Author: bugman
Date: Sun Mar 24 17:52:33 2013
New Revision: 19131
URL: http://svn.gna.org/viewcvs/relax?rev=19131&view=rev
Log:
Moved the residual pipe_control.structure.api_base module to
lib.structure.internal.displacements.
This is because the base module still contained the Displacements class.
Added:
trunk/lib/structure/internal/displacements.py
- copied, changed from r19128, trunk/pipe_control/structure/api_base.py
Removed:
trunk/pipe_control/structure/api_base.py
Modified:
trunk/lib/structure/internal/__init__.py
trunk/pipe_control/structure/__init__.py
trunk/pipe_control/structure/internal.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=19131&r1=19130&r2=19131&view=diff
==============================================================================
--- trunk/lib/structure/internal/__init__.py (original)
+++ trunk/lib/structure/internal/__init__.py Sun Mar 24 17:52:33 2013
@@ -23,6 +23,7 @@
"""The relax-lib structure.internal package - the internal structural
object."""
__all__ = [
+ 'displacements',
'models',
'molecules'
]
Copied: trunk/lib/structure/internal/displacements.py (from r19128,
trunk/pipe_control/structure/api_base.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/displacements.py?p2=trunk/lib/structure/internal/displacements.py&p1=trunk/pipe_control/structure/api_base.py&r1=19128&r2=19131&rev=19131&view=diff
==============================================================================
--- trunk/pipe_control/structure/api_base.py (original)
+++ trunk/lib/structure/internal/displacements.py Sun Mar 24 17:52:33 2013
@@ -20,12 +20,7 @@
###############################################################################
# Module docstring.
-"""The API for accessing, creating, and modifying structural information.
-
-The full API is documented within this base class object. Each available
API call is given as a
-prototype method stub (or functional method) with all arguments, raised
errors, and return values
-documented.
-"""
+"""The objects representing displacement information in the internal
structural object."""
# relax module import.
from data_store.relax_xml import object_to_xml, xml_to_object
Modified: trunk/pipe_control/structure/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/__init__.py?rev=19131&r1=19130&r2=19131&view=diff
==============================================================================
--- trunk/pipe_control/structure/__init__.py (original)
+++ trunk/pipe_control/structure/__init__.py Sun Mar 24 17:52:33 2013
@@ -36,7 +36,6 @@
"""
__all__ = [
- 'api_base',
'geometric',
'internal',
'main',
Removed: trunk/pipe_control/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/api_base.py?rev=19130&view=auto
==============================================================================
--- trunk/pipe_control/structure/api_base.py (original)
+++ trunk/pipe_control/structure/api_base.py (removed)
@@ -1,182 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2008-2013 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.
-"""The API for accessing, creating, and modifying structural information.
-
-The full API is documented within this base class object. Each available
API call is given as a
-prototype method stub (or functional method) with all arguments, raised
errors, and return values
-documented.
-"""
-
-# relax module import.
-from data_store.relax_xml import object_to_xml, xml_to_object
-from lib.structure.superimpose import kabsch
-from lib.structure.internal.models import ModelContainer
-
-
-class Displacements:
- """A special object for representing rotational and translational
displacements between models."""
-
- def __init__(self):
- """Initialise the storage objects."""
-
- # The displacement structures.
- self._translation_vector = {}
- self._translation_distance = {}
- self._rotation_matrix = {}
- self._rotation_axis = {}
- self._rotation_angle = {}
-
-
- def _calculate(self, model_from=None, model_to=None, coord_from=None,
coord_to=None, centroid=None):
- """Calculate the rotational and translational displacements using
the given coordinate sets.
-
- This uses the U{Kabsch
algorithm<http://en.wikipedia.org/wiki/Kabsch_algorithm>}.
-
-
- @keyword model_from: The model number of the starting structure.
- @type model_from: int
- @keyword model_to: The model number of the ending structure.
- @type model_to: int
- @keyword coord_from: The list of atomic coordinates for the
starting structure.
- @type coord_from: numpy rank-2, Nx3 array
- @keyword coord_to: The list of atomic coordinates for the
ending structure.
- @type coord_to: numpy rank-2, Nx3 array
- @keyword centroid: An alternative position of the centroid,
used for studying pivoted systems.
- @type centroid: list of float or numpy rank-1, 3D array
- """
-
- # Initialise structures if necessary.
- if not model_from in self._translation_vector:
- self._translation_vector[model_from] = {}
- if not model_from in self._translation_distance:
- self._translation_distance[model_from] = {}
- if not model_from in self._rotation_matrix:
- self._rotation_matrix[model_from] = {}
- if not model_from in self._rotation_axis:
- self._rotation_axis[model_from] = {}
- if not model_from in self._rotation_angle:
- self._rotation_angle[model_from] = {}
-
- # The Kabsch algorithm.
- trans_vect, trans_dist, R, axis, angle, pivot =
kabsch(name_from='model %s'%model_from, name_to='model %s'%model_to,
coord_from=coord_from, coord_to=coord_to, centroid=centroid)
-
- # Store the data.
- self._translation_vector[model_from][model_to] = trans_vect
- self._translation_distance[model_from][model_to] = trans_dist
- self._rotation_matrix[model_from][model_to] = R
- self._rotation_axis[model_from][model_to] = axis
- self._rotation_angle[model_from][model_to] = angle
-
-
- def from_xml(self, str_node, dir=None, file_version=1):
- """Recreate the structural object from the XML structural object
node.
-
- @param str_node: The structural object XML node.
- @type str_node: xml.dom.minicompat.Element instance
- @keyword dir: The name of the directory containing the
results file.
- @type dir: str
- @keyword file_version: The relax XML version of the XML file.
- @type file_version: int
- """
-
- # Get the pairs of displacements.
- pair_nodes = str_node.getElementsByTagName('pair')
-
- # Loop over the pairs.
- for pair_node in pair_nodes:
- # Get the two models.
- model_from = int(pair_node.getAttribute('model_from'))
- model_to = int(pair_node.getAttribute('model_to'))
-
- # Initialise structures if necessary.
- if not model_from in self._translation_vector:
- self._translation_vector[model_from] = {}
- if not model_from in self._translation_distance:
- self._translation_distance[model_from] = {}
- if not model_from in self._rotation_matrix:
- self._rotation_matrix[model_from] = {}
- if not model_from in self._rotation_axis:
- self._rotation_axis[model_from] = {}
- if not model_from in self._rotation_angle:
- self._rotation_angle[model_from] = {}
-
- # A temporary container to place the Python objects into.
- cont = ModelContainer()
-
- # Recreate the Python objects.
- xml_to_object(pair_node, cont, file_version=file_version)
-
- # Repackage the data.
- for name in ['translation_vector', 'translation_distance',
'rotation_matrix', 'rotation_axis', 'rotation_angle']:
- # The objects.
- obj = getattr(self, '_'+name)
- obj_temp = getattr(cont, name)
-
- # Store.
- obj[model_from][model_to] = obj_temp
-
-
- def to_xml(self, doc, element):
- """Create XML elements for each model.
-
- @param doc: The XML document object.
- @type doc: xml.dom.minidom.Document instance
- @param element: The element to add the displacement XML elements to.
- @type element: XML element object
- """
-
- # Loop over the starting models.
- start_models = sorted(self._translation_vector.keys())
- for model_from in start_models:
- # Loop over the ending models.
- end_models = sorted(self._translation_vector[model_from].keys())
- for model_to in end_models:
- # Create an XML element for each pair.
- pair_element = doc.createElement('pair')
- element.appendChild(pair_element)
-
- # Set the attributes.
- pair_element.setAttribute('desc', 'The displacement from
model %s to model %s' % (model_from, model_to))
- pair_element.setAttribute('model_from', str(model_from))
- pair_element.setAttribute('model_to', str(model_to))
-
- # The objects to store.
- obj_names = [
- '_translation_vector',
- '_translation_distance',
- '_rotation_matrix',
- '_rotation_axis',
- '_rotation_angle'
- ]
-
- # Store the objects.
- for i in range(len(obj_names)):
- # Create a new element for this object, and add it to
the main element.
- sub_elem = doc.createElement(obj_names[i][1:])
- pair_element.appendChild(sub_elem)
-
- # Get the sub-object.
- subobj = getattr(self,
obj_names[i])[model_from][model_to]
-
- # Add the value to the sub element.
- object_to_xml(doc, sub_elem, value=subobj)
Modified: trunk/pipe_control/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/internal.py?rev=19131&r1=19130&r2=19131&view=diff
==============================================================================
--- trunk/pipe_control/structure/internal.py (original)
+++ trunk/pipe_control/structure/internal.py Sun Mar 24 17:52:33 2013
@@ -34,12 +34,12 @@
# relax module imports.
from data_store.relax_xml import object_to_xml, xml_to_object
from pipe_control.mol_res_spin import Selection
-from pipe_control.structure.api_base import Displacements
from lib import regex
from lib.check_types import is_float
from lib.errors import RelaxError, RelaxNoneIntError, RelaxNoPdbError
from lib.io import file_root, open_read_file
from lib.structure import pdb_read, pdb_write
+from lib.structure.displacements import Displacements
from lib.structure.internal.models import ModelList
from lib.structure.internal.molecules import MolContainer
from lib.warnings import RelaxWarning
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=19131&r1=19130&r2=19131&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Sun Mar 24 17:52:33 2013
@@ -34,13 +34,13 @@
from pipe_control.interatomic import interatomic_loop
from pipe_control.mol_res_spin import create_spin, exists_mol_res_spin_data,
generate_spin_id_unique, linear_ave, return_molecule, return_residue,
return_spin, spin_loop
from pipe_control import pipes
-from pipe_control.structure.api_base import Displacements
from pipe_control.structure.internal import Internal
-from lib.structure.statistics import atomic_rmsd
-from lib.structure.superimpose import fit_to_first, fit_to_mean
from target_functions.ens_pivot_finder import Pivot_finder
from lib.errors import RelaxError, RelaxFileError, RelaxNoPdbError,
RelaxNoSequenceError
from lib.io import get_file_path, open_write_file, write_data,
write_spin_data
+from lib.structure.displacements import Displacements
+from lib.structure.statistics import atomic_rmsd
+from lib.structure.superimpose import fit_to_first, fit_to_mean
from lib.warnings import RelaxWarning, RelaxNoPDBFileWarning,
RelaxZeroVectorWarning
r19131 - in /trunk: lib/structure/internal/ pipe_control/structure/