Author: bugman
Date: Fri Mar 12 19:56:55 2010
New Revision: 10989
URL: http://svn.gna.org/viewcvs/relax?rev=10989&view=rev
Log:
Renamed the initialised PyMOL executable object from 'pymol' to 'pymol_ob'.
This is to avoid the name clash with the pymol python package.
Modified:
1.3/generic_fns/pymol_control.py
Modified: 1.3/generic_fns/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pymol_control.py?rev=10989&r1=10988&r2=10989&view=diff
==============================================================================
--- 1.3/generic_fns/pymol_control.py (original)
+++ 1.3/generic_fns/pymol_control.py Fri Mar 12 19:56:55 2010
@@ -158,8 +158,8 @@
-# Initialise the Pymol data container.
-pymol = Pymol()
+# Initialise the Pymol executable object.
+pymol_obj = Pymol()
"""Pymol data container instance."""
@@ -192,13 +192,13 @@
open_files.append(pdb_file)
# Hide everything.
- pymol.exec_cmd("cmd.hide('everything'," + repr(id) + ")")
+ pymol_obj.exec_cmd("cmd.hide('everything'," + repr(id) + ")")
# Show the cartoon style.
- pymol.exec_cmd("cmd.show('cartoon'," + repr(id) + ")")
+ pymol_obj.exec_cmd("cmd.show('cartoon'," + repr(id) + ")")
# Colour by secondary structure.
- pymol.exec_cmd("util.cbss(" + repr(id) + ", 'red', 'yellow',
'green')")
+ pymol_obj.exec_cmd("util.cbss(" + repr(id) + ", 'red', 'yellow',
'green')")
def command(command):
@@ -209,7 +209,7 @@
"""
# Pass the command to PyMOL.
- pymol.exec_cmd(command)
+ pymol_obj.exec_cmd(command)
def cone_pdb(file=None):
@@ -220,55 +220,55 @@
"""
# Read in the cone PDB file.
- pymol.exec_cmd("load " + file)
+ pymol_obj.exec_cmd("load " + file)
# The cone axis.
################
# Select the AVE, AXE, and SIM residues.
- pymol.exec_cmd("select (resn AVE,AXE,SIM)")
+ pymol_obj.exec_cmd("select (resn AVE,AXE,SIM)")
# Show the vector as a stick.
- pymol.exec_cmd("show stick, 'sele'")
+ pymol_obj.exec_cmd("show stick, 'sele'")
# Colour it blue.
- pymol.exec_cmd("color cyan, 'sele'")
+ pymol_obj.exec_cmd("color cyan, 'sele'")
# Select the atom used for labelling.
- pymol.exec_cmd("select (resn AVE,AXE,SIM and symbol N)")
+ pymol_obj.exec_cmd("select (resn AVE,AXE,SIM and symbol N)")
# Hide the atom.
- pymol.exec_cmd("hide ('sele')")
+ pymol_obj.exec_cmd("hide ('sele')")
# Label using the atom name.
- pymol.exec_cmd("cmd.label(\"sele\",\"name\")")
+ pymol_obj.exec_cmd("cmd.label(\"sele\",\"name\")")
# The cone object.
##################
# Select the CON residue.
- pymol.exec_cmd("select (resn CON,EDG)")
+ pymol_obj.exec_cmd("select (resn CON,EDG)")
# Hide everything.
- pymol.exec_cmd("hide ('sele')")
+ pymol_obj.exec_cmd("hide ('sele')")
# Show as 'sticks'.
- pymol.exec_cmd("show sticks, 'sele'")
+ pymol_obj.exec_cmd("show sticks, 'sele'")
# Colour it white.
- pymol.exec_cmd("color white, 'sele'")
+ pymol_obj.exec_cmd("color white, 'sele'")
# Shorten the stick width from 0.25 to 0.15.
- pymol.exec_cmd("set stick_radius,0.15000")
+ pymol_obj.exec_cmd("set stick_radius,0.15000")
# Clean up.
###########
# Remove the selection.
- pymol.exec_cmd("cmd.delete('sele')")
+ pymol_obj.exec_cmd("cmd.delete('sele')")
def create_macro(data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None):
@@ -327,7 +327,7 @@
# Loop over the commands and execute them.
for command in commands:
- pymol.exec_cmd(command)
+ pymol_obj.exec_cmd(command)
def tensor_pdb(file=None):
@@ -341,42 +341,42 @@
pipes.test()
# Read in the tensor PDB file.
- pymol.exec_cmd("load " + file)
+ pymol_obj.exec_cmd("load " + file)
# Centre of mass.
#################
# Select the COM residue.
- pymol.exec_cmd("select resn COM")
+ pymol_obj.exec_cmd("select resn COM")
# Show the centre of mass as the dots representation.
- pymol.exec_cmd("show dots, 'sele'")
+ pymol_obj.exec_cmd("show dots, 'sele'")
# Colour it blue.
- pymol.exec_cmd("color blue, 'sele'")
+ pymol_obj.exec_cmd("color blue, 'sele'")
# The diffusion tensor axes.
############################
# Select the AXS residue.
- pymol.exec_cmd("select resn AXS")
+ pymol_obj.exec_cmd("select resn AXS")
# Hide everything.
- pymol.exec_cmd("hide ('sele')")
+ pymol_obj.exec_cmd("hide ('sele')")
# Show as 'sticks'.
- pymol.exec_cmd("show sticks, 'sele'")
+ pymol_obj.exec_cmd("show sticks, 'sele'")
# Colour it cyan.
- pymol.exec_cmd("color cyan, 'sele'")
+ pymol_obj.exec_cmd("color cyan, 'sele'")
# Select the N atoms of the AXS residue (used to display the axis
labels).
- pymol.exec_cmd("select (resn AXS and elem N)")
+ pymol_obj.exec_cmd("select (resn AXS and elem N)")
# Label the atoms.
- pymol.exec_cmd("label 'sele', name")
+ pymol_obj.exec_cmd("label 'sele', name")
@@ -384,17 +384,17 @@
##########################
# Select the SIM residue.
- pymol.exec_cmd("select resn SIM")
+ pymol_obj.exec_cmd("select resn SIM")
# Colour it.
- pymol.exec_cmd("colour cyan, 'sele'")
+ pymol_obj.exec_cmd("colour cyan, 'sele'")
# Clean up.
###########
# Remove the selection.
- pymol.exec_cmd("cmd.delete('sele')")
+ pymol_obj.exec_cmd("cmd.delete('sele')")
def vector_dist(file=None):
@@ -411,24 +411,24 @@
id = file_root(file)
# Read in the vector distribution PDB file.
- pymol.exec_cmd("load " + file)
+ pymol_obj.exec_cmd("load " + file)
# Create a surface.
###################
# Select the vector distribution.
- pymol.exec_cmd("cmd.show('surface', " + repr(id) + ")")
+ pymol_obj.exec_cmd("cmd.show('surface', " + repr(id) + ")")
def view():
"""Start PyMOL."""
# Open PyMOL.
- if pymol.running():
+ if pymol_obj.running():
raise RelaxError("PyMOL is already running.")
else:
- pymol.open_gui()
+ pymol_obj.open_gui()
def write(data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None, file=None, dir=None, force=False):
r10989 - /1.3/generic_fns/pymol_control.py