Author: bugman
Date: Fri Jan 30 16:55:13 2015
New Revision: 27395
URL: http://svn.gna.org/viewcvs/relax?rev=27395&view=rev
Log:
Spun out the atomic assembly code of the assemble_coord_array() function.
The code from the lib.structure.internal.coordinates.assemble_coord_array()
function has been
shifted to the new assemble_atomic_coordinates(). This is to simplify
assemble_coord_array() as
well as to isolate the individual functionality for reuse.
Modified:
trunk/lib/structure/internal/coordinates.py
Modified: trunk/lib/structure/internal/coordinates.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/coordinates.py?rev=27395&r1=27394&r2=27395&view=diff
==============================================================================
--- trunk/lib/structure/internal/coordinates.py (original)
+++ trunk/lib/structure/internal/coordinates.py Fri Jan 30 16:55:13 2015
@@ -28,6 +28,127 @@
# relax module imports.
from lib.errors import RelaxFault
from lib.sequence_alignment.msa import central_star
+
+
+def assemble_atomic_coordinates(objects=None, object_names=None,
molecules=None, models=None, atom_id=None, seq_info_flag=False):
+ """Assemble the atomic coordinates of all structures.
+
+ @keyword objects: The list of internal structural
objects to assemble the coordinates from.
+ @type objects: list of str
+ @keyword object_names: The list of names for each structural
object to use in printouts.
+ @type object_names: 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
+ @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 list of structure IDs for each
molecule, the atom positions per molecule and per residue, the molecule names
per molecule and per residue, the residue names per molecule and per residue,
the residue numbers per molecule and per residue, the atom names per molecule
and per residue, the atomic elements per molecule and per residue, the one
letter codes for the residue sequence, the number of molecules.
+ @rtype: list of str, list of list of dict of
str, list of list of dict of str, list of list of dict of str, list of list of
dict of str, list of list of dict of str, list of list of dict of str, list of
str, int
+ """
+
+ print("Assembling all atomic coordinates:")
+ ids = []
+ atom_pos = []
+ mol_names = []
+ res_names = []
+ res_nums = []
+ atom_names = []
+ elements = []
+ one_letter_codes = []
+ for struct_index in range(len(objects)):
+ # Printout.
+ print(" Data pipe: %s" % object_names[struct_index])
+
+ # 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
+
+ # Printout.
+ print(" Model: %s" % model.num)
+
+ # Add all coordinates and elements.
+ current_mol = ''
+ current_res = None
+ 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:
+ # Printout.
+ print(" Molecule: %s" % mol_name)
+
+ # Change the current molecule name and residue number.
+ current_mol = mol_name
+ current_res = None
+
+ # Store the one letter codes for sequence alignment.
+
one_letter_codes.append(objects[struct_index].one_letter_codes(mol_name=mol_name))
+
+ # Extend the lists.
+ atom_names.append([])
+ atom_pos.append([])
+ if seq_info_flag:
+ mol_names.append([])
+ res_names.append([])
+ res_nums.append([])
+ elements.append([])
+
+ # Create a new structure ID.
+ if len(object_names) > 1 and num_models > 1:
+ ids.append('%s, model %i, %s' %
(object_names[struct_index], model.num, mol_name))
+ elif len(object_names) > 1:
+ ids.append('%s, %s' % (object_names[struct_index],
mol_name))
+ elif num_models > 1:
+ ids.append('model %i, %s' % (model.num, mol_name))
+ else:
+ ids.append('%s' % mol_name)
+
+ # A new residue.
+ if res_num != current_res:
+ # Change the current residue
+ current_res = res_num
+
+ # Extend the lists.
+ atom_names[-1].append([])
+ atom_pos[-1].append({})
+ if seq_info_flag:
+ mol_names[-1].append({})
+ res_names[-1].append({})
+ res_nums[-1].append({})
+ elements[-1].append({})
+
+ # Store the per-structure ID and coordinate.
+ atom_names[-1][-1].append(atom_name)
+ atom_pos[-1][-1][atom_name] = pos[0]
+
+ # Store the per-structure sequence information.
+ if seq_info_flag:
+ mol_names[-1][-1][atom_name] = mol_name
+ res_names[-1][-1][atom_name] = res_name
+ res_nums[-1][-1][atom_name] = res_num
+ elements[-1][-1][atom_name] = elem
+
+ # The total number of molecules.
+ num_mols = len(atom_names)
+
+ # Return the data.
+ return ids, atom_pos, mol_names, res_names, res_nums, atom_names,
elements, one_letter_codes, num_mols
def assemble_coord_array(objects=None, object_names=None, molecules=None,
models=None, atom_id=None, algorithm='NW70', matrix='BLOSUM62',
gap_open_penalty=1.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0,
end_gap_extend_penalty=0.0, seq_info_flag=False):
@@ -62,103 +183,7 @@
"""
# Assemble the atomic coordinates of all structures.
- print("Assembling all atomic coordinates:")
- ids = []
- atom_pos = []
- mol_names = []
- res_names = []
- res_nums = []
- atom_names = []
- elements = []
- one_letter_codes = []
- for struct_index in range(len(objects)):
- # Printout.
- print(" Data pipe: %s" % object_names[struct_index])
-
- # 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
-
- # Printout.
- print(" Model: %s" % model.num)
-
- # Add all coordinates and elements.
- current_mol = ''
- current_res = None
- 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:
- # Printout.
- print(" Molecule: %s" % mol_name)
-
- # Change the current molecule name and residue number.
- current_mol = mol_name
- current_res = None
-
- # Store the one letter codes for sequence alignment.
-
one_letter_codes.append(objects[struct_index].one_letter_codes(mol_name=mol_name))
-
- # Extend the lists.
- atom_names.append([])
- atom_pos.append([])
- if seq_info_flag:
- mol_names.append([])
- res_names.append([])
- res_nums.append([])
- elements.append([])
-
- # Create a new structure ID.
- if len(object_names) > 1 and num_models > 1:
- ids.append('%s, model %i, %s' %
(object_names[struct_index], model.num, mol_name))
- elif len(object_names) > 1:
- ids.append('%s, %s' % (object_names[struct_index],
mol_name))
- elif num_models > 1:
- ids.append('model %i, %s' % (model.num, mol_name))
- else:
- ids.append('%s' % mol_name)
-
- # A new residue.
- if res_num != current_res:
- # Change the current residue
- current_res = res_num
-
- # Extend the lists.
- atom_names[-1].append([])
- atom_pos[-1].append({})
- if seq_info_flag:
- mol_names[-1].append({})
- res_names[-1].append({})
- res_nums[-1].append({})
- elements[-1].append({})
-
- # Store the per-structure ID and coordinate.
- atom_names[-1][-1].append(atom_name)
- atom_pos[-1][-1][atom_name] = pos[0]
-
- # Store the per-structure sequence information.
- if seq_info_flag:
- mol_names[-1][-1][atom_name] = mol_name
- res_names[-1][-1][atom_name] = res_name
- res_nums[-1][-1][atom_name] = res_num
- elements[-1][-1][atom_name] = elem
-
- # The total number of molecules.
- num_mols = len(atom_names)
+ ids, atom_pos, mol_names, res_names, res_nums, atom_names, elements,
one_letter_codes, num_mols = assemble_atomic_coordinates(objects=objects,
object_names=object_names, molecules=molecules, models=models, atom_id=atom_id,
seq_info_flag=seq_info_flag)
# Multiple sequence alignment.
if algorithm != None:
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