Author: bugman
Date: Mon Apr 7 18:08:05 2008
New Revision: 5379
URL: http://svn.gna.org/viewcvs/relax?rev=5379&view=rev
Log:
Converted all the class methods into module functions.
Modified:
1.3/generic_fns/pymol.py
Modified: 1.3/generic_fns/pymol.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pymol.py?rev=5379&r1=5378&r2=5379&view=diff
==============================================================================
--- 1.3/generic_fns/pymol.py (original)
+++ 1.3/generic_fns/pymol.py Mon Apr 7 18:08:05 2008
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2006-2007 Edward d'Auvergne
#
+# Copyright (C) 2006-2008 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -29,324 +29,310 @@
from relax_errors import RelaxError, RelaxImplementError, RelaxNoPipeError,
RelaxNoSequenceError
-# The relax data storage object.
-
-
-
-class Pymol:
- def __init__(self, relax):
- """Class containing the functions for viewing molecules using
PyMOL."""
-
- self.relax = relax
-
- # Initialise the command history (for reopening PyMOL pipes).
- self.clear_history()
-
-
- def cartoon(self, run=None):
- """Apply the PyMOL cartoon style and colour by secondary
structure."""
-
- # Arguments.
+def cartoon(run=None):
+ """Apply the PyMOL cartoon style and colour by secondary structure."""
+
+ # Arguments.
+ self.run = run
+
+ # Test if the run exists.
+ if not self.run in relax_data_store.run_names:
+ raise RelaxNoPipeError, self.run
+
+ # Identifier.
+ pdb_file = relax_data_store.pdb[self.run].file_name
+ id = self.relax.IO.file_root(pdb_file)
+
+ # Hide everything.
+ self.pipe_write("cmd.hide('everything'," + `id` + ")")
+
+ # Show the cartoon style.
+ self.pipe_write("cmd.show('cartoon'," + `id` + ")")
+
+ # Colour by secondary structure.
+ self.pipe_write("util.cbss(" + `id` + ", 'red', 'yellow', 'green')")
+
+
+def clear_history():
+ """Function for clearing the PyMOL command history."""
+
+ self.command_history = ""
+
+
+def command(run, command):
+ """Function for sending PyMOL commands to the program pipe."""
+
+ # Arguments.
+ self.run = run
+
+ # Test if the run exists.
+ if not self.run in relax_data_store.run_names:
+ raise RelaxNoPipeError, self.run
+
+ # Pass the command to PyMOL.
+ self.pipe_write(command)
+
+
+def create_macro():
+ """Function for creating an array of PyMOL commands."""
+
+ # Function type.
+ self.function_type =
relax_data_store.run_types[relax_data_store.run_names.index(self.run)]
+
+ # Specific PyMOL macro creation function.
+ pymol_macro = self.relax.specific_setup.setup('pymol_macro',
self.function_type)
+
+ # Get the macro.
+ self.commands = pymol_macro(self.run, self.data_type, self.style,
self.colour_start, self.colour_end, self.colour_list)
+
+
+def macro_exec(run=None, data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None):
+ """Function for executing a PyMOL macro."""
+
+ # Arguments.
+ self.run = run
+ self.data_type = data_type
+ self.style = style
+ self.colour_start = colour_start
+ self.colour_end = colour_end
+ self.colour_list = colour_list
+
+ # No coded yet.
+ raise RelaxImplementError
+
+ # Test if the run exists.
+ if not self.run in relax_data_store.run_names:
+ raise RelaxNoPipeError, self.run
+
+ # Test if the sequence data is loaded.
+ if not relax_data_store.res.has_key(self.run):
+ raise RelaxNoSequenceError, self.run
+
+ # Create the macro.
+ self.create_macro()
+
+ # Loop over the commands and execute them.
+ for command in self.commands:
+ self.pipe_write(command)
+
+
+def open_pdb(run=None):
+ """Function for opening the PDB file in PyMOL."""
+
+ # Argument.
+ if run:
self.run = run
- # Test if the run exists.
- if not self.run in relax_data_store.run_names:
- raise RelaxNoPipeError, self.run
-
- # Identifier.
- pdb_file = relax_data_store.pdb[self.run].file_name
- id = self.relax.IO.file_root(pdb_file)
-
- # Hide everything.
- self.pipe_write("cmd.hide('everything'," + `id` + ")")
-
- # Show the cartoon style.
- self.pipe_write("cmd.show('cartoon'," + `id` + ")")
-
- # Colour by secondary structure.
- self.pipe_write("util.cbss(" + `id` + ", 'red', 'yellow', 'green')")
-
-
- def clear_history(self):
- """Function for clearing the PyMOL command history."""
-
- self.command_history = ""
-
-
- def command(self, run, command):
- """Function for sending PyMOL commands to the program pipe."""
-
- # Arguments.
- self.run = run
-
- # Test if the run exists.
- if not self.run in relax_data_store.run_names:
- raise RelaxNoPipeError, self.run
-
- # Pass the command to PyMOL.
- self.pipe_write(command)
-
-
- def create_macro(self):
- """Function for creating an array of PyMOL commands."""
-
- # Function type.
- self.function_type =
relax_data_store.run_types[relax_data_store.run_names.index(self.run)]
-
- # Specific PyMOL macro creation function.
- pymol_macro = self.relax.specific_setup.setup('pymol_macro',
self.function_type)
-
- # Get the macro.
- 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 PyMOL macro."""
-
- # Arguments.
- self.run = run
- self.data_type = data_type
- self.style = style
- self.colour_start = colour_start
- self.colour_end = colour_end
- self.colour_list = colour_list
-
- # No coded yet.
- raise RelaxImplementError
-
- # Test if the run exists.
- if not self.run in relax_data_store.run_names:
- raise RelaxNoPipeError, self.run
-
- # Test if the sequence data is loaded.
- if not relax_data_store.res.has_key(self.run):
- raise RelaxNoSequenceError, self.run
-
- # Create the macro.
- self.create_macro()
-
- # Loop over the commands and execute them.
- for command in self.commands:
- self.pipe_write(command)
-
-
- def open_pdb(self, run=None):
- """Function for opening the PDB file in PyMOL."""
-
- # Argument.
- if run:
- self.run = run
-
- # Test if the pipe is open.
- if not self.pipe_open_test():
- return
-
- # Reinitialise PyMOL.
- self.pipe_write("reinitialize")
-
- # Open the PDB file.
- self.pipe_write("load " + relax_data_store.pdb[self.run].file_name)
-
-
- def pipe_open(self):
- """Function for opening a PyMOL pipe."""
-
- # Test that the PyMOL binary exists.
- self.relax.IO.test_binary('pymol')
-
- # Open the PyMOL pipe.
- relax_data_store.pymol = popen("pymol -qpK", 'w', 0)
-
- # Execute the command history.
- if len(self.command_history) > 0:
- self.pipe_write(self.command_history, store_command=0)
- return
-
- # Test if the PDB file has been loaded.
- if hasattr(relax_data_store, 'pdb') and
relax_data_store.pdb.has_key(self.run):
- self.open_pdb()
-
-
- def pipe_open_test(self):
- """Function for testing if the PyMOL pipe is open."""
-
- # Test if a pipe has been opened.
- if not hasattr(relax_data_store, 'pymol'):
- return 0
-
- # Test if the pipe has been broken.
- try:
- relax_data_store.pymol.write('\n')
- except IOError:
- return 0
-
- # The pipe is open.
- return 1
-
-
- def pipe_write(self, command=None, store_command=1):
- """Function for writing to the PyMOL pipe.
-
- This function is also used to execute a user supplied PyMOL command.
- """
-
- # Reopen the pipe if needed.
- if not self.pipe_open_test():
- self.pipe_open()
-
- # Write the command to the pipe.
- relax_data_store.pymol.write(command + '\n')
-
- # Place the command in the command history.
- if store_command:
- self.command_history = self.command_history + command + "\n"
-
-
- def tensor_pdb(self, run=None, file=None):
- """Display the diffusion tensor geometric structure."""
-
- # Arguments.
- self.run = run
-
- # Test if the run exists.
- if not self.run in relax_data_store.run_names:
- raise RelaxNoPipeError, self.run
-
- # Read in the tensor PDB file.
- self.pipe_write("load " + file)
-
-
- # Centre of mass.
- #################
-
- # Select the COM residue.
- self.pipe_write("select resn COM")
-
- # Show the centre of mass as the dots representation.
- self.pipe_write("show dots, 'sele'")
-
- # Colour it blue.
- self.pipe_write("color blue, 'sele'")
-
-
- # The diffusion tensor axes.
- ############################
-
- # Select the AXS residue.
- self.pipe_write("select resn AXS")
-
- # Hide everything.
- self.pipe_write("hide ('sele')")
-
- # Show as 'sticks'.
- self.pipe_write("show sticks, 'sele'")
-
- # Colour it cyan.
- self.pipe_write("color cyan, 'sele'")
-
- # Select the N atoms of the AXS residue (used to display the axis
labels).
- self.pipe_write("select (resn AXS and elem N)")
-
- # Label the atoms.
- self.pipe_write("label 'sele', name")
-
-
-
- # Monte Carlo simulations.
- ##########################
-
- # Select the SIM residue.
- self.pipe_write("select resn SIM")
-
- # Colour it.
- self.pipe_write("colour cyan, 'sele'")
-
-
- # Clean up.
- ###########
-
- # Remove the selection.
- self.pipe_write("cmd.delete('sele')")
-
-
- def vector_dist(self, run=None, file=None):
- """Display the XH bond vector distribution.
-
- @param run: The run
- @type run: str
- @param file: The vector distribution PDB file.
- @type file: str
- """
-
- # Arguments.
- self.run = run
-
- # Test if the run exists.
- if not self.run in relax_data_store.run_names:
- raise RelaxNoPipeError, self.run
-
- # The file root.
- file_root = self.relax.IO.file_root(file)
-
- # Read in the vector distribution PDB file.
- self.pipe_write("load " + file)
-
-
- # Create a surface.
- ###################
-
- # Select the vector distribution.
- self.pipe_write("cmd.show('surface', " + `file_root` + ")")
-
-
- def view(self, run=None):
- """Function for running PyMOL."""
-
- # Arguments.
- self.run = run
-
- # Open a PyMOL pipe.
- if self.pipe_open_test():
- raise RelaxError, "The PyMOL pipe already exists."
- else:
- self.pipe_open()
-
-
- 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 PyMOL macro."""
-
- # Arguments.
- self.run = run
- self.data_type = data_type
- self.style = style
- self.colour_start = colour_start
- self.colour_end = colour_end
- self.colour_list = colour_list
-
- # No coded yet.
- raise RelaxImplementError
-
- # Test if the run exists.
- if not self.run in relax_data_store.run_names:
- raise RelaxNoPipeError, self.run
-
- # Test if the sequence data is loaded.
- if not relax_data_store.res.has_key(self.run):
- raise RelaxNoSequenceError, self.run
-
- # Create the macro.
- self.create_macro()
-
- # File name.
- if file == None:
- file = data_type + '.mac'
-
- # Open the file for writing.
- file = self.relax.IO.open_write_file(file, dir, force)
-
- # Loop over the commands and write them.
- for command in self.commands:
- file.write(command + "\n")
-
- # Close the file.
- file.close()
+ # Test if the pipe is open.
+ if not self.pipe_open_test():
+ return
+
+ # Reinitialise PyMOL.
+ self.pipe_write("reinitialize")
+
+ # Open the PDB file.
+ self.pipe_write("load " + relax_data_store.pdb[self.run].file_name)
+
+
+def pipe_open():
+ """Function for opening a PyMOL pipe."""
+
+ # Test that the PyMOL binary exists.
+ self.relax.IO.test_binary('pymol')
+
+ # Open the PyMOL pipe.
+ relax_data_store.pymol = popen("pymol -qpK", 'w', 0)
+
+ # Execute the command history.
+ if len(self.command_history) > 0:
+ self.pipe_write(self.command_history, store_command=0)
+ return
+
+ # Test if the PDB file has been loaded.
+ if hasattr(relax_data_store, 'pdb') and
relax_data_store.pdb.has_key(self.run):
+ self.open_pdb()
+
+
+def pipe_open_test():
+ """Function for testing if the PyMOL pipe is open."""
+
+ # Test if a pipe has been opened.
+ if not hasattr(relax_data_store, 'pymol'):
+ return 0
+
+ # Test if the pipe has been broken.
+ try:
+ relax_data_store.pymol.write('\n')
+ except IOError:
+ return 0
+
+ # The pipe is open.
+ return 1
+
+
+def pipe_write(command=None, store_command=1):
+ """Function for writing to the PyMOL pipe.
+
+ This function is also used to execute a user supplied PyMOL command.
+ """
+
+ # Reopen the pipe if needed.
+ if not self.pipe_open_test():
+ self.pipe_open()
+
+ # Write the command to the pipe.
+ relax_data_store.pymol.write(command + '\n')
+
+ # Place the command in the command history.
+ if store_command:
+ self.command_history = self.command_history + command + "\n"
+
+
+def tensor_pdb(run=None, file=None):
+ """Display the diffusion tensor geometric structure."""
+
+ # Arguments.
+ self.run = run
+
+ # Test if the run exists.
+ if not self.run in relax_data_store.run_names:
+ raise RelaxNoPipeError, self.run
+
+ # Read in the tensor PDB file.
+ self.pipe_write("load " + file)
+
+
+ # Centre of mass.
+ #################
+
+ # Select the COM residue.
+ self.pipe_write("select resn COM")
+
+ # Show the centre of mass as the dots representation.
+ self.pipe_write("show dots, 'sele'")
+
+ # Colour it blue.
+ self.pipe_write("color blue, 'sele'")
+
+
+ # The diffusion tensor axes.
+ ############################
+
+ # Select the AXS residue.
+ self.pipe_write("select resn AXS")
+
+ # Hide everything.
+ self.pipe_write("hide ('sele')")
+
+ # Show as 'sticks'.
+ self.pipe_write("show sticks, 'sele'")
+
+ # Colour it cyan.
+ self.pipe_write("color cyan, 'sele'")
+
+ # Select the N atoms of the AXS residue (used to display the axis
labels).
+ self.pipe_write("select (resn AXS and elem N)")
+
+ # Label the atoms.
+ self.pipe_write("label 'sele', name")
+
+
+
+ # Monte Carlo simulations.
+ ##########################
+
+ # Select the SIM residue.
+ self.pipe_write("select resn SIM")
+
+ # Colour it.
+ self.pipe_write("colour cyan, 'sele'")
+
+
+ # Clean up.
+ ###########
+
+ # Remove the selection.
+ self.pipe_write("cmd.delete('sele')")
+
+
+def vector_dist(run=None, file=None):
+ """Display the XH bond vector distribution.
+
+ @param run: The run
+ @type run: str
+ @param file: The vector distribution PDB file.
+ @type file: str
+ """
+
+ # Arguments.
+ self.run = run
+
+ # Test if the run exists.
+ if not self.run in relax_data_store.run_names:
+ raise RelaxNoPipeError, self.run
+
+ # The file root.
+ file_root = self.relax.IO.file_root(file)
+
+ # Read in the vector distribution PDB file.
+ self.pipe_write("load " + file)
+
+
+ # Create a surface.
+ ###################
+
+ # Select the vector distribution.
+ self.pipe_write("cmd.show('surface', " + `file_root` + ")")
+
+
+def view(run=None):
+ """Function for running PyMOL."""
+
+ # Arguments.
+ self.run = run
+
+ # Open a PyMOL pipe.
+ if self.pipe_open_test():
+ raise RelaxError, "The PyMOL pipe already exists."
+ else:
+ self.pipe_open()
+
+
+def write(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 PyMOL macro."""
+
+ # Arguments.
+ self.run = run
+ self.data_type = data_type
+ self.style = style
+ self.colour_start = colour_start
+ self.colour_end = colour_end
+ self.colour_list = colour_list
+
+ # No coded yet.
+ raise RelaxImplementError
+
+ # Test if the run exists.
+ if not self.run in relax_data_store.run_names:
+ raise RelaxNoPipeError, self.run
+
+ # Test if the sequence data is loaded.
+ if not relax_data_store.res.has_key(self.run):
+ raise RelaxNoSequenceError, self.run
+
+ # Create the macro.
+ self.create_macro()
+
+ # File name.
+ if file == None:
+ file = data_type + '.mac'
+
+ # Open the file for writing.
+ file = self.relax.IO.open_write_file(file, dir, force)
+
+ # Loop over the commands and write them.
+ for command in self.commands:
+ file.write(command + "\n")
+
+ # Close the file.
+ file.close()
r5379 - /1.3/generic_fns/pymol.py