Author: semor
Date: Thu Apr 3 20:48:09 2008
New Revision: 5278
URL: http://svn.gna.org/viewcvs/relax?rev=5278&view=rev
Log:
More removal of the run argument as part of the moving to the new design.
Modified:
1.3/prompt/pymol.py
Modified: 1.3/prompt/pymol.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/pymol.py?rev=5278&r1=5277&r2=5278&view=diff
==============================================================================
--- 1.3/prompt/pymol.py (original)
+++ 1.3/prompt/pymol.py Thu Apr 3 20:48:09 2008
@@ -42,13 +42,8 @@
self.__relax__ = relax
- def cartoon(self, run=None):
+ def cartoon(self):
"""Apply the PyMOL cartoon style and colour by secondary structure.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- run: The name of the run.
Description
@@ -68,23 +63,18 @@
Example
~~~~~~~
- To apply this user function to the run 'final', type:
-
- relax> pymol.cartoon("final")
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "pymol.cartoon("
- text = text + "run=" + `run` + ")"
- print text
-
- # The run name.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
-
- # Execute the functional code.
- self.__relax__.generic.pymol.cartoon(run=run)
+ To apply this user function, type:
+
+ relax> pymol.cartoon()
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "pymol.cartoon()"
+ print text
+
+ # Execute the functional code.
+ pymol_obj.cartoon()
def clear_history(self):
@@ -99,14 +89,12 @@
self.__relax__.generic.pymol.clear_history()
- def command(self, run=None, command=None):
+ def command(self, command=None):
"""Function for executing a user supplied PyMOL command.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- run: The name of the run.
-
command: The PyMOL command to execute.
@@ -120,37 +108,30 @@
Example
~~~~~~~
- To reinitialise the PyMOL instance for the run 'aic', type:
-
- relax> pymol.command("aic", "reinitialise")
+ To reinitialise the PyMOL instance, type:
+
+ relax> pymol.command("reinitialise")
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "pymol.command("
- text = text + "run=" + `run`
- text = text + ", command=" + `command` + ")"
- print text
-
- # The run name.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
+ text = text + "command=" + `command` + ")"
+ print text
# The command argument.
if type(command) != str:
raise RelaxStrError, ('command', command)
# Execute the functional code.
- self.__relax__.generic.pymol.command(run=run, command=command)
-
-
- def macro_exec(self, run=None, data_type=None, style="classic",
colour_start=None, colour_end=None, colour_list=None):
+ pymol_obj.command(command=command)
+
+
+ def macro_exec(self, data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None):
"""Function for executing PyMOL macros.
Keyword Arguments
~~~~~~~~~~~~~~~~~
-
- run: The name of the run.
data_type: The data type to map to the structure.
@@ -192,28 +173,22 @@
Examples
~~~~~~~~
- To map the order parameter values, S2, of the run 'final' onto the
structure using the
- classic style, type:
-
- relax> pymol.macro_exec('final', 'S2')
- relax> pymol.macro_exec('final', data_type='S2')
- relax> pymol.macro_exec('final', data_type='S2', style="classic")
+ To map the order parameter values, S2, onto the structure using the
classic style, type:
+
+ relax> pymol.macro_exec('S2')
+ relax> pymol.macro_exec(data_type='S2')
+ relax> pymol.macro_exec(data_type='S2', style="classic")
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "pymol.macro_exec("
- text = text + "run=" + `run`
- text = text + ", data_type=" + `data_type`
+ text = text + "data_type=" + `data_type`
text = text + ", style=" + `style`
text = text + ", colour_start=" + `colour_start`
text = text + ", colour_end=" + `colour_end`
text = text + ", colour_list=" + `colour_list` + ")"
print text
-
- # The run name.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
# Data type for mapping to the structure.
if type(data_type) != str:
@@ -240,28 +215,26 @@
raise RelaxListNumError, ('ending colour of the linear
gradient', colour_end)
# Execute the functional code.
- self.__relax__.generic.pymol.macro_exec(run=run,
data_type=data_type, style=style, colour_start=colour_start,
colour_end=colour_end, colour_list=colour_list)
-
-
- def tensor_pdb(self, run=None, file=None):
+ pymol_obj.macro_exec(data_type=data_type, style=style,
colour_start=colour_start, colour_end=colour_end, colour_list=colour_list)
+
+
+ def tensor_pdb(self, file=None):
"""Function displaying the diffusion tensor PDB geometric object
over the loaded PDB.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- run: The name of the run.
-
file: The name of the PDB file containing the tensor geometric
object.
Description
~~~~~~~~~~~
- In executing this user function, a PDB file must have previously
been loaded into this run,
- a geometric object or polygon representing the Brownian rotational
diffusion tensor will be
- overlain with the loaded PDB file and displayed within PyMOL. The
PDB file containing the
- geometric object must be created using the complementary
'pdb.create_diff_tensor_pdb()' user
- function.
+ In executing this user function, a PDB file must have previously
been loaded into this data
+ pipe a geometric object or polygon representing the Brownian
rotational diffusion tensor
+ will be overlain with the loaded PDB file and displayed within
PyMOL. The PDB file
+ containing the geometric object must be created using the
complementary
+ 'pdb.create_diff_tensor_pdb()' user function.
The tensor PDB file is read in using the command:
@@ -290,29 +263,22 @@
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "pymol.tensor_pdb("
- text = text + "run=" + `run`
- text = text + ", file=" + `file` + ")"
- print text
-
- # The run name.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
+ text = text + "file=" + `file` + ")"
+ print text
# The file name.
if type(file) != str:
raise RelaxStrError, ('file name', file)
# Execute the functional code.
- self.__relax__.generic.pymol.tensor_pdb(run=run, file=file)
-
-
- def vector_dist(self, run=None, file='XH_dist.pdb'):
+ pymol_obj.tensor_pdb(file=file)
+
+
+ def vector_dist(self, file='XH_dist.pdb'):
"""Function displaying the PDB file representation of the XH vector
distribution.
Keyword Arguments
~~~~~~~~~~~~~~~~~
-
- run: The name of the run.
file: The name of the PDB file containing the vector distribution.
@@ -334,59 +300,41 @@
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "pymol.vector_dist("
- text = text + "run=" + `run`
- text = text + ", file=" + `file` + ")"
- print text
-
- # The run name.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
+ text = text + "file=" + `file` + ")"
+ print text
# The file name.
if type(file) != str:
raise RelaxStrError, ('file name', file)
# Execute the functional code.
- self.__relax__.generic.pymol.vector_dist(run=run, file=file)
-
-
- def view(self, run=None):
+ pymol_obj.vector_dist(file=file)
+
+
+ def view(self):
"""Function for viewing the collection of molecules extracted from
the PDB file.
+
+
+ Example
+ ~~~~~~~
+
+ relax> pymol.view()
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "pymol.view()"
+ print text
+
+ # Execute the functional code.
+ pymol_obj.view()
+
+
+ def write(self, data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None, file=None, dir='pymol', force=0):
+ """Function for creating PyMOL macros.
Keyword Arguments
~~~~~~~~~~~~~~~~~
-
- run: The name of the run which the PDB belongs to.
-
-
- Example
- ~~~~~~~
-
- relax> pymol.view('m1')
- relax> pymol.view(run='pdb')
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "pymol.view("
- text = text + "run=" + `run` + ")"
- print text
-
- # The run argument.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
-
- # Execute the functional code.
- self.__relax__.generic.pymol.view(run=run)
-
-
- def write(self, run=None, data_type=None, style="classic",
colour_start=None, colour_end=None, colour_list=None, file=None, dir='pymol',
force=0):
- """Function for creating PyMOL macros.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- run: The name of the run.
data_type: The data type to map to the structure.
@@ -436,19 +384,18 @@
Examples
~~~~~~~~
- To create a PyMOL macro mapping the order parameter values, S2, of
the run 'final' onto the
- structure using the classic style, type:
-
- relax> pymol.write('final', 'S2')
- relax> pymol.write('final', data_type='S2')
- relax> pymol.write('final', data_type='S2', style="classic",
file='s2.mac', dir='pymol')
+ To create a PyMOL macro mapping the order parameter values, S2, onto
the structure using
+ the classic style, type:
+
+ relax> pymol.write('S2')
+ relax> pymol.write(data_type='S2')
+ relax> pymol.write(data_type='S2', style="classic", file='s2.mac',
dir='pymol')
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "pymol.write("
- text = text + "run=" + `run`
- text = text + ", data_type=" + `data_type`
+ text = text + "data_type=" + `data_type`
text = text + ", style=" + `style`
text = text + ", colour_start=" + `colour_start`
text = text + ", colour_end=" + `colour_end`
@@ -458,10 +405,6 @@
text = text + ", force=" + `force` + ")"
print text
- # The run name.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
-
# Data type for mapping to the structure.
if type(data_type) != str:
raise RelaxStrError, ('data type', data_type)
@@ -499,7 +442,7 @@
raise RelaxBinError, ('force flag', force)
# Execute the functional code.
- self.__relax__.generic.pymol.write(run=run, data_type=data_type,
style=style, colour_start=colour_start, colour_end=colour_end,
colour_list=colour_list, file=file, dir=dir, force=force)
+ pymol_obj.write(data_type=data_type, style=style,
colour_start=colour_start, colour_end=colour_end, colour_list=colour_list,
file=file, dir=dir, force=force)
r5278 - /1.3/prompt/pymol.py