Author: bugman
Date: Fri Mar 12 19:45:37 2010
New Revision: 10987
URL: http://svn.gna.org/viewcvs/relax?rev=10987&view=rev
Log:
Started to redesign the generic_fns.pymol module to use the pymol python
package.
This involves much renaming of the PyMOL pipe object which is not the PyMOL
executable object. This
attempts to use the pymol python package, and if not available PyMOL will be
run from the command
line as a pipe.
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=10987&r1=10986&r2=10987&view=diff
==============================================================================
--- 1.3/generic_fns/pymol.py (original)
+++ 1.3/generic_fns/pymol.py Fri Mar 12 19:45:37 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2006-2009 Edward d'Auvergne
#
+# Copyright (C) 2006-2010 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -23,8 +23,14 @@
# Module docstring.
"""Module for interfacing with PyMOL."""
+# Dependency check module.
+import dep_check
+
# Python module imports.
-from os import popen, sep
+if dep_check.pymol_module:
+ import pymol
+from os import sep
+from subprocess import PIPE, Popen
# relax module imports.
from generic_fns.mol_res_spin import exists_mol_res_spin_data
@@ -35,37 +41,42 @@
class Pymol:
- """Data container for storing PyMOL related data.
-
- This includes information such as the PyMOL command history. Also
stored is the file handle to
- the PyMOL child process pipe.
- """
-
- def __init__(self):
- """Class initialisation method used to set the command history and
the PyMOL pipe."""
-
+ """The PyMOL execution object."""
+
+ def __init__(self, exec_mode=None):
+ """Set up the PyMOL execution object.
+
+ @keyword exec_mode: The execution mode which can be either 'module'
or 'external'.
+ @type exec_mode: None or str
+ """
+
+ # Variable for storing the pymol command history.
self.command_history = ""
- """Variable for storing the pymol command history."""
-
- self.pipe = None
- """Writable pipe (file handle) to the PyMOL child process."""
+
+ # The pymol mode of operation.
+ self.exec_mode = exec_mode
+ if not exec_mode:
+ if dep_check.pymol_module:
+ self.exec_mode = 'module'
+ else:
+ self.exec_mode = 'external'
def clear_history(self):
- """Method for clearing the PyMOL command history."""
+ """Clear the PyMOL command history."""
self.command_history = ""
def open_pdb(self):
- """Function for opening the PDB file in PyMOL."""
-
- # Test if the pipe is open.
- if not self.pipe_open_test():
+ """Open the PDB file in PyMOL."""
+
+ # Test if PyMOL is running.
+ if not self.running():
return
# Reinitialise PyMOL.
- self.pipe_write("reinitialize")
+ self.exec_cmd("reinitialize")
# Open the PDB files.
open_files = []
@@ -81,24 +92,31 @@
continue
# Open the file in PyMOL.
- self.pipe_write("load " + file)
+ self.exec_cmd("load " + file)
# Add to the open file list.
open_files.append(file)
- def pipe_open(self):
- """Function for opening a PyMOL pipe."""
-
- # Test that the PyMOL binary exists.
- test_binary('pymol')
-
- # Open the PyMOL pipe.
- self.pymol = popen("pymol -qpK", 'w', 0)
+ def open_gui(self):
+ """Open the PyMOL GUI."""
+
+ # Use the PyMOL python modules.
+ if self.exec_mode == 'module':
+ # Open the GUI.
+ pymol.gui.pymol.start_pymol()
+
+ # Otherwise execute PyMOL on the command line.
+ if self.exec_mode == 'external':
+ # Test that the PyMOL binary exists.
+ test_binary('pymol')
+
+ # Open PyMOL as a pipe.
+ self.pymol = Popen(['pymol', '-qpK'], stdin=PIPE).stdin
# Execute the command history.
if len(self.command_history) > 0:
- self.pipe_write(self.command_history, store_command=0)
+ self.exec_cmd(self.command_history, store_command=0)
return
# Test if the PDB file has been loaded.
@@ -106,35 +124,33 @@
self.open_pdb()
- def pipe_open_test(self):
- """Function for testing if the PyMOL pipe is open."""
-
- # Test if a pipe has been opened.
+ def running(self):
+ """Test if PyMOL is running."""
+
+ # Test if PyMOL is already running.
if not hasattr(self, 'pymol'):
- return 0
+ return False
# Test if the pipe has been broken.
try:
self.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()
+ return False
+
+ # PyMOL is running.
+ return True
+
+
+ def exec_cmd(self, command=None, store_command=1):
+ """Execute a PyMOL command."""
+
+ # Reopen the GUI if needed.
+ if not self.running():
+ self.open_gui()
# Write the command to the pipe.
- self.pymol.write(command + '\n')
+ if self.exec_mode == 'external':
+ self.pymol.write(command + '\n')
# Place the command in the command history.
if store_command:
@@ -176,13 +192,13 @@
open_files.append(pdb_file)
# Hide everything.
- pymol.pipe_write("cmd.hide('everything'," + repr(id) + ")")
+ pymol.exec_cmd("cmd.hide('everything'," + repr(id) + ")")
# Show the cartoon style.
- pymol.pipe_write("cmd.show('cartoon'," + repr(id) + ")")
+ pymol.exec_cmd("cmd.show('cartoon'," + repr(id) + ")")
# Colour by secondary structure.
- pymol.pipe_write("util.cbss(" + repr(id) + ", 'red', 'yellow',
'green')")
+ pymol.exec_cmd("util.cbss(" + repr(id) + ", 'red', 'yellow',
'green')")
def command(command):
@@ -193,7 +209,7 @@
"""
# Pass the command to PyMOL.
- pymol.pipe_write(command)
+ pymol.exec_cmd(command)
def cone_pdb(file=None):
@@ -204,55 +220,55 @@
"""
# Read in the cone PDB file.
- pymol.pipe_write("load " + file)
+ pymol.exec_cmd("load " + file)
# The cone axis.
################
# Select the AVE, AXE, and SIM residues.
- pymol.pipe_write("select (resn AVE,AXE,SIM)")
+ pymol.exec_cmd("select (resn AVE,AXE,SIM)")
# Show the vector as a stick.
- pymol.pipe_write("show stick, 'sele'")
+ pymol.exec_cmd("show stick, 'sele'")
# Colour it blue.
- pymol.pipe_write("color cyan, 'sele'")
+ pymol.exec_cmd("color cyan, 'sele'")
# Select the atom used for labelling.
- pymol.pipe_write("select (resn AVE,AXE,SIM and symbol N)")
+ pymol.exec_cmd("select (resn AVE,AXE,SIM and symbol N)")
# Hide the atom.
- pymol.pipe_write("hide ('sele')")
+ pymol.exec_cmd("hide ('sele')")
# Label using the atom name.
- pymol.pipe_write("cmd.label(\"sele\",\"name\")")
+ pymol.exec_cmd("cmd.label(\"sele\",\"name\")")
# The cone object.
##################
# Select the CON residue.
- pymol.pipe_write("select (resn CON,EDG)")
+ pymol.exec_cmd("select (resn CON,EDG)")
# Hide everything.
- pymol.pipe_write("hide ('sele')")
+ pymol.exec_cmd("hide ('sele')")
# Show as 'sticks'.
- pymol.pipe_write("show sticks, 'sele'")
+ pymol.exec_cmd("show sticks, 'sele'")
# Colour it white.
- pymol.pipe_write("color white, 'sele'")
+ pymol.exec_cmd("color white, 'sele'")
# Shorten the stick width from 0.25 to 0.15.
- pymol.pipe_write("set stick_radius,0.15000")
+ pymol.exec_cmd("set stick_radius,0.15000")
# Clean up.
###########
# Remove the selection.
- pymol.pipe_write("cmd.delete('sele')")
+ pymol.exec_cmd("cmd.delete('sele')")
def create_macro(data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None):
@@ -311,7 +327,7 @@
# Loop over the commands and execute them.
for command in commands:
- pymol.pipe_write(command)
+ pymol.exec_cmd(command)
def tensor_pdb(file=None):
@@ -325,42 +341,42 @@
pipes.test()
# Read in the tensor PDB file.
- pymol.pipe_write("load " + file)
+ pymol.exec_cmd("load " + file)
# Centre of mass.
#################
# Select the COM residue.
- pymol.pipe_write("select resn COM")
+ pymol.exec_cmd("select resn COM")
# Show the centre of mass as the dots representation.
- pymol.pipe_write("show dots, 'sele'")
+ pymol.exec_cmd("show dots, 'sele'")
# Colour it blue.
- pymol.pipe_write("color blue, 'sele'")
+ pymol.exec_cmd("color blue, 'sele'")
# The diffusion tensor axes.
############################
# Select the AXS residue.
- pymol.pipe_write("select resn AXS")
+ pymol.exec_cmd("select resn AXS")
# Hide everything.
- pymol.pipe_write("hide ('sele')")
+ pymol.exec_cmd("hide ('sele')")
# Show as 'sticks'.
- pymol.pipe_write("show sticks, 'sele'")
+ pymol.exec_cmd("show sticks, 'sele'")
# Colour it cyan.
- pymol.pipe_write("color cyan, 'sele'")
+ pymol.exec_cmd("color cyan, 'sele'")
# Select the N atoms of the AXS residue (used to display the axis
labels).
- pymol.pipe_write("select (resn AXS and elem N)")
+ pymol.exec_cmd("select (resn AXS and elem N)")
# Label the atoms.
- pymol.pipe_write("label 'sele', name")
+ pymol.exec_cmd("label 'sele', name")
@@ -368,17 +384,17 @@
##########################
# Select the SIM residue.
- pymol.pipe_write("select resn SIM")
+ pymol.exec_cmd("select resn SIM")
# Colour it.
- pymol.pipe_write("colour cyan, 'sele'")
+ pymol.exec_cmd("colour cyan, 'sele'")
# Clean up.
###########
# Remove the selection.
- pymol.pipe_write("cmd.delete('sele')")
+ pymol.exec_cmd("cmd.delete('sele')")
def vector_dist(file=None):
@@ -395,24 +411,24 @@
id = file_root(file)
# Read in the vector distribution PDB file.
- pymol.pipe_write("load " + file)
+ pymol.exec_cmd("load " + file)
# Create a surface.
###################
# Select the vector distribution.
- pymol.pipe_write("cmd.show('surface', " + repr(id) + ")")
+ pymol.exec_cmd("cmd.show('surface', " + repr(id) + ")")
def view():
- """Function for running PyMOL."""
-
- # Open a PyMOL pipe.
- if pymol.pipe_open_test():
- raise RelaxError("The PyMOL pipe already exists.")
+ """Start PyMOL."""
+
+ # Open PyMOL.
+ if pymol.running():
+ raise RelaxError("PyMOL is already running.")
else:
- pymol.pipe_open()
+ pymol.open_gui()
def write(data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None, file=None, dir=None, force=False):
r10987 - /1.3/generic_fns/pymol.py