Author: bugman
Date: Mon Apr 8 16:45:13 2013
New Revision: 19402
URL: http://svn.gna.org/viewcvs/relax?rev=19402&view=rev
Log:
The grace.write user function data type argument sequence values have changed.
Instead of 'spin', this can now be 'res_num' or 'spin_num' to specify that
either the residue number
or spin number should be plotted on the desired axis. The x_data_type now
defaults to 'res_num'.
Modified:
trunk/pipe_control/grace.py
trunk/user_functions/grace.py
Modified: trunk/pipe_control/grace.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/grace.py?rev=19402&r1=19401&r2=19402&view=diff
==============================================================================
--- trunk/pipe_control/grace.py (original)
+++ trunk/pipe_control/grace.py Mon Apr 8 16:45:13 2013
@@ -60,7 +60,7 @@
axis_labels = [None, None]
for i in range(2):
# Determine the sequence data type.
- if data_type[i] == 'spin':
+ if data_type[i] == 'res_num':
seq_type[i] = 'res'
# Analysis specific methods for making labels.
@@ -74,12 +74,12 @@
return_grace_string =
specific_analyses.setup.get_specific_fn('return_grace_string',
pipes.get_type())
# Test if the axis data type is a minimisation statistic.
- if data_type[i] and data_type[i] != 'spin' and
pipe_control.minimise.return_data_name(data_type[i]):
+ if data_type[i] and data_type[i] != 'res_num' and
pipe_control.minimise.return_data_name(data_type[i]):
return_units = pipe_control.minimise.return_units
return_grace_string =
pipe_control.minimise.return_grace_string
# Some axis default values for spin data.
- if data_type[i] == 'spin':
+ if data_type[i] == 'res_num':
# Residue only data.
if seq_type[i] == 'res':
# Axis limits.
@@ -184,8 +184,8 @@
data_dict = False
# Specific x and y value returning functions.
- x_return_value, x_return_conversion_factor, x_get_type =
determine_functions(category=x_data_type)
- y_return_value, y_return_conversion_factor, y_get_type =
determine_functions(category=y_data_type)
+ x_return_value, x_return_conversion_factor, x_get_type =
determine_functions(data_name=x_data_type)
+ y_return_value, y_return_conversion_factor, y_get_type =
determine_functions(data_name=y_data_type)
# Number of graph sets.
if plot_data == 'sim':
@@ -215,7 +215,7 @@
continue
# The X data (plotted as residue numbers).
- if x_data_type == 'spin':
+ if x_data_type == 'res_num':
x_val = res_num
x_err = None
@@ -225,7 +225,7 @@
x_val, x_err = x_return_value(spin, x_data_type, sim=sim)
# The Y data (plotted as residue numbers).
- if y_data_type == 'spin':
+ if y_data_type == 'res_num':
y_val = res_num
y_err = None
@@ -320,12 +320,12 @@
point = data[0][index][-1]
# Conversion factors.
- if x_data_type != 'spin':
+ if x_data_type != 'res_num':
x_val[j] = x_val[j] /
x_return_conversion_factor(x_data_type)
- if x_err[j] and x_data_type != 'spin':
+ if x_err[j] and x_data_type != 'res_num':
x_err[j] = x_err[j] /
x_return_conversion_factor(x_data_type)
y_val[j] = y_val[j] / y_return_conversion_factor(y_data_type)
- if y_err[j] and y_data_type != 'spin':
+ if y_err[j] and y_data_type != 'res_num':
y_err[j] = y_err[j] /
y_return_conversion_factor(y_data_type)
# Append the data.
@@ -437,7 +437,7 @@
system(grace_exe + " " + file_path + " &")
-def write(x_data_type='spin', y_data_type=None, spin_id=None,
plot_data='value', file=None, dir=None, force=False, norm=True):
+def write(x_data_type='res_num', y_data_type=None, spin_id=None,
plot_data='value', file=None, dir=None, force=False, norm=True):
"""Writing data to a file.
@keyword x_data_type: The category of the X-axis data.
Modified: trunk/user_functions/grace.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/grace.py?rev=19402&r1=19401&r2=19402&view=diff
==============================================================================
--- trunk/user_functions/grace.py (original)
+++ trunk/user_functions/grace.py Mon Apr 8 16:45:13 2013
@@ -100,7 +100,7 @@
uf.title_short = "Grace file creation."
uf.add_keyarg(
name = "x_data_type",
- default = "spin",
+ default = "res_num",
py_type = "str",
desc_short = "x data type",
desc = "The data type for the X-axis (no regular expression is
allowed).",
@@ -119,7 +119,7 @@
name = "spin_id",
py_type = "str",
desc_short = "spin ID string",
- desc = "The spin identification string.",
+ desc = "The spin ID string.",
can_be_none = True
)
uf.add_keyarg(
@@ -175,9 +175,12 @@
)
# Description.
uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This is designed to be as flexible as possible so
that any combination of data can be plotted. The output is in the format of
a Grace plot (also known as ACE/gr, Xmgr, and xmgrace) which only supports
two dimensional plots. Three types of information can be used to create
various types of plot. These include the x-axis and y-axis data types, the
spin identification string, and the type of data plot.")
-uf.desc[-1].add_paragraph("The x-axis and y-axis data types should be plain
strings, regular expression is not allowed. If the x-axis data type is not
given, the plot will default to having the spin sequence along the x-axis.
The two axes of the Grace plot can be absolutely any of the data types listed
in the tables below. The only limitation, currently anyway, is that the data
must belong to the same data pipe.")
-uf.desc[-1].add_paragraph("The spin identification string can be used to
limit which spins are used in the plot. The default is that all spins will
be used, however, the ID string can be used to select a subset of all spins,
or a single spin for plots of Monte Carlo simulations, etc.")
+uf.desc[-1].add_paragraph("This is designed to be as flexible as possible so
that any combination of data can be plotted. The output is in the format of
a Grace plot (also known as ACE/gr, Xmgr, and xmgrace) which only supports
two dimensional plots. Three types of information can be used to create
various types of plot. These include the x-axis and y-axis data types, the
spin ID string, and the type of data plot.")
+uf.desc[-1].add_paragraph("The x-axis and y-axis data types should be plain
strings, regular expression is not allowed. The two axes of the Grace plot
can be any of the data types listed in the tables below. The only limitation
is that the data must belong to the same data pipe.")
+uf.desc[-1].add_paragraph("If the x-axis data type is not given, the plot
will default to having the residue numbering along the x-axis.Two special
data types for the axes are:")
+uf.desc[-1].add_item_list_element("'res_num'", "The axis will consist of the
residue numbering.")
+uf.desc[-1].add_item_list_element("'spin_num'", "The axis will consist of
the spin numbering.")
+uf.desc[-1].add_paragraph("The spin ID string can be used to limit which
spins are used in the plot. The default is that all spins will be used,
however, the ID string can be used to select a subset of all spins, or a
single spin for plots of Monte Carlo simulations, etc.")
uf.desc[-1].add_paragraph("The property which is actually plotted can be
controlled by the plot data setting. This can be one of the following:")
uf.desc[-1].add_item_list_element("'value'", "Plot values (with errors if
they exist).")
uf.desc[-1].add_item_list_element("'error'", "Plot errors.")
@@ -193,9 +196,9 @@
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To write the NOE values for all spins to the
Grace file 'noe.agr', type one of:")
-uf.desc[-1].add_prompt("relax> grace.write('spin', 'noe', file='noe.agr')")
+uf.desc[-1].add_prompt("relax> grace.write('res_num', 'noe',
file='noe.agr')")
uf.desc[-1].add_prompt("relax> grace.write(y_data_type='noe',
file='noe.agr')")
-uf.desc[-1].add_prompt("relax> grace.write(x_data_type='spin',
y_data_type='noe', file='noe.agr')")
+uf.desc[-1].add_prompt("relax> grace.write(x_data_type='res_num',
y_data_type='noe', file='noe.agr')")
uf.desc[-1].add_prompt("relax> grace.write(y_data_type='noe',
file='noe.agr', force=True)")
uf.desc[-1].add_paragraph("To create a Grace file of 's2' vs. 'te' for all
spins, type one of:")
uf.desc[-1].add_prompt("relax> grace.write('s2', 'te', file='s2_te.agr')")
r19402 - in /trunk: pipe_control/grace.py user_functions/grace.py