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List: relax-commits
Subject: r2711 - in /branches/tensor_pdb: generic_fns/pymol.py prompt/pymol.py
From: edward.dauvergne () domain ! hid
Date: 2006-10-31 8:02:17
Message-ID: E1GeoZd-0004xJ-LG () subversion ! gna ! org
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Author: bugman
Date: Tue Oct 31 09:02:16 2006
New Revision: 2711
URL: http://svn.gna.org/viewcvs/relax?rev=2711&view=rev
Log:
Changed all references from Molmol to PyMOL in the PyMOL code. The macro fns raise \
RelaxErrors.
The 'self.macro_exec()' and 'self.write()' functions raise RelaxErrors saying that \
the functions have not been implemented yet. The 'pymol.cartoon()' user function has \
been shifted to the top of the function list in the 'prompt/pymol.py' file.
Modified:
branches/tensor_pdb/generic_fns/pymol.py
branches/tensor_pdb/prompt/pymol.py
Modified: branches/tensor_pdb/generic_fns/pymol.py
URL: http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/generic_fns/pymol.py?rev=2711&r1=2710&r2=2711&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pymol.py (original)
+++ branches/tensor_pdb/generic_fns/pymol.py Tue Oct 31 09:02:16 2006
@@ -26,11 +26,11 @@
class Pymol:
def __init__(self, relax):
- """Class containing the functions for viewing molecules."""
+ """Class containing the functions for viewing molecules using PyMOL."""
self.relax = relax
- # Initialise the command history (for reopening Molmol pipes).
+ # Initialise the command history (for reopening PyMOL pipes).
self.clear_history()
@@ -58,40 +58,40 @@
def clear_history(self):
- """Function for clearing the Molmol command history."""
+ """Function for clearing the PyMOL command history."""
self.command_history = ""
def command(self, run, command):
- """Function for sending Molmol commands to the program pipe."""
-
- # Arguments.
- self.run = run
-
- # Test if the run exists.
- if not self.run in self.relax.data.run_names:
- raise RelaxNoRunError, self.run
-
- # Pass the command to Molmol.
+ """Function for sending PyMOL commands to the program pipe."""
+
+ # Arguments.
+ self.run = run
+
+ # Test if the run exists.
+ if not self.run in self.relax.data.run_names:
+ raise RelaxNoRunError, self.run
+
+ # Pass the command to PyMOL.
self.pipe_write(command)
def create_macro(self):
- """Function for creating an array of Molmol commands."""
+ """Function for creating an array of PyMOL commands."""
# Function type.
self.function_type = \
self.relax.data.run_types[self.relax.data.run_names.index(self.run)]
- # Specific Molmol macro creation function.
- molmol_macro = self.relax.specific_setup.setup('molmol_macro', \
self.function_type) + # Specific PyMOL macro creation function.
+ pymol_macro = self.relax.specific_setup.setup('pymol_macro', \
self.function_type)
# Get the macro.
- self.commands = molmol_macro(self.run, self.data_type, self.style, \
self.colour_start, self.colour_end, self.colour_list) + self.commands = \
pymol_macro(self.run, self.data_type, self.style, self.colour_start, self.colour_end, \
self.colour_list)
def macro_exec(self, run=None, data_type=None, style="classic", \
colour_start=None, colour_end=None, colour_list=None):
- """Function for executing a Molmol macro."""
+ """Function for executing a PyMOL macro."""
# Arguments.
self.run = run
@@ -101,6 +101,9 @@
self.colour_end = colour_end
self.colour_list = colour_list
+ # No coded yet.
+ raise RelaxError, "This function has not yet been implemented."
+
# Test if the run exists.
if not self.run in self.relax.data.run_names:
raise RelaxNoRunError, self.run
@@ -172,9 +175,9 @@
def pipe_write(self, command=None, store_command=1):
- """Function for writing to the Molmol pipe.
-
- This function is also used to execute a user supplied Molmol command.
+ """Function for writing to the PyMOL pipe.
+
+ This function is also used to execute a user supplied PyMOL command.
"""
# Reopen the pipe if needed.
@@ -204,7 +207,7 @@
def view(self, run=None):
- """Function for running Molmol."""
+ """Function for running PyMOL."""
# Arguments.
self.run = run
@@ -217,7 +220,7 @@
def write(self, run=None, data_type=None, style="classic", colour_start=None, \
colour_end=None, colour_list=None, file=None, dir=None, force=0):
- """Function for creating a Molmol macro."""
+ """Function for creating a PyMOL macro."""
# Arguments.
self.run = run
@@ -227,6 +230,9 @@
self.colour_end = colour_end
self.colour_list = colour_list
+ # No coded yet.
+ raise RelaxError, "This function has not yet been implemented."
+
# Test if the run exists.
if not self.run in self.relax.data.run_names:
raise RelaxNoRunError, self.run
Modified: branches/tensor_pdb/prompt/pymol.py
URL: http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/prompt/pymol.py?rev=2711&r1=2710&r2=2711&view=diff
==============================================================================
--- branches/tensor_pdb/prompt/pymol.py (original)
+++ branches/tensor_pdb/prompt/pymol.py Tue Oct 31 09:02:16 2006
@@ -30,7 +30,7 @@
def __init__(self, relax):
# Help.
self.__relax_help__ = \
- """Class for interfacing with Molmol."""
+ """Class for interfacing with PyMOL."""
# Add the generic help string.
self.__relax_help__ = self.__relax_help__ + "\n" + help.relax_class_help
@@ -39,42 +39,87 @@
self.__relax__ = relax
- def clear_history(self):
- """Function for clearing the Molmol command history."""
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "pymol.clear_history()"
- print text
-
- # Execute the functional code.
- self.__relax__.generic.pymol.clear_history()
-
-
- def command(self, run=None, command=None):
- """Function for executing a user supplied Molmol command.
+ def cartoon(self, run=None):
+ """Apply the PyMOL cartoon style and colour by secondary structure.
Keyword Arguments
~~~~~~~~~~~~~~~~~
run: The name of the run.
-
- command: The Molmol command to execute.
Description
~~~~~~~~~~~
- This user function allows you to pass Molmol commands to the program. This \
can be useful
- for automation or scripting.
+ This function applies the PyMOL cartoon style which is equivalent to hiding \
everything and + clicking on show cartoon. It also colours the cartoon with \
red helices, yellow strands, and + green loops. The following commands are \
executed: +
+ cmd.hide('everything', file)
+ cmd.show('cartoon', file)
+ util.cbss(file, 'red', 'yellow', 'green')
+
+ where file is the file name without the '.pdb' extension.
Example
~~~~~~~
- To reinitialise the Molmol instance for the run 'aic', type:
-
- relax> pymol.command("aic", "InitAll yes")
+ 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)
+
+
+ def clear_history(self):
+ """Function for clearing the PyMOL command history."""
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "pymol.clear_history()"
+ print text
+
+ # Execute the functional code.
+ self.__relax__.generic.pymol.clear_history()
+
+
+ def command(self, run=None, command=None):
+ """Function for executing a user supplied PyMOL command.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ run: The name of the run.
+
+ command: The PyMOL command to execute.
+
+
+ Description
+ ~~~~~~~~~~~
+
+ This user function allows you to pass PyMOL commands to the program. This \
can be useful + for automation or scripting.
+
+
+ Example
+ ~~~~~~~
+
+ To reinitialise the PyMOL instance for the run 'aic', type:
+
+ relax> pymol.command("aic", "reinitialise")
"""
# Function intro text.
@@ -97,7 +142,7 @@
def macro_exec(self, run=None, data_type=None, style="classic", \
colour_start=None, colour_end=None, colour_list=None):
- """Function for executing Molmol macros.
+ """Function for executing PyMOL macros.
Keyword Arguments
~~~~~~~~~~~~~~~~~
@@ -119,7 +164,7 @@
Description
~~~~~~~~~~~
- This function allows residues specific values to be mapped to a structure \
through Molmol + This function allows residues specific values to be mapped to \
a structure through PyMOL
macros. Currently only the 'classic' style, which is described below, is \
availible.
@@ -134,7 +179,7 @@
will select the default colour gradient which for each type of analysis is \
described below.
When supplying the colours as strings, two lists of colours can be selected \
from which to
- match the strings. These are the default Molmol colour list and the X11 \
colour list, both + match the strings. These are the default PyMOL colour \
list and the X11 colour list, both
of which are described in the tables below. The default behaviour is to \
first search the
Molmol list and then the X11 colour list, raising an error if neither \
contain the string.
To explicitly select these lists, set the 'colour_list' argument to either \
'molmol' or @@ -195,68 +240,23 @@
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 cartoon(self, run=None):
- """Apply the PyMOL cartoon style and colour by secondary structure.
+ def tensor_pdb(self, run=None, 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
~~~~~~~~~~~
- This function applies the PyMOL cartoon style which is equivalent to hiding \
everything and
- clicking on show cartoon. It also colours the cartoon with red helices, \
yellow strands, and
- green loops. The following commands are executed:
-
- cmd.hide('everything', file)
- cmd.show('cartoon', file)
- util.cbss(file, 'red', 'yellow', 'green')
-
- where file is the file name without the '.pdb' extension.
-
-
- 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)
-
-
- def tensor_pdb(self, run=None, 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 Molmol. The PDB file \
containing the + 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_tensor_pdb()' user function.
@@ -314,7 +314,7 @@
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='molmol', force=0): + 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
@@ -344,7 +344,7 @@
~~~~~~~~~~~
This function allows residues specific values to be mapped to a structure \
through the
- creation of a Molmol '*.mac' macro which can be executed in Molmol by \
clicking on 'File, + creation of a PyMOL macro which can be executed in PyMOL \
by clicking on 'File,
Macro, Execute User...'. Currently only the 'classic' style, which is \
described below, is availible.
@@ -360,9 +360,9 @@
will select the default colour gradient which for each type of analysis is \
described below.
When supplying the colours as strings, two lists of colours can be selected \
from which to
- match the strings. These are the default Molmol colour list and the X11 \
colour list, both + match the strings. These are the default PyMOL colour \
list and the X11 colour list, both
of which are described in the tables below. The default behaviour is to \
first search the
- Molmol list and then the X11 colour list, raising an error if neither \
contain the string. + PyMOL list and then the X11 colour list, raising an \
error if neither contain the string.
To explicitly select these lists, set the 'colour_list' argument to either \
'molmol' or 'x11'.
@@ -370,12 +370,12 @@
Examples
~~~~~~~~
- To create a Molmol macro mapping the order parameter values, S2, of the run \
'final' onto the + 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='molmol') + relax> pymol.write('final', data_type='S2', style="classic", \
file='s2.mac', dir='pymol') """
# Function intro text.
@@ -441,7 +441,7 @@
#########################
# Write function.
- #write.__doc__ = write.__doc__ + "\n\n" + Molmol.classic.__doc__ + "\n\n"
+ #write.__doc__ = write.__doc__ + "\n\n" + Pymol.classic.__doc__ + "\n\n"
# Molmol RGB colour list.
write.__doc__ = write.__doc__ + "\n\n" + Colour.molmol_colours.__doc__ + "\n\n"
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