Author: bugman
Date: Wed Apr 16 15:44:09 2008
New Revision: 5753
URL: http://svn.gna.org/viewcvs/relax?rev=5753&view=rev
Log:
Converted the map() user function interface to the new relax design.
Modified:
1.3/prompt/dx.py
Modified: 1.3/prompt/dx.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/dx.py?rev=5753&r1=5752&r2=5753&view=diff
==============================================================================
--- 1.3/prompt/dx.py (original)
+++ 1.3/prompt/dx.py Wed Apr 16 15:44:09 2008
@@ -95,21 +95,19 @@
opendx.run(file=file, dir=dir, dx_exe=dx_exe, vp_exec=vp_exec)
- def map(self, run=None, params=None, map_type="Iso3D", res_num=None,
inc=20, lower=None, upper=None, axis_incs=5, file="map", dir="dx",
point=None, point_file="point", remap=None):
+ def map(self, params=None, map_type="Iso3D", spin_id=None, inc=20,
lower=None, upper=None, axis_incs=5, file_prefix="map", dir="dx", point=None,
point_file="point", remap=None):
"""Function for creating a map of the given space in OpenDX format.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- run: The name of the run.
-
- params: The parameters to be mapped. This argument should be an
array of strings, values
- of which are described below.
+ params: The parameters to be mapped. This argument should be an
array of strings, the
+ meanings of which are described below.
map_type: The type of map to create. For example the default, a 3D
isosurface, the type is
'Iso3D'. See below for more details.
- res_num: The residue number.
+ spin_id: The spin identification numbe.
inc: The number of increments to map in each dimension. This value
controls the resolution
of the map.
@@ -127,7 +125,7 @@
axis_incs: The number of increments or ticks displaying parameter
values along the axes of
the OpenDX plot.
- file: The file name. All the output files are prefixed with this
name. The main file
+ file_prefix: The file name. All the output files are prefixed with
this name. The main file
containing the data points will be called the value of 'file'. The
OpenDX program will be
called 'file.net' and the OpenDX import file will be called
'file.general'.
@@ -153,42 +151,40 @@
| Surface type | Pattern
|
|___________________________________________|_______________________________|
| |
|
- | 3D isosurface | '^[Ii]so3[Dd]'
|
+ | 3D isosurface | 'Iso3D'
|
|___________________________________________|_______________________________|
- Pattern syntax is simply regular expression syntax where square
brackets '[]' means any
- character within the brackets, '^' means the start of the string,
etc.
+ This argument is case insensitive.
Examples
~~~~~~~~
- The following commands will generate a map of the extended
model-free space defined as run
- 'm5' which consists of the parameters {S2, S2f, ts}. Files will be
output into the
- directory 'dx' and will be prefixed by 'map'. The residue, in this
case, is number 6.
-
- relax> dx.map('m5', ['S2', 'S2f', 'ts'], 6)
- relax> dx.map('m5', ['S2', 'S2f', 'ts'], 6, 20, 'map', 'dx')
- relax> dx.map('m5', ['S2', 'S2f', 'ts'], res_num=6, file='map',
dir='dx')
- relax> dx.map(run='m5', params=['S2', 'S2f', 'ts'], res_num=6,
inc=20, file='map', dir='dx')
- relax> dx.map(run='m5', params=['S2', 'S2f', 'ts'], res_num=6,
type='Iso3D', inc=20,
- swap=[0, 1, 2], file='map', dir='dx')
-
-
- To map the model-free space 'm4' defined by the parameters {S2, te,
Rex}, name the results
- 'test', and not place the files in a subdirectory, use the following
commands (assuming
- residue 2).
-
- relax> dx.map('m4', ['S2', 'te', 'Rex'], res_num=2, file='test',
dir=None)
- relax> dx.map(run='m4', params=['S2', 'te', 'Rex'], res_num=2,
inc=100, file='test',
- dir=None)
+ The following commands will generate a map of the extended
model-free space for model 'm5'
+ consisting of the parameters {S2, S2f, ts}. Files will be output
into the
+ directory 'dx' and will be prefixed by 'map'. In this case, the
system is a protein and
+ residue number 6 will be mapped.
+
+ relax> dx.map(['S2', 'S2f', 'ts'], ':6')
+ relax> dx.map(['S2', 'S2f', 'ts'], ':6', 20, 'map', 'dx')
+ relax> dx.map(['S2', 'S2f', 'ts'], spin_id=':6', file='map',
dir='dx')
+ relax> dx.map(params=['S2', 'S2f', 'ts'], spin_id=':6', inc=20,
file='map', dir='dx')
+ relax> dx.map(params=['S2', 'S2f', 'ts'], spin_id=':6',
type='Iso3D', inc=20,
+ file='map', dir='dx')
+
+
+ To map the model-free space 'm4' for residue 2, spin N6 defined by
the parameters {S2, te,
+ Rex}, name the results 'test', and to place the files in the current
directory, use one of
+ the following commands:
+
+ relax> dx.map(['S2', 'te', 'Rex'], spin_id=':2@N6', file='test',
dir=None)
+ relax> dx.map(params=['S2', 'te', 'Rex'], spin_id=':2@N6', inc=100,
file='test', dir=None)
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "map("
- text = text + "run=" + `run`
- text = text + ", params=" + `params`
+ text = text + "params=" + `params`
text = text + ", map_type=" + `map_type`
text = text + ", res_num=" + `res_num`
text = text + ", inc=" + `inc`
@@ -202,10 +198,6 @@
text = text + ", remap=" + `remap` + ")"
print text
- # The run argument.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
-
# The parameters to map.
if type(params) != list:
raise RelaxListError, ('parameters', params)
@@ -279,7 +271,7 @@
raise RelaxFunctionError, ('remap function', remap)
# Execute the functional code.
- self.__relax__.generic.opendx.map(run=run, params=params,
map_type=map_type, res_num=res_num, inc=inc, lower=lower, upper=upper,
axis_incs=axis_incs, file=file, dir=dir, point=point, point_file=point_file,
remap=remap)
+ opendx.main.map(params=params, map_type=map_type, res_num=res_num,
inc=inc, lower=lower, upper=upper, axis_incs=axis_incs, file=file, dir=dir,
point=point, point_file=point_file, remap=remap)
# Docstring modification.
r5753 - /1.3/prompt/dx.py