Author: bugman
Date: Thu Dec 18 12:23:42 2014
New Revision: 27130
URL: http://svn.gna.org/viewcvs/relax?rev=27130&view=rev
Log:
Shifted the matrix output of the structure.atomic_fluctuations user function
into lib.plotting.text.
The new lib.plotting.text module will be used by the relax library plotting API
to output data into
plain text format. The current correlation_matrix() function, which has been
added to the API
correlation_matrix() function dictionary, simply has the file writing code of
the
structure.atomic_fluctuations user function. This significantly simplifies the
user function.
Added:
trunk/lib/plotting/text.py
- copied, changed from r27128, trunk/lib/plotting/gnuplot.py
Modified:
trunk/lib/plotting/__init__.py
trunk/lib/plotting/api.py
trunk/pipe_control/structure/main.py
Modified: trunk/lib/plotting/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/plotting/__init__.py?rev=27130&r1=27129&r2=27130&view=diff
==============================================================================
--- trunk/lib/plotting/__init__.py (original)
+++ trunk/lib/plotting/__init__.py Thu Dec 18 12:23:42 2014
@@ -25,5 +25,6 @@
# The package content list.
__all__ = [
'api',
- 'gnuplot'
+ 'gnuplot',
+ 'text'
]
Modified: trunk/lib/plotting/api.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/plotting/api.py?rev=27130&r1=27129&r2=27130&view=diff
==============================================================================
--- trunk/lib/plotting/api.py (original)
+++ trunk/lib/plotting/api.py Thu Dec 18 12:23:42 2014
@@ -25,6 +25,7 @@
# relax module imports.
from lib.errors import RelaxError
from lib.plotting import gnuplot
+from lib.plotting import text
def correlation_matrix(format=None, matrix=None, labels=None, file=None,
dir=None, force=False):
@@ -44,7 +45,8 @@
# The supported formats.
function = {
- 'gnuplot': gnuplot.correlation_matrix
+ 'gnuplot': gnuplot.correlation_matrix,
+ 'text': text.correlation_matrix
}
# Unsupported format.
Copied: trunk/lib/plotting/text.py (from r27128, trunk/lib/plotting/gnuplot.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/plotting/text.py?p2=trunk/lib/plotting/text.py&p1=trunk/lib/plotting/gnuplot.py&r1=27128&r2=27130&rev=27130&view=diff
==============================================================================
--- trunk/lib/plotting/gnuplot.py (original)
+++ trunk/lib/plotting/text.py Thu Dec 18 12:23:42 2014
@@ -20,10 +20,10 @@
###############################################################################
# Module docstring.
-"""Module for data plotting using gnuplot."""
+"""Module for data plotting in plain text format."""
# relax module imports.
-from lib.io import open_write_file, swap_extension
+from lib.io import open_write_file
def correlation_matrix(matrix=None, labels=None, file=None, dir=None,
force=False):
@@ -39,17 +39,32 @@
@type dir: str or None
"""
- # The script file name.
- file_name = swap_extension(file=file, ext='gnu')
+ # Open the text file for writing.
+ output = open_write_file(file, dir=dir, force=force)
- # Open the script file for writing.
- output = open_write_file(file_name, dir=dir, force=force)
+ # The dimensions.
+ n = len(matrix)
- # Set the plot type.
- output.write("set pm3d map\n")
+ # The header line.
+ output.write('#')
+ for i in range(n):
+ if i == 0:
+ output.write(" %18s" % labels[i])
+ else:
+ output.write(" %20s" % labels[i])
+ output.write('\n')
- # Load and show the text data.
- output.write("splot \"%s\" matrix\n" % file)
+ # Output the matrix.
+ for i in range(n):
+ for j in range(n):
+ # Output the matrix.
+ if j == 0:
+ output.write("%20.15f" % matrix[i, j])
+ else:
+ output.write(" %20.15f" % matrix[i, j])
+
+ # End of the current line.
+ output.write('\n')
# Close the file.
output.close()
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27130&r1=27129&r2=27130&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Thu Dec 18 12:23:42 2014
@@ -251,9 +251,6 @@
# Checks.
check_pipe()
check_structure()
- format_list = ['text', 'gnuplot']
- if format not in format_list:
- raise RelaxError("The format '%s' must be one of %s." % (format,
format_list))
# 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)
@@ -266,18 +263,10 @@
output = open_write_file(file, dir=dir, force=force)
# The header line.
- output.write('#')
labels = []
for i in range(len(atom_names)):
# The spin identification string.
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]))
-
- # Output the spin ID.
- if i == 0:
- output.write(" %18s" % labels[i])
- else:
- output.write(" %20s" % labels[i])
- output.write('\n')
# Generate the pairwise matrix.
n = len(atom_names)
@@ -292,22 +281,8 @@
# Calculate and store the corrected sample standard deviation.
matrix[i, j] = std(array(dist, float64), ddof=1)
- # Output the matrix.
- if j == 0:
- output.write("%20.15f" % matrix[i, j])
- else:
- output.write(" %20.15f" % matrix[i, j])
-
- # End of the current line.
- output.write('\n')
-
- # Close the file.
- output.close()
-
- # The gnuplot script.
- if format == 'gnuplot':
- # Call the plotting API.
- correlation_matrix(format=format, matrix=matrix, labels=labels,
file=file, dir=dir, force=force)
+ # Call the plotting API.
+ correlation_matrix(format=format, matrix=matrix, labels=labels, file=file,
dir=dir, force=force)
def connect_atom(index1=None, index2=None):
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