Author: bugman
Date: Thu Dec 11 16:00:21 2014
New Revision: 27091
URL: http://svn.gna.org/viewcvs/relax?rev=27091&view=rev
Log:
Changed the design of the
lib.structure.internal.coordinates.assemble_coord_array() function.
The elements_flag argument has been renamed to seq_info_flag. If this is
set, then in addition to
the atomic elements, the molecule name, residue name, residue number, and
atom name is now assembled
and returned. This information is now the common information between the
structures, hence the
return values for the elements are a list of str rather than list of lists.
All of the code in pipe_control.structure.main has been updated for the
change.
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=27091&r1=27090&r2=27091&view=diff
==============================================================================
--- trunk/lib/structure/internal/coordinates.py (original)
+++ trunk/lib/structure/internal/coordinates.py Thu Dec 11 16:00:21 2014
@@ -26,7 +26,7 @@
from numpy import array, float64
-def assemble_coord_array(objects=None, object_names=None, molecules=None,
models=None, atom_id=None, elements_flag=False):
+def assemble_coord_array(objects=None, object_names=None, molecules=None,
models=None, atom_id=None, seq_info_flag=False):
"""Assemble the atomic coordinates
@keyword objects: The list of internal structural objects to
assemble the coordinates from.
@@ -39,8 +39,10 @@
@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 array of atomic coordinates (first dimension
is the model and/or molecule, the second are the atoms, and the third are the
coordinates); a list of unique IDs for each structural object, model, and
molecule; the list of element names for each structural object and each atom
(if the elements flag is set).
- @rtype: numpy rank-3 float64 array, list of str, list of
list of str
+ @keyword seq_info_flag: A flag which if True will cause the atomic
sequence information to be assembled and returned. This includes the
molecule names, residue names, residue numbers, atom names, and elements.
+ @type seq_info_flag: bool
+ @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); a list of unique IDs for each structural object, model, and
molecule; the common list of molecule names (if the seq_info_flag is set);
the common list of residue names (if the seq_info_flag is set); the common
list of residue numbers (if the seq_info_flag is set); the common list of
atom names (if the seq_info_flag is set); the common list of element names
(if the seq_info_flag is set).
+ @rtype: numpy rank-3 float64 array, list of str, list of
str, list of str, list of int, list of str, list of str
"""
# Assemble the atomic coordinates of all structures.
@@ -48,7 +50,11 @@
ids = []
atom_ids = []
atom_pos = []
- atom_elem = []
+ mol_names = []
+ res_names = []
+ res_nums = []
+ atom_names = []
+ elements = []
for struct_index in range(len(objects)):
# Printout.
print(" Data pipe: %s" % object_names[struct_index])
@@ -75,7 +81,12 @@
if molecules == None:
atom_ids.append([])
atom_pos.append({})
- atom_elem.append({})
+ if seq_info_flag:
+ mol_names.append({})
+ res_names.append({})
+ res_nums.append({})
+ atom_names.append({})
+ elements.append({})
# Add all coordinates and elements.
current_mol = ''
@@ -96,7 +107,12 @@
if molecules != None:
atom_ids.append([])
atom_pos.append({})
- atom_elem.append({})
+ if seq_info_flag:
+ mol_names.append({})
+ res_names.append({})
+ res_nums.append({})
+ atom_names.append({})
+ elements.append({})
# Create a new structure ID.
if len(object_names) > 1 and num_models > 1:
@@ -114,17 +130,28 @@
else:
id = "#%s:%s&%s@%s" % (mol_name, res_num, res_name,
atom_name)
+ # Store the per-structure ID and coordinate.
atom_ids[-1].append(id)
atom_pos[-1][id] = pos[0]
- atom_elem[-1][id] = elem
+
+ # Store the per-structure sequence information.
+ if seq_info_flag:
+ mol_names[-1][id] = mol_name
+ res_names[-1][id] = res_name
+ res_nums[-1][id] = res_num
+ atom_names[-1][id] = atom_name
+ elements[-1][id] = elem
# Set up the structures for the superimposition algorithm.
num = len(atom_ids)
coord = []
- elements = []
+ mol_name_common = []
+ res_name_common = []
+ res_num_common = []
+ atom_name_common = []
+ element_common = []
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]:
@@ -142,14 +169,21 @@
# 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])
+
+ # The common sequence information.
+ if seq_info_flag:
+ mol_name_common.append(mol_names[0][id])
+ res_name_common.append(res_names[0][id])
+ res_num_common.append(res_nums[0][id])
+ atom_name_common.append(atom_names[0][id])
+ element_common.append(elements[0][id])
# Convert to a numpy array.
coord = array(coord, float64)
# Return the information.
- if elements_flag:
- return coord, ids, elements
+ if seq_info_flag:
+ return coord, ids, mol_name_common, res_name_common, res_num_common,
atom_name_common, element_common
else:
return coord, ids
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27091&r1=27090&r2=27091&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Thu Dec 11 16:00:21 2014
@@ -136,13 +136,13 @@
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, ids, elements = assemble_coordinates(pipes=pipes,
molecules=molecules, models=models, atom_id=atom_id, elements_flag=True)
+ coord, ids, mol_names, res_names, res_nums, atom_names, elements =
assemble_coordinates(pipes=pipes, molecules=molecules, models=models,
atom_id=atom_id, seq_info_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[0], centroid=centroid)
+ T, R, pivot = fit_to_mean(models=list(range(len(ids))), 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[0], centroid=centroid)
+ T, R, pivot = fit_to_first(models=list(range(len(ids))),
coord=coord, centre_type=centre_type, elements=elements, centroid=centroid)
# Loop over all pipes, models, and molecules.
i = 0
@@ -160,7 +160,7 @@
i += 1
-def assemble_coordinates(pipes=None, molecules=None, models=None,
atom_id=None, elements_flag=False):
+def assemble_coordinates(pipes=None, molecules=None, models=None,
atom_id=None, seq_info_flag=False):
"""Assemble the atomic coordinates
@keyword pipes: The data pipes to assemble the coordinates from.
@@ -171,8 +171,8 @@
@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 array of atomic coordinates (first dimension
is the model and/or molecule, the second are the atoms, and the third are the
coordinates); a list of unique IDs for each pipe, model, and molecule; the
list of element names for each atom (if the elements flag is set).
- @rtype: numpy rank-3 float64 array, list of str, list of
str
+ @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); a list of unique IDs for each structural object, model, and
molecule; the common list of molecule names (if the seq_info_flag is set);
the common list of residue names (if the seq_info_flag is set); the common
list of residue numbers (if the seq_info_flag is set); the common list of
atom names (if the seq_info_flag is set); the common list of element names
(if the seq_info_flag is set).
+ @rtype: numpy rank-3 float64 array, list of str, list of
str, list of str, list of int, list of str, list of str
"""
# The data pipes to use.
@@ -201,7 +201,7 @@
object_names.append(pipes[pipe_index])
# Call the library method to do all of the work.
- return assemble_coord_array(objects=objects, object_names=object_names,
molecules=molecules, models=models, atom_id=atom_id,
elements_flag=elements_flag)
+ return assemble_coord_array(objects=objects, object_names=object_names,
molecules=molecules, models=models, atom_id=atom_id,
seq_info_flag=seq_info_flag)
def connect_atom(index1=None, index2=None):
@@ -1136,13 +1136,13 @@
models = cdp.structure.model_list()
# Assemble the atomic coordinates and obtain the corresponding element
information.
- coord, ids, elements = assemble_coordinates(models=[models],
atom_id=atom_id, elements_flag=True)
+ coord, ids, mol_names, res_names, res_nums, atom_names, elements =
assemble_coordinates(models=[models], atom_id=atom_id, seq_info_flag=True)
# The different algorithms.
if method == 'fit to mean':
- T, R, pivot = fit_to_mean(models=models, coord=coord,
centre_type=centre_type, elements=elements[0], centroid=centroid)
+ T, R, pivot = fit_to_mean(models=models, coord=coord,
centre_type=centre_type, elements=elements, centroid=centroid)
elif method == 'fit to first':
- T, R, pivot = fit_to_first(models=models, coord=coord,
centre_type=centre_type, elements=elements[0], centroid=centroid)
+ T, R, pivot = fit_to_first(models=models, coord=coord,
centre_type=centre_type, elements=elements, centroid=centroid)
# Update to the new coordinates.
for i in range(len(models)):
r27091 - in /trunk: lib/structure/internal/coordinates.py pipe_control/structure/main.py