (original)
+++ trunk/lib/structure/internal/coordinates.py Thu Dec 11 12:25:03 2014
@@ -152,3 +152,51 @@
return coord, ids, elements
else:
return coord, ids
+
+
+def loop_coord_structures(objects=None, molecules=None, models=None,
atom_id=None):
+ """Generator function for looping over all internal structural objects,
models and molecules.
+
+ @keyword objects: The list of internal structural objects to loop
over.
+ @type objects: list of str
+ @keyword models: The list of models for each structural object.
The number of elements must match the objects 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 for each structural
object. The number of elements must match the objects argument. If set to
None, then all molecules will be used.
+ @type molecules: None or list of lists of str
+ @keyword atom_id: The molecule, residue, and atom identifier
string of the coordinates of interest. This matches the spin ID string
format.
+ @type atom_id: None or str
+ @return: The structural object index, model number, and
molecule name.
+ @rtype: int, int or None, str
+ """
+
+ # Loop over all structural objects.
+ for struct_index in range(len(objects)):
+ # Validate the models.
+ objects[struct_index].validate_models(verbosity=0)
+
+ # The number of models.
+ num_models = objects[struct_index].num_models()
+
+ # The selection object.
+ selection = objects[struct_index].selection(atom_id=atom_id)
+
+ # Loop over the models.
+ for model in objects[struct_index].model_loop():
+ # No model match.
+ if models != None and model.num not in models[struct_index]:
+ continue
+
+ # Coordinate loop.
+ current_mol = ''
+ for mol_name, res_num, res_name, atom_name, elem, pos in
objects[struct_index].atom_loop(selection=selection, model_num=model.num,
mol_name_flag=True, res_num_flag=True, res_name_flag=True,
atom_name_flag=True, pos_flag=True, element_flag=True):
+ # No molecule match, so skip.
+ if molecules != None and mol_name not in
molecules[struct_index]:
+ continue
+
+ # A new molecule.
+ if mol_name != current_mol:
+ # Change the current molecule name.
+ current_mol = mol_name
+
+ # Yield the data.
+ yield struct_index, model.num, mol_name
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27088&r1=27087&r2=27088&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Thu Dec 11 12:25:03 2014
@@ -34,7 +34,7 @@
from lib.io import get_file_path, open_write_file, write_data
from lib.selection import tokenise
from lib.sequence import write_spin_data
-from lib.structure.internal.coordinates import assemble_coord_array
+from lib.structure.internal.coordinates import assemble_coord_array,
loop_coord_structures
from lib.structure.internal.displacements import Displacements
from lib.structure.internal.object import Internal
from lib.structure.represent.diffusion_tensor import diffusion_tensor
@@ -144,44 +144,20 @@
elif method == 'fit to first':
T, R, pivot = fit_to_first(models=list(range(len(elements))),
coord=coord, centre_type=centre_type, elements=elements[0], centroid=centroid)
- # Update to the new coordinates.
+ # Loop over all pipes, models, and molecules.
i = 0
- for pipe_index in range(len(pipes)):
- # The data pipe object.
- dp = get_pipe(pipes[pipe_index])
-
- # The selection object.
- selection = dp.structure.selection(atom_id=atom_id)
-
- # Loop over the models.
- for model in dp.structure.model_loop():
- # No model match.
- if models != None and model.num not in models[pipe_index]:
- continue
-
- # Loop over the molecules.
- current_mol = ''
- for mol_name in dp.structure.atom_loop(selection=selection,
model_num=model.num, mol_name_flag=True):
- # No molecule match, so skip.
- if molecules != None and mol_name not in
molecules[pipe_index]:
- continue
-
- # A new molecule.
- if mol_name != current_mol:
- # Change the current molecule name.
- current_mol = mol_name
-
- # The atom ID from the molecule name.
- id = '#%s' % mol_name
-
- # Translate the molecule first (the rotational pivot is
defined in the first model).
- translate(T=T[i], model=model.num,
pipe_name=pipes[pipe_index], atom_id=id)
-
- # Rotate the molecule.
- rotate(R=R[i], origin=pivot[i], model=model.num,
pipe_name=pipes[pipe_index], atom_id=id)
-
- # Increment the index.
- i += 1
+ for pipe_index, model_num, mol_name in structure_loop(pipes=pipes,
molecules=molecules, models=models, atom_id=atom_id):
+ # The atom ID from the molecule name.
+ id = '#%s' % mol_name
+
+ # Translate the molecule first (the rotational pivot is defined in
the first model).
+ translate(T=T[i], model=model_num, pipe_name=pipes[pipe_index],
atom_id=id)
+
+ # Rotate the molecule.
+ rotate(R=R[i], origin=pivot[i], model=model_num,
pipe_name=pipes[pipe_index], atom_id=id)
+
+ # Increment the index.
+ i += 1
def assemble_coordinates(pipes=None, molecules=None, models=None,
atom_id=None, elements_flag=False):
@@ -1078,6 +1054,49 @@
spin.xh_vect = xh_vect
+def structure_loop(pipes=None, molecules=None, models=None, atom_id=None):
+ """Generator function for looping over all internal structural objects,
models and molecules.
+
+ @keyword pipes: The data pipes to loop over.
+ @type pipes: None or list of str
+ @keyword models: The list of models for each data pipe. 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 for each data pipe. 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 of the coordinates of interest. This matches the spin ID string
format.
+ @type atom_id: None or str
+ @return: The data pipe index, model number, and molecule
name.
+ @rtype: int, int or None, str
+ """
+
+ # The data pipes to use.
+ if pipes == None:
+ pipes = [cdp_name()]
+ num_pipes = len(pipes)
+
+ # Checks.
+ for pipe in pipes:
+ check_pipe(pipe)
+
+ # Check the models and molecules arguments.
+ if models != None:
+ if len(models) != num_pipes:
+ raise RelaxError("The %i elements of the models argument does
not match the %i data pipes." % (len(models), num_pipes))
+ if molecules != None:
+ if len(molecules) != num_pipes:
+ raise RelaxError("The %i elements of the molecules argument does
not match the %i data pipes." % (len(molecules), num_pipes))
+
+ # Assemble the structural objects.
+ objects = []
+ for pipe_index in range(len(pipes)):
+ dp = get_pipe(pipes[pipe_index])
+ objects.append(dp.structure)
+
+ # Call the library method to do all of the work.
+ for pipe_index, model_num, mol_name in
loop_coord_structures(objects=objects, molecules=molecules, models=models,
atom_id=atom_id):
+ yield pipe_index, model_num, mol_name
+
+
def superimpose(models=None, method='fit to mean', atom_id=None,
centre_type="centroid", centroid=None):
"""Superimpose a set of structural models.
r27088 - in /trunk: lib/structure/internal/coordinates.py pipe_control/structure/main.py