Author: bugman
Date: Wed Oct 1 19:44:24 2014
New Revision: 26112
URL: http://svn.gna.org/viewcvs/relax?rev=26112&view=rev
Log:
Implemented the structure.align user function backend.
This is similar to the structure.superimpose user function, however the
coordinate data structure
only contains atoms which are in common to all structures.
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=26112&r1=26111&r2=26112&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Wed Oct 1 19:44:24 2014
@@ -42,7 +42,7 @@
from pipe_control import molmol, pipes
from pipe_control.interatomic import interatomic_loop
from pipe_control.mol_res_spin import check_mol_res_spin_data, create_spin,
generate_spin_id_unique, linear_ave, return_spin, spin_loop
-from pipe_control.pipes import check_pipe
+from pipe_control.pipes import check_pipe, get_pipe
from pipe_control.structure.mass import pipe_centre_of_mass
from status import Status; status = Status()
from target_functions.ens_pivot_finder import Pivot_finder
@@ -101,6 +101,133 @@
# Add a model.
cdp.structure.structural_data.add_item(model_num=model_num)
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):
+ """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
+ @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'.
+ @type method: 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 centre_type: The type of centre to superimpose over. This
can either be the standard centroid superimposition or the CoM could be used
instead.
+ @type centre_type: str
+ @keyword centroid: An alternative position of the centroid to allow
for different superpositions, for example of pivot point motions.
+ @type centroid: list of float or numpy rank-1, 3D array
+ """
+
+ # Check the method.
+ allowed = ['fit to mean', 'fit to first']
+ if method not in allowed:
+ raise RelaxError("The superimposition method '%s' is unknown. It
must be one of %s." % (method, allowed))
+
+ # Check the type.
+ allowed = ['centroid', 'CoM']
+ if centre_type not in allowed:
+ raise RelaxError("The superimposition centre type '%s' is unknown.
It must be one of %s." % (centre_type, allowed))
+
+ # The data pipes to use.
+ if pipes == None:
+ pipes = [pipes.cdp_name()]
+
+ # 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)
+
+ # Assemble the atomic coordinates of all structures.
+ atom_ids = []
+ atom_pos = []
+ atom_elem = []
+ for pipe_index in range(len(pipes)):
+ # The data pipe object.
+ dp = get_pipe(pipes[pipe_index])
+
+ # Validate the models.
+ dp.structure.validate_models(verbosity=0)
+
+ # 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]:
+ # Extend the lists.
+ 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):
+ # A unique identifier.
+ id = "#%s:%s&%s@%s" % (mol_name, res_num, res_name,
atom_name)
+ if id == "#uniform_mol1:1&NH@N":
+ print id, pos[0]
+
+ atom_ids[-1].append(id)
+ atom_pos[-1][id] = pos[0]
+ atom_elem[-1][id] = elem
+
+ # Set up the structures for the superimposition algorithm.
+ num = len(atom_ids)
+ coord = []
+ elements = []
+ for i in range(num):
+ coord.append([])
+ elements.append([])
+
+ # Find the common atoms and create the coordinate data structure.
+ for id in atom_ids[0]:
+ # Is the atom ID present in all other structures?
+ present = True
+ for i in range(num):
+ if id not in atom_ids[i]:
+ present = False
+ break
+
+ # Not present, so skip the atom.
+ if not present:
+ continue
+
+ # Add the atomic position to the coordinate list and the element to
the element list.
+ for i in range(num):
+ coord[i].append(atom_pos[i][id])
+ elements[i].append(atom_elem[i][id])
+
+ # Convert to a numpy array.
+ coord = array(coord, float64)
+ for i in range(num):
+ print coord[i][0]
+
+
+ # The different algorithms.
+ if method == 'fit to mean':
+ T, R, pivot = fit_to_mean(models=range(num), coord=coord,
centre_type=centre_type, elements=elements, centroid=centroid)
+ elif method == 'fit to first':
+ T, R, pivot = fit_to_first(models=range(num), coord=coord,
centre_type=centre_type, elements=elements, centroid=centroid)
+
+ # Update to the new coordinates.
+ 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])
def check_structure_func():
r26112 - /trunk/pipe_control/structure/main.py