Author: bugman
Date: Wed Dec 10 15:56:46 2014
New Revision: 27057
URL: http://svn.gna.org/viewcvs/relax?rev=27057&view=rev
Log:
Implemented the new molecules argument for the structure.align user function.
In addition to accepting the new argument, the user function backend has been
redesigned for
flexibility. The assembly of coordinates and final rotations and
translations now consist of three
loops over desired data pipes, all models, and all molecules. If the models
or molecules arguments
are supplied, then the models or molecules in the loop which do not match are
skipped. This logic
simplifies and cleans up the backend.
Modified:
trunk/pipe_control/structure/main.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=27057&r1=27056&r2=27057&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Wed Dec 10 15:56:46 2014
@@ -105,11 +105,13 @@
print("Created the empty model number %s." % model_num)
-def align(pipes=None, models=None, method='fit to mean', atom_id=None,
centre_type="centroid", centroid=None):
+def align(pipes=None, molecules=None, models=None, method='fit to mean',
atom_id=None, centre_type="centroid", centroid=None):
"""Superimpose a set of related, but not identical structures.
@keyword pipes: The data pipes to include in the alignment and
superimposition.
- @type pipes: list of str
+ @type pipes: None or list of str
+ @keyword molecules: The molecule names to include in the alignment
and superimposition.
+ @type molecules: 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 method: The superimposition method. It must be one of
'fit to mean' or 'fit to first'.
@@ -135,23 +137,25 @@
# The data pipes to use.
if pipes == None:
pipes = [cdp_name()]
+ num_pipes = len(pipes)
# Checks.
for pipe in pipes:
check_pipe(pipe)
- # Initialise the models data structure.
- if models == None:
- models = []
- for i in range(len(pipes)):
- models.append(None)
+ # 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 atomic coordinates of all structures.
print("Assembling all atomic coordinates:")
atom_ids = []
atom_pos = []
atom_elem = []
- mol_ids = []
for pipe_index in range(len(pipes)):
# Printout.
print(" Data pipe: %s" % pipes[pipe_index])
@@ -165,42 +169,51 @@
# The selection object.
selection = dp.structure.selection(atom_id=atom_id)
- # Create a list of all models for this pipe.
- if models[pipe_index] == None:
- models[pipe_index] = []
- for model in dp.structure.model_loop():
- models[pipe_index].append(model.num)
-
# Loop over the models.
- for model in models[pipe_index]:
+ for model in dp.structure.model_loop():
+ # No model match.
+ if models != None and model.num not in models[pipe_index]:
+ continue
+
# Printout.
- print(" Model: %s" % model)
+ print(" Model: %s" % model.num)
# Extend the lists.
- atom_ids.append([])
- atom_pos.append({})
- atom_elem.append({})
- mol_ids.append([])
+ if molecules == None:
+ atom_ids.append([])
+ atom_pos.append({})
+ atom_elem.append({})
# Add all coordinates and elements.
- for mol_name, res_num, res_name, atom_name, elem, pos in
dp.structure.atom_loop(selection=selection, model_num=model,
mol_name_flag=True, res_num_flag=True, res_name_flag=True,
atom_name_flag=True, pos_flag=True, element_flag=True):
+ current_mol = ''
+ for mol_name, res_num, res_name, atom_name, elem, pos in
dp.structure.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[pipe_index]:
+ continue
+
+ # A new molecule.
+ if mol_name != current_mol:
+ # Printout.
+ print(" Molecule: %s" % mol_name)
+
+ # Change the current molecule name.
+ current_mol = mol_name
+
+ # Extend the lists.
+ if molecules != None:
+ atom_ids.append([])
+ atom_pos.append({})
+ atom_elem.append({})
+
# A unique identifier.
- id = "#%s:%s&%s@%s" % (mol_name, res_num, res_name,
atom_name)
+ if molecules != None:
+ id = ":%s&%s@%s" % (res_num, res_name, atom_name)
+ else:
+ id = "#%s:%s&%s@%s" % (mol_name, res_num, res_name,
atom_name)
atom_ids[-1].append(id)
atom_pos[-1][id] = pos[0]
atom_elem[-1][id] = elem
-
- # Store the molecule name for later checks.
- if mol_name not in mol_ids[-1]:
- print(" Molecule: %s" % mol_name)
- mol_ids[-1].append(mol_name)
-
- # Check for the molecule names.
- for mol_name in mol_ids[0]:
- for i in range(len(mol_ids)):
- if mol_name not in mol_ids[i]:
- raise RelaxError("The molecule name '%s' cannot be found in
all data pipes." % mol_name)
# Set up the structures for the superimposition algorithm.
num = len(atom_ids)
@@ -240,15 +253,48 @@
# Update to the new coordinates.
i = 0
for pipe_index in range(len(pipes)):
- for model in models[pipe_index]:
- # Translate the molecule first (the rotational pivot is defined
in the first model).
- translate(T=T[i], model=model, pipe_name=pipes[pipe_index])
-
- # Rotate the molecule.
- rotate(R=R[i], origin=pivot[i], model=model,
pipe_name=pipes[pipe_index])
-
- # Increment the index.
- i += 1
+ # The data pipe object.
+ dp = get_pipe(pipes[pipe_index])
+
+ print(" Data pipe: %s" % 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
+
+ print(" Model: %s" % model.num)
+
+ # 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:
+
+ print(" Molecule: %s" % mol_name)
+
+ # 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 connect_atom(index1=None, index2=None):
Modified: trunk/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=27057&r1=27056&r2=27057&view=diff
==============================================================================
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Wed Dec 10 15:56:46 2014
@@ -171,8 +171,15 @@
uf.add_keyarg(
name = "models",
py_type = "int_list_of_lists",
- desc_short = "model list",
- desc = "The list of models for each data pipe to superimpose. The
number of elements must match the pipes argument.",
+ desc_short = "model list for each data pipe",
+ desc = "The list of models for each data pipe to superimpose. 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 molecules to include in the alignment and superimposition.
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(
r27057 - in /trunk: pipe_control/structure/main.py user_functions/structure.py