Author: bugman
Date: Thu Dec 11 09:44:53 2014
New Revision: 27070
URL: http://svn.gna.org/viewcvs/relax?rev=27070&view=rev
Log:
Shift of the atomic coordinate assembly code into the relax library.
Most of the pipe_control.structure.main.assemble_coordinates() function has
been shifted into the
assemble_coord_array() function of the new lib.structure.internal.coordinates
module. The
pipe_control function now only checks the arguments and assembles the
structural objects from the
relax data store, and then calls assemble_coord_array() to do all of the work.
This code abstraction increases the usefulness of the atomic coordinate
assembly and allows it to be
significantly expanded in the future, for example by being able to take
sequence alignments into
consideration.
Added:
trunk/lib/structure/internal/coordinates.py
Modified:
trunk/lib/structure/internal/__init__.py
trunk/pipe_control/structure/main.py
Modified: trunk/lib/structure/internal/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/__init__.py?rev=27070&r1=27069&r2=27070&view=diff
==============================================================================
--- trunk/lib/structure/internal/__init__.py (original)
+++ trunk/lib/structure/internal/__init__.py Thu Dec 11 09:44:53 2014
@@ -23,6 +23,7 @@
"""The relax-lib structure.internal package - the internal structural
object."""
__all__ = [
+ 'coordinates',
'displacements',
'models',
'molecules',
Added: trunk/lib/structure/internal/coordinates.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/coordinates.py?rev=27070&view=auto
==============================================================================
--- trunk/lib/structure/internal/coordinates.py (added)
+++ trunk/lib/structure/internal/coordinates.py Thu Dec 11 09:44:53 2014
@@ -0,0 +1,140 @@
+###############################################################################
+#
#
+# Copyright (C) 2014 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax (http://www.nmr-relax.com).
#
+#
#
+# This program is free software: you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation, either version 3 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# This program is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
+#
#
+###############################################################################
+
+# Module docstring.
+"""Module for handling atomic coordinate information."""
+
+# Python module imports.
+from numpy import array, float64
+
+
+def assemble_coord_array(objects=None, object_names=None, molecules=None,
models=None, atom_id=None, elements_flag=False):
+ """Assemble the atomic coordinates
+
+ @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
+ @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
+ """
+
+ # Assemble the atomic coordinates of all structures.
+ print("Assembling all atomic coordinates:")
+ atom_ids = []
+ atom_pos = []
+ atom_elem = []
+ 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 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)
+
+ # Extend the lists.
+ if molecules == None:
+ atom_ids.append([])
+ atom_pos.append({})
+ atom_elem.append({})
+
+ # Add all coordinates and elements.
+ current_mol = ''
+ 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.
+ current_mol = mol_name
+
+ # Extend the lists.
+ if molecules != None:
+ atom_ids.append([])
+ atom_pos.append({})
+ atom_elem.append({})
+
+ # A unique identifier.
+ 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
+
+ # 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)
+
+ # Return the information.
+ if elements_flag:
+ return coord, elements
+ else:
+ return coord
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27070&r1=27069&r2=27070&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Thu Dec 11 09:44:53 2014
@@ -34,6 +34,7 @@
from lib.io import get_file_path, open_write_file, write_data
from lib.selection import tokenise
from lib.sequence import write_spin_data
+from lib.structure.internal.coordinates import assemble_coord_array
from lib.structure.internal.displacements import Displacements
from lib.structure.internal.object import Internal
from lib.structure.represent.diffusion_tensor import diffusion_tensor
@@ -186,14 +187,14 @@
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.
+ @keyword pipes: The data pipes to assemble the coordinates from.
@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.
+ @keyword models: The list of models for each data pipe. 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.
+ @keyword molecules: The list of molecules for each data pipe. 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
+ @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), and the list of element names for each atom (if the elements
flag is set).
@rtype: numpy rank-3 float64 array, list of str
"""
@@ -215,104 +216,16 @@
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 = []
+ # Assemble the structural objects.
+ objects = []
+ object_names = []
for pipe_index in range(len(pipes)):
- # Printout.
- print(" Data pipe: %s" % pipes[pipe_index])
-
- # 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)
-
- # 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
-
- # Printout.
- print(" Model: %s" % model.num)
-
- # Extend the lists.
- if molecules == None:
- atom_ids.append([])
- atom_pos.append({})
- atom_elem.append({})
-
- # Add all coordinates and elements.
- 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.
- 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
-
- # 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)
-
- # Return the information.
- if elements_flag:
- return coord, elements
- else:
- return coord
+ objects.append(dp.structure)
+ 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)
def connect_atom(index1=None, index2=None):
r27070 - in /trunk: lib/structure/internal/__init__.py lib/structure/internal/coordinates.py pipe_control/structure/main.py