Author: bugman
Date: Thu Dec 11 08:58:36 2014
New Revision: 27067
URL: http://svn.gna.org/viewcvs/relax?rev=27067&view=rev
Log:
Shifted the atomic assembly code from the structure.align user function into
its own function.
The new function assemble_coordinates() of the pipe_control.structure.main
module will be used to
standardise the process of assembling atomic coordinates for all of the
structure user functions.
This will improve the support for comparing different molecules rather than
different models as
missing atoms or divergent primary sequence are properly handled, and it has
multi-pipe support.
Modified:
trunk/pipe_control/structure/main.py
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27067&r1=27066&r2=27067&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Thu Dec 11 08:58:36 2014
@@ -134,6 +134,70 @@
if centre_type not in allowed:
raise RelaxError("The superimposition centre type '%s' is unknown.
It must be one of %s." % (centre_type, allowed))
+ # Assemble the atomic coordinates and obtain the corresponding element
information.
+ coord, elements = assemble_coordinates(pipes=pipes, molecules=molecules,
models=models, atom_id=atom_id, elements_flag=True)
+
+ # The different algorithms.
+ if method == 'fit to mean':
+ T, R, pivot = fit_to_mean(models=list(range(len(elements))),
coord=coord, centre_type=centre_type, elements=elements, centroid=centroid)
+ elif method == 'fit to first':
+ T, R, pivot = fit_to_first(models=list(range(len(elements))),
coord=coord, centre_type=centre_type, elements=elements, centroid=centroid)
+
+ # Update to the new coordinates.
+ 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
+
+
+def assemble_coordinates(pipes=None, molecules=None, models=None,
atom_id=None, elements_flag=False):
+ """Assemble the atomic coordinates
+
+ @keyword pipes: The data pipes to include in the alignment and
superimposition.
+ @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: None or list of lists of int
+ @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 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
+ @return: The array of atomic coordinates (first dimension
is the model and/or molecule, the second are the atoms, and the third are the
coordinates), and the list of element names for each atom (if the elements
flag is set).
+ @rtype: numpy rank-3 float64 array, list of str
+ """
+
# The data pipes to use.
if pipes == None:
pipes = [cdp_name()]
@@ -244,50 +308,11 @@
# Convert to a numpy array.
coord = array(coord, float64)
- # The different algorithms.
- if method == 'fit to mean':
- T, R, pivot = fit_to_mean(models=list(range(num)), coord=coord,
centre_type=centre_type, elements=elements, centroid=centroid)
- elif method == 'fit to first':
- T, R, pivot = fit_to_first(models=list(range(num)), coord=coord,
centre_type=centre_type, elements=elements, centroid=centroid)
-
- # Update to the new coordinates.
- 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
+ # Return the information.
+ if elements_flag:
+ return coord, elements
+ else:
+ return coord
def connect_atom(index1=None, index2=None):
r27067 - /trunk/pipe_control/structure/main.py