Author: bugman
Date: Wed Sep 24 17:54:52 2008
New Revision: 7250
URL: http://svn.gna.org/viewcvs/relax?rev=7250&view=rev
Log:
Updated the grace.write() user function interface to the new design.
Modified:
1.3/prompt/grace.py
Modified: 1.3/prompt/grace.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/grace.py?rev=7250&r1=7249&r2=7250&view=diff
==============================================================================
--- 1.3/prompt/grace.py (original)
+++ 1.3/prompt/grace.py Wed Sep 24 17:54:52 2008
@@ -101,7 +101,7 @@
self.__relax__.generic.grace.view(file=file, dir=dir,
grace_exe=grace_exe)
- def write(self, x_data_type='res', y_data_type=None, res_num=None,
res_name=None, plot_data='value', norm=0, file=None, dir='grace',
force=False):
+ def write(self, x_data_type='spin', y_data_type=None, spin_id=None,
plot_data='value', file=None, dir='grace', force=False, norm=False):
"""Function for creating a grace '.agr' file.
Keyword Arguments
@@ -111,9 +111,7 @@
y_data_type: The data type for the Y-axis (no regular expression is
allowed).
- res_num: The residue number (regular expression is allowed).
-
- res_name: The residue name (regular expression is allowed).
+ spin_id: The spin identification string.
plot_data: The data to use for the plot.
@@ -133,20 +131,17 @@
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
keyword arguments can
be used to create various types of plot. These include the X-axis
and Y-axis data types,
- the residue number and name selection arguments, and an argument for
selecting what to
- actually plot.
+ the spin identification string, and an argument for selecting what
to actually plot.
The X-axis and Y-axis data type arguments should be plain strings,
regular expression is not
allowed. If the X-axis data type argument is not given, the plot
will default to having the
- residue number along the x-axis. The two axes of the Grace plot can
be absolutely any of
+ 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 run.
-
- The residue number and name arguments can be used to limit the
residues used in the plot.
- The default is that all residues will be used, however, these
arguments can be used to
- select a subset of all residues, or a single residue for plots of
Monte Carlo simulations,
- etc. Regular expression is allowed for both the residue number and
name, and the number can
- either be an integer or a string.
+ the data must belong to the same data pipe.
+
+ 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, these arguments can
be used to select a
+ subset of all spins, or a single spin for plots of Monte Carlo
simulations, etc.
The property which is actually plotted can be controlled by the
'plot_data' argument. It
can be one of the following:
@@ -155,24 +150,23 @@
'sims': Plot the simulation values.
Normalisation is only allowed for series type data, for example the
R2 exponential curves,
- and will be ignored for all other data types. If the norm flag is
set to one then the
+ and will be ignored for all other data types. If the norm flag is
set to True then the
y-value of the first point of the series will be set to 1. This
normalisation is useful for
- emphasising errors in the data sets.
+ highlighting errors in the data sets.
Examples
~~~~~~~~
- To write the NOE values for all residues to the Grace file 'noe.agr',
- type:
-
- relax> grace.write('res', 'noe', file='noe.agr')
+ To write the NOE values for all spins to the Grace file 'noe.agr',
type one of:
+
+ relax> grace.write('spin', 'noe', file='noe.agr')
relax> grace.write(y_data_type='noe', file='noe.agr')
- relax> grace.write(x_data_type='res', y_data_type='noe',
file='noe.agr')
+ relax> grace.write(x_data_type='spin', y_data_type='noe',
file='noe.agr')
relax> grace.write(y_data_type='noe', file='noe.agr', force=True)
- To create a Grace file of 'S2' vs. 'te' for all residues, type:
+ To create a Grace file of 'S2' vs. 'te' for all spins, type one of:
relax> grace.write('S2', 'te', file='s2_te.agr')
relax> grace.write(x_data_type='S2', y_data_type='te',
file='s2_te.agr')
@@ -180,10 +174,10 @@
To create a Grace file of the Monte Carlo simulation values of 'Rex'
vs. 'te' for residue
- 123, type:
-
- relax> grace.write('Rex', 'te', res_num=123, plot_data='sims',
file='s2_te.agr')
- relax> grace.write(x_data_type='Rex', y_data_type='te', res_num=123,
+ 123, type one of:
+
+ relax> grace.write('Rex', 'te', spin_id=':123', plot_data='sims',
file='s2_te.agr')
+ relax> grace.write(x_data_type='Rex', y_data_type='te',
spin_id=':123',
plot_data='sims', file='s2_te.agr')
@@ -194,8 +188,8 @@
normalisation, whereby the initial peak intensity of each residue
I(0) is set to 1,
emphasises any problems. To produce this Grace file, type:
- relax> grace.write(name, x_data_type='relax_times',
y_data_type='ave_int',
- norm=1, file='intensities_norm.agr', force=True)
+ relax> grace.write(x_data_type='relax_times', y_data_type='ave_int',
+ file='intensities_norm.agr', force=True,
norm=True)
"""
# Function intro text.
@@ -203,13 +197,12 @@
text = sys.ps3 + "grace.write("
text = text + "x_data_type=" + `x_data_type`
text = text + ", y_data_type=" + `y_data_type`
- text = text + ", res_num=" + `res_num`
- text = text + ", res_name=" + `res_name`
+ text = text + ", spin_id=" + `spin_id`
text = text + ", plot_data=" + `plot_data`
- text = text + ", norm=" + `norm`
text = text + ", file=" + `file`
text = text + ", dir=" + `dir`
- text = text + ", force=" + `force` + ")"
+ text = text + ", force=" + `force`
+ text = text + ", norm=" + `norm` + ")"
print text
# Data type for x-axis.
@@ -220,13 +213,9 @@
if type(y_data_type) != str:
raise RelaxStrError, ('y data type', y_data_type)
- # Residue number.
- if res_num != None and type(res_num) != int and type(res_num) != str:
- raise RelaxNoneIntStrError, ('residue number', res_num)
-
- # Residue name.
- if res_name != None and type(res_name) != str:
- raise RelaxNoneStrError, ('residue name', res_name)
+ # Spin ID string.
+ if spin_id != None and type(spin_id) != str:
+ raise RelaxNoneStrError, ('spin identification string', spin_id)
# The plot data.
if type(plot_data) != str:
@@ -244,8 +233,12 @@
if type(force) != bool:
raise RelaxBoolError, ('force flag', force)
+ # The normalisation flag.
+ if type(norm) != bool:
+ raise RelaxBoolError, ('normalisation flag', norm)
+
# Execute the functional code.
- grace.write(x_data_type=x_data_type, y_data_type=y_data_type,
res_num=res_num, res_name=res_name, plot_data=plot_data, norm=norm,
file=file, dir=dir, force=force)
+ grace.write(x_data_type=x_data_type, y_data_type=y_data_type,
res_num=res_num, res_name=res_name, plot_data=plot_data, file=file, dir=dir,
force=force, norm=norm)
r7250 - /1.3/prompt/grace.py