Author: bugman
Date: Thu Feb 19 10:38:59 2009
New Revision: 8831
URL: http://svn.gna.org/viewcvs/relax?rev=8831&view=rev
Log:
Converted all the remaining value user function to the new relax design.
Modified:
1.3/prompt/value.py
Modified: 1.3/prompt/value.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/value.py?rev=8831&r1=8830&r2=8831&view=diff
==============================================================================
--- 1.3/prompt/value.py (original)
+++ 1.3/prompt/value.py Thu Feb 19 10:38:59 2009
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2008 Edward d'Auvergne
#
+# Copyright (C) 2003-2009 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -53,15 +53,15 @@
self.__relax__ = relax
- def copy(self, run1=None, run2=None, param=None):
- """Function for copying residue specific data values from run1 to
run2.
+ def copy(self, pipe_from=None, pipe_to=None, param=None):
+ """Copy spin specific data values from one data pipe to another.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- run1: The name of the run to copy from.
-
- run2: The name of the run to copy to.
+ pipe_from: The name of the pipe to copy from.
+
+ pipe_to: The name of the pipe to copy to.
param: The parameter to copy.
@@ -71,15 +71,15 @@
Only one parameter may be selected, therefore the 'param' argument
should be a string.
- If this function is used to change values of previously minimised
runs, then the
+ If this function is used to change values of previously minimised
parameters, then the
minimisation statistics (chi-squared value, iteration count,
function count, gradient count,
- and Hessian count) will be reset to None.
+ and Hessian count) will be reset.
Examples
~~~~~~~~
- To copy the CSA values from the run 'm1' to 'm2', type:
+ To copy the CSA values from the data pipe 'm1' to 'm2', type:
relax> value.copy('m1', 'm2', 'CSA')
"""
@@ -87,35 +87,33 @@
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "value.copy("
- text = text + "run1=" + `run1`
- text = text + ", run2=" + `run2`
+ text = text + "pipe_from=" + `pipe_from`
+ text = text + ", pipe_to=" + `pipe_to`
text = text + ", param=" + `param` + ")"
print text
- # The run1 argument.
- if type(run1) != str:
- raise RelaxStrError, ('run1', run1)
-
- # The run2 argument.
- if type(run2) != str:
- raise RelaxStrError, ('run2', run2)
+ # The pipe_from argument.
+ if type(pipe_from) != str:
+ raise RelaxStrError, ('pipe_from', pipe_from)
+
+ # The pipe_to argument.
+ if type(pipe_to) != str:
+ raise RelaxStrError, ('pipe_to', pipe_to)
# The parameter.
if type(param) != str:
raise RelaxStrError, ('parameter', param)
# Execute the functional code.
- self.__relax__.generic.value.copy(run1=run1, run2=run2, param=param)
-
-
- def display(self, run=None, param=None):
- """Function for displaying residue specific data values.
+ self.__relax__.generic.value.copy(pipe_from=pipe_from,
pipe_to=pipe_to, param=param)
+
+
+ def display(self, param=None):
+ """Display spin specific data values.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- run: The name of the run.
-
param: The parameter to display.
@@ -128,38 +126,31 @@
Examples
~~~~~~~~
- To show all CSA values for the run 'm1', type:
-
- relax> value.display('m1', 'CSA')
+ To show all CSA values, type:
+
+ relax> value.display('CSA')
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "value.display("
- text = text + "run=" + `run`
- text = text + ", param=" + `param` + ")"
+ text = text + "param=" + `param` + ")"
print text
-
- # The run name.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
# The parameter.
if type(param) != str:
raise RelaxStrError, ('parameter', param)
# Execute the functional code.
- self.__relax__.generic.value.display(run=run, param=param)
-
-
- def read(self, run=None, param=None, scaling=1.0, file=None, num_col=0,
name_col=1, data_col=2, error_col=3, sep=None):
- """Function for reading residue specific data values from a file.
+ self.__relax__.generic.value.display(param=param)
+
+
+ def read(self, param=None, scaling=1.0, file=None, num_col=0,
name_col=1, data_col=2, error_col=3, sep=None):
+ """Read spin specific data values from a file.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- run: The name of the run.
-
param: The parameter.
scaling: The factor to scale parameters by.
@@ -183,7 +174,7 @@
Only one parameter may be selected, therefore the 'param' argument
should be a string. If
the file only contains values and no errors, set the error column
argument to None.
- If this function is used to change values of previously minimised
runs, then the
+ If this function is used to change values of previously minimised
parameters, then the
minimisation statistics (chi-squared value, iteration count,
function count, gradient count,
and Hessian count) will be reset to None.
@@ -191,20 +182,19 @@
Examples
~~~~~~~~
- To load CSA values for the run 'm1' from the file 'csa_values' in
the directory 'data', type
- any of the following:
-
- relax> value.read('m1', 'CSA', 'data/csa_value')
- relax> value.read('m1', 'CSA', 'data/csa_value', 0, 1, 2, 3, None, 1)
- relax> value.read(run='m1', param='CSA', file='data/csa_value',
num_col=0, name_col=1,
+ To load CSA values from the file 'csa_values' in the directory
'data', type one of the
+ following:
+
+ relax> value.read('CSA', 'data/csa_value')
+ relax> value.read('CSA', 'data/csa_value', 0, 1, 2, 3, None, 1)
+ relax> value.read(param='CSA', file='data/csa_value', num_col=0,
name_col=1,
data_col=2, error_col=3, sep=None)
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "value.read("
- text = text + "run=" + `run`
- text = text + ", param=" + `param`
+ text = text + "param=" + `param`
text = text + ", scaling=" + `scaling`
text = text + ", file=" + `file`
text = text + ", num_col=" + `num_col`
@@ -214,10 +204,6 @@
text = text + ", sep=" + `sep` + ")"
print text
- # The run name.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
-
# The parameter.
if type(param) != str:
raise RelaxStrError, ('parameter', param)
@@ -251,11 +237,11 @@
raise RelaxNoneStrError, ('column separator', sep)
# Execute the functional code.
- self.__relax__.generic.value.read(run=run, param=param,
scaling=scaling, file=file, num_col=num_col, name_col=name_col,
data_col=data_col, error_col=error_col, sep=sep)
+ self.__relax__.generic.value.read(param=param, scaling=scaling,
file=file, num_col=num_col, name_col=name_col, data_col=data_col,
error_col=error_col, sep=sep)
def set(self, val=None, param=None, spin_id=None):
- """Function for setting spin specific data values.
+ """Set spin specific data values.
Keyword arguments
~~~~~~~~~~~~~~~~~
@@ -428,13 +414,11 @@
def write(self, param=None, file=None, dir=None, force=False):
- """Function for writing residue specific data values to a file.
+ """Write spin specific data values to a file.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- run: The name of the run.
-
param: The parameter.
file: The name of the file.
@@ -461,7 +445,7 @@
relax> value.write(param='CSA', file='csa.txt')
- To write the NOE values to the file 'noe', type:
+ To write the NOE values to the file 'noe', type one of:
relax> value.write('noe', 'noe.out')
relax> value.write(param='noe', file='noe.out')
r8831 - /1.3/prompt/value.py