Author: bugman
Date: Sun Dec 9 12:15:34 2007
New Revision: 4137
URL: http://svn.gna.org/viewcvs/relax?rev=4137&view=rev
Log:
Updated the value.set() 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=4137&r1=4136&r2=4137&view=diff
==============================================================================
--- 1.3/prompt/value.py (original)
+++ 1.3/prompt/value.py Sun Dec 9 12:15:34 2007
@@ -248,27 +248,23 @@
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)
- def set(self, run=None, value=None, param=None, res_num=None,
res_name=None):
- """Function for setting residue specific data values.
+ def set(self, value=None, param=None, spin_id=None):
+ """Function for setting spin specific data values.
Keyword arguments
~~~~~~~~~~~~~~~~~
- run: The run to assign the values to.
-
value: The value(s).
param: The parameter(s).
- res_num: The residue number.
-
- res_name: The residue name.
+ spin_id: The spin identifier.
Description
~~~~~~~~~~~
- 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
results, then the
minimisation statistics (chi-squared value, iteration count,
function count, gradient count,
and Hessian count) will be reset to None.
@@ -311,86 +307,73 @@
|_______|_______|__________________________________________________________________________|
- Residue number and name argument
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- If the 'res_num' and 'res_name' arguments are left as the defaults
of None, then the
- function will be applied to all residues. Otherwise the residue
number can be set to either
- an integer for selecting a single residue or a python regular
expression string for
- selecting multiple residues. The residue name argument must be a
string and can use regular
- expression as well. If the data is global non-residue specific
data, such as diffusion
- tensor parameters, supplying the residue number and name will
terminate the program with an
- error.
+ Spin identification
+ ~~~~~~~~~~~~~~~~~~~
+
+ If the 'spin_id' argument is left as the default of None, then the
function will be applied
+ to all spins. If the data is global non-residue specific data, such
as diffusion tensor
+ parameters, supplying the spin identifier will terminate the program
with an error.
Examples
~~~~~~~~
- To set the parameter values for the run 'test' to the default
values, for all residues,
+ To set the parameter values for the current data pipe to the default
values, for all spins,
type:
- relax> value.set('test')
-
-
- To set the parameter values of residue 10, which is the model-free
run 'm4' and has the
- parameters {S2, te, Rex}, the following can be used. Rex term is
the value for the first
- given field strength.
-
- relax> value.set('m4', [0.97, 2.048*1e-9, 0.149], res_num=10)
- relax> value.set('m4', value=[0.97, 2.048*1e-9, 0.149], res_num=10)
-
-
- To set the CSA value for the model-free run 'tm3' to the default
value, type:
-
- relax> value.set('tm3', param='csa')
-
-
- To set the CSA value of all residues in the reduced spectral density
mapping run '600MHz' to
- -172 ppm, type:
-
- relax> value.set('600MHz', -172 * 1e-6, 'csa')
- relax> value.set('600MHz', value=-172 * 1e-6, param='csa')
-
-
- To set the NH bond length of all residues in the model-free run 'm5'
to 1.02 Angstroms,
- type:
-
- relax> value.set('m5', 1.02 * 1e-10, 'bond_length')
- relax> value.set('m5', value=1.02 * 1e-10, param='r')
-
-
- To set both the bond length and the CSA value for the run 'new' to
the default values, type:
-
- relax> value.set('new', param=['bond length', 'csa'])
-
-
- To set both tf and ts in the model-free run 'm6' to 100 ps, type:
-
- relax> value.set('m6', 100e-12, ['tf', 'ts'])
- relax> value.set('m6', value=100e-12, param=['tf', 'ts'])
-
-
- To set the S2 and te parameter values for model-free run 'm4' which
has the parameters
- {S2, te, Rex} to 0.56 and 13 ps, type:
-
- relax> value.set('m4', [0.56, 13e-12], ['S2', 'te'], 10)
- relax> value.set('m4', value=[0.56, 13e-12], param=['S2', 'te'],
res_num=10)
- relax> value.set(run='m4', value=[0.56, 13e-12], param=['S2', 'te'],
res_num=10)
+ relax> value.set()
+
+
+ To set the parameter values of residue 10, which is in the current
model-free data pipe 'm4'
+ and has the parameters {S2, te, Rex}, the following can be used.
Rex term is the value for
+ the first given field strength.
+
+ relax> value.set([0.97, 2.048*1e-9, 0.149], spin_id=':10')
+ relax> value.set(value=[0.97, 2.048*1e-9, 0.149], spin_id=':10')
+
+
+ To set the CSA value of all spins to the default value, type:
+
+ relax> value.set(param='csa')
+
+
+ To set the CSA value of all spins to -172 ppm, type:
+
+ relax> value.set(-172 * 1e-6, 'csa')
+ relax> value.set(value=-172 * 1e-6, param='csa')
+
+
+ To set the NH bond length of all spins to 1.02 Angstroms, type:
+
+ relax> value.set(1.02 * 1e-10, 'bond_length')
+ relax> value.set(value=1.02 * 1e-10, param='r')
+
+
+ To set both the bond length and the CSA value to the default values,
type:
+
+ relax> value.set(param=['bond length', 'csa'])
+
+
+ To set both tf and ts to 100 ps, type:
+
+ relax> value.set(100e-12, ['tf', 'ts'])
+ relax> value.set(value=100e-12, param=['tf', 'ts'])
+
+
+ To set the S2 and te parameter values of residue 126, Ca spins to
0.56 and 13 ps, type:
+
+ relax> value.set([0.56, 13e-12], ['S2', 'te'], ':126@Ca')
+ relax> value.set(value=[0.56, 13e-12], param=['S2', 'te'],
spin_id=':126@Ca')
+ relax> value.set(value=[0.56, 13e-12], param=['S2', 'te'],
spin_id=':126@Ca')
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "value.set("
- text = text + "run=" + `run`
- text = text + ", value=" + `value`
+ text = text + "value=" + `value`
text = text + ", param=" + `param`
- text = text + ", res_num=" + `res_num`
- text = text + ", res_name=" + `res_name` + ")"
+ text = text + ", spin_id=" + `spin_id` + ")"
print text
-
- # The run name.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
# The value.
if value != None and type(value) != float and type(value) != int and
type(value) != list:
@@ -420,16 +403,12 @@
if type(value) == list and type(param) == list and len(value) !=
len(param):
raise RelaxError, "Both the value array and parameter array must
be of equal length."
- # 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 identifier.
+ if spin_id != None and type(spin_id) != str:
+ raise RelaxNoneStrError, ('spin identifier', spin_id)
# Execute the functional code.
- self.__relax__.generic.value.set(run=run, value=value, param=param,
res_num=res_num, res_name=res_name)
+ value.set(value=value, param=param, spin_id=spin_id)
def write(self, run=None, param=None, file=None, dir=None, force=0):
r4137 - /1.3/prompt/value.py