Author: bugman
Date: Fri Dec 19 11:23:46 2014
New Revision: 27144
URL: http://svn.gna.org/viewcvs/relax?rev=27144&view=rev
Log:
Implemented angular fluctuations for the structure.atomic_fluctuations user
function.
This adds the measure argument to the user function to allow either the
default of 'distance' or the
'angle' setting to be chosen. The implementation is confirmed by the
Structure.test_atomic_fluctuations_angle system test which now passes.
Modified:
trunk/pipe_control/structure/main.py
trunk/test_suite/system_tests/structure.py
trunk/user_functions/structure.py
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27144&r1=27143&r2=27144&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Fri Dec 19 11:23:46 2014
@@ -21,7 +21,7 @@
# Python module imports.
from minfx.generic import generic_minimise
-from numpy import array, float64, std, zeros
+from numpy import array, average, float64, std, zeros
from numpy.linalg import norm
from os import F_OK, access, getcwd
from re import search
@@ -31,6 +31,7 @@
# relax module imports.
from lib.check_types import is_float
from lib.errors import RelaxError, RelaxFileError
+from lib.geometry.vectors import vector_angle_atan2
from lib.io import get_file_path, open_write_file, write_data
from lib.plotting.api import correlation_matrix
from lib.selection import tokenise
@@ -227,7 +228,7 @@
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 atomic_fluctuations(pipes=None, models=None, molecules=None,
atom_id=None, file=None, format='text', dir=None, force=False):
+def atomic_fluctuations(pipes=None, models=None, molecules=None,
atom_id=None, measure='distance', file=None, format='text', dir=None,
force=False):
"""Write out a correlation matrix of pairwise interatomic distance
fluctuations between different structures.
@keyword pipes: The data pipes to generate the interatomic distance
fluctuation correlation matrix for.
@@ -238,6 +239,8 @@
@type molecules: None or list of lists of str
@keyword atom_id: The atom identification string of the coordinates of
interest. This matches the spin ID string format.
@type atom_id: str or None
+ @keyword measure: The type of fluctuation to measure. This can be
either 'distance' or 'angle'.
+ @type measure: str
@keyword file: The name of the file to write.
@type file: str
@keyword format: The output format. This can be set to "text" for
text file output, or "gnuplot" for creating a gnuplot script.
@@ -251,6 +254,9 @@
# Checks.
check_pipe()
check_structure()
+ allowed_measures = ['distance', 'angle']
+ if measure not in allowed_measures:
+ raise RelaxError("The measure '%s' must be one of %s." % (measure,
allowed_measures))
# Assemble the atomic coordinates.
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)
@@ -267,17 +273,41 @@
for i in range(n):
labels.append(generate_spin_id_unique(mol_name=mol_names[i],
res_num=res_nums[i], res_name=res_names[i], spin_name=atom_names[i]))
- # Generate the pairwise matrix.
+ # Initialise the SD matrix and other structures.
matrix = zeros((n, n), float64)
- for i in range(n):
- for j in range(n):
- # The interatomic distances between each structure.
- dist = []
- for k in range(len(coord)):
- dist.append(norm(coord[k, i] - coord[k, j]))
-
- # Calculate and store the corrected sample standard deviation.
- matrix[i, j] = std(array(dist, float64), ddof=1)
+ vectors = zeros((len(coord), 3), float64)
+ angles = zeros(len(coord), float64)
+
+ # Generate the pairwise distance SD matrix.
+ if measure == 'distance':
+ for i in range(n):
+ for j in range(n):
+ # The interatomic distances between each structure.
+ dist = []
+ for k in range(len(coord)):
+ dist.append(norm(coord[k, i] - coord[k, j]))
+
+ # Calculate and store the corrected sample standard
deviation.
+ matrix[i, j] = std(array(dist, float64), ddof=1)
+
+ # Generate the pairwise angle SD matrix.
+ elif measure == 'angle':
+ # Loop over the atom pairs.
+ for i in range(n):
+ for j in range(n):
+ # The interatomic vectors.
+ for k in range(len(coord)):
+ vectors[k] = coord[k, i] - coord[k, j]
+
+ # The average vector.
+ ave_vect = average(vectors, axis=0)
+
+ # The intervector angles.
+ for k in range(len(coord)):
+ angles[k] = vector_angle_atan2(ave_vect, vectors[k])
+
+ # Calculate and store the corrected sample standard
deviation.
+ matrix[i, j] = std(angles, ddof=1)
# Call the plotting API.
correlation_matrix(format=format, matrix=matrix, labels=labels,
file=file, dir=dir, force=force)
Modified: trunk/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=27144&r1=27143&r2=27144&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Fri Dec 19 11:23:46 2014
@@ -353,7 +353,7 @@
# Run the structure.atomic_fluctuations user function and collect
the results in a dummy file object.
file = DummyFileObject()
- self.interpreter.structure.atomic_fluctuations(measure='angles',
atom_id='@N,CA', file=file, format='text')
+ self.interpreter.structure.atomic_fluctuations(measure='angle',
atom_id='@N,CA', file=file, format='text')
# The atom positions.
n = array([[ 9.464, -9.232, 27.573], [ 9.211, -9.425, 26.970],
[ 7.761, -6.392, 27.161]], float64)
Modified: trunk/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=27144&r1=27143&r2=27144&view=diff
==============================================================================
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Fri Dec 19 11:23:46 2014
@@ -294,6 +294,16 @@
can_be_none = True
)
uf.add_keyarg(
+ name = "measure",
+ py_type = "str",
+ default = "distance",
+ desc_short = "measure",
+ desc = "The type of fluctuation to investigate. This allows for both
interatomic distance and vector angle fluctuations to be calculated.",
+ wiz_element_type = "combo",
+ wiz_combo_choices = ["Interatomic distance fluctuations", "Interatomic
vector angle fluctuations"],
+ wiz_combo_data = ["distance", "angle"]
+)
+uf.add_keyarg(
name = "file",
py_type = "str_or_inst",
arg_type = "file sel",
@@ -328,7 +338,9 @@
)
# Description.
uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This is used to visualise the interatomic
distance fluctuations between different structures. The corrected sample
standard deviation (SD) is calculated for the distances between all atom
pairs, resulting in a pairwise matrix of SD values. The matrix will be
output into a text file.")
+uf.desc[-1].add_paragraph("This is used to visualise the interatomic
fluctuations between different structures. By setting the measure argument,
this can be set to either the fluctuations of the interatomic distances or
the fluctuations of the interatomic vector angles:")
+uf.desc[-1].add_item_list_element("'distance'", "This is the default. The
corrected sample standard deviation (SD) is calculated for the distances
between all atom pairs, resulting in a pairwise matrix of SD values.")
+uf.desc[-1].add_item_list_element("'angle'", "The corrected sample standard
deviation (SD) is calculated for the angles between the inter atom vectors
all atom pairs to an average vector. This also produces a pairwise matrix of
SD values.")
uf.desc[-1].add_paragraph("In addition to creating the text file, a second
file will be created if the format argument is set to anything other than the
text file. It will have the same name as the text file, however the file
extension will be changed to match the format. The currently supported
formats are:")
uf.desc[-1].add_item_list_element("'text'", "This is the default value and
will result in a single text file being created.")
uf.desc[-1].add_item_list_element("'gnuplot'", "This will create a script
for visualising the correlation matrix using gnuplot.")
r27144 - in /trunk: pipe_control/structure/main.py test_suite/system_tests/structure.py user_functions/structure.py