Author: bugman
Date: Sun Oct 29 09:17:10 2006
New Revision: 2702
URL: http://svn.gna.org/viewcvs/relax?rev=2702&view=rev
Log:
Initial support for PyMOL.
The 'prompt' and 'generic_fns' Molmol files have been copied to new PyMOL
files. The classes have
been renamed and setup within the prompt interface or the main generic
functions class. A number of
instances where 'molmol' was written have been replaced with 'pymol'. Much
work is still left. For
example PyMOL will not execute in script mode as it terminates saying:
PyMOL: normal program termination.
once the pipe is closed (after finishing the script and relax terminating).
Added:
branches/tensor_pdb/generic_fns/pymol.py
- copied, changed from r2700, branches/tensor_pdb/generic_fns/molmol.py
branches/tensor_pdb/prompt/pymol.py
- copied, changed from r2700, branches/tensor_pdb/prompt/molmol.py
Modified:
branches/tensor_pdb/generic_fns/main.py
branches/tensor_pdb/prompt/__init__.py
branches/tensor_pdb/prompt/interpreter.py
Modified: branches/tensor_pdb/generic_fns/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/generic_fns/main.py?rev=2702&r1=2701&r2=2702&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/main.py (original)
+++ branches/tensor_pdb/generic_fns/main.py Sun Oct 29 09:17:10 2006
@@ -35,6 +35,7 @@
from nuclei import Nuclei
from palmer import Palmer
from pdb import PDB
+from pymol import Pymol
from results import Results
from runs import Runs
from selection import Selection
@@ -67,6 +68,7 @@
self.opendx = OpenDX(self.relax)
self.palmer = Palmer(self.relax)
self.pdb = PDB(self.relax)
+ self.pymol = Pymol(self.relax)
self.results = Results(self.relax)
self.runs = Runs(self.relax)
self.selection = Selection(self.relax)
Copied: branches/tensor_pdb/generic_fns/pymol.py (from r2700,
branches/tensor_pdb/generic_fns/molmol.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/generic_fns/pymol.py?p2=branches/tensor_pdb/generic_fns/pymol.py&p1=branches/tensor_pdb/generic_fns/molmol.py&r1=2700&r2=2702&rev=2702&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/molmol.py (original)
+++ branches/tensor_pdb/generic_fns/pymol.py Sun Oct 29 09:17:10 2006
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004, 2006 Edward d'Auvergne
#
+# Copyright (C) 2006 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -24,7 +24,7 @@
from string import split
-class Molmol:
+class Pymol:
def __init__(self, relax):
"""Class containing the functions for viewing molecules."""
@@ -113,13 +113,13 @@
def pipe_open(self):
- """Function for opening a Molmol pipe."""
-
- # Test that the Molmol binary exists.
- self.relax.IO.test_binary('molmol')
-
- # Open the Molmol pipe.
- self.relax.data.molmol = popen("molmol -f -", 'w', 0)
+ """Function for opening a PyMOL pipe."""
+
+ # Test that the PyMOL binary exists.
+ self.relax.IO.test_binary('pymol')
+
+ # Open the PyMOL pipe.
+ self.relax.data.molmol = popen("pymol -qp", 'w', 0)
# Execute the command history.
if len(self.command_history) > 0:
@@ -130,16 +130,12 @@
if hasattr(self.relax.data, 'pdb') and
self.relax.data.pdb.has_key(self.run):
self.open_pdb()
- # Run InitAll to remove everything from molmol.
- else:
- self.pipe_write("InitAll yes")
-
def pipe_open_test(self):
- """Function for testing if the Molmol pipe is open."""
+ """Function for testing if the PyMOL pipe is open."""
# Test if a pipe has been opened.
- if not hasattr(self.relax.data, 'molmol'):
+ if not hasattr(self.relax.data, 'pymol'):
return 0
# Test if the pipe has been broken.
@@ -235,9 +231,9 @@
# Arguments.
self.run = run
- # Open a Molmol pipe.
+ # Open a PyMOL pipe.
if self.pipe_open_test():
- raise RelaxError, "The Molmol pipe already exists."
+ raise RelaxError, "The PyMOL pipe already exists."
else:
self.pipe_open()
Modified: branches/tensor_pdb/prompt/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/prompt/__init__.py?rev=2702&r1=2701&r2=2702&view=diff
==============================================================================
--- branches/tensor_pdb/prompt/__init__.py (original)
+++ branches/tensor_pdb/prompt/__init__.py Sun Oct 29 09:17:10 2006
@@ -43,6 +43,7 @@
'nuclei',
'palmer',
'pdb',
+ 'pymol',
'relax_data',
'relax_fit',
'run',
Modified: branches/tensor_pdb/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/prompt/interpreter.py?rev=2702&r1=2701&r2=2702&view=diff
==============================================================================
--- branches/tensor_pdb/prompt/interpreter.py (original)
+++ branches/tensor_pdb/prompt/interpreter.py Sun Oct 29 09:17:10 2006
@@ -59,6 +59,7 @@
from noe import Noe
from palmer import Palmer
from pdb import PDB
+from pymol import Pymol
from relax_data import Relax_data
from relax_fit import Relax_fit
from results import Results
@@ -116,6 +117,7 @@
self._Noe = Noe(relax)
self._Palmer = Palmer(relax)
self._PDB = PDB(relax)
+ self._Pymol = Pymol(relax)
self._Relax_data = Relax_data(relax)
self._Relax_fit = Relax_fit(relax)
self._Results = Results(relax)
@@ -173,6 +175,7 @@
noe = self._Noe
palmer = self._Palmer
pdb = self._PDB
+ pymol = self._Pymol
relax_data = self._Relax_data
relax_fit = self._Relax_fit
results = self._Results
Copied: branches/tensor_pdb/prompt/pymol.py (from r2700,
branches/tensor_pdb/prompt/molmol.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/prompt/pymol.py?p2=branches/tensor_pdb/prompt/pymol.py&p1=branches/tensor_pdb/prompt/molmol.py&r1=2700&r2=2702&rev=2702&view=diff
==============================================================================
--- branches/tensor_pdb/prompt/molmol.py (original)
+++ branches/tensor_pdb/prompt/pymol.py Sun Oct 29 09:17:10 2006
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004, 2006 Edward d'Auvergne
#
+# Copyright (C) 2006 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -23,15 +23,10 @@
import sys
from colour import Colour
-from doc_string import regexp_doc
import help
-from generic_fns.minimise import Minimise
-from specific_fns.model_free import Molmol
-from specific_fns.jw_mapping import Jw_mapping
-from specific_fns.noe import Noe
-
-
-class Molmol:
+
+
+class Pymol:
def __init__(self, relax):
# Help.
self.__relax_help__ = \
@@ -49,11 +44,11 @@
# Function intro text.
if self.__relax__.interpreter.intro:
- text = sys.ps3 + "molmol.clear_history()"
- print text
-
- # Execute the functional code.
- self.__relax__.generic.molmol.clear_history()
+ 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):
@@ -79,12 +74,12 @@
To reinitialise the Molmol instance for the run 'aic', type:
- relax> molmol.command("aic", "InitAll yes")
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "molmol.command("
+ relax> pymol.command("aic", "InitAll yes")
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "pymol.command("
text = text + "run=" + `run`
text = text + ", command=" + `command` + ")"
print text
@@ -98,7 +93,7 @@
raise RelaxStrError, ('command', command)
# Execute the functional code.
- self.__relax__.generic.molmol.command(run=run, command=command)
+ 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):
@@ -152,14 +147,14 @@
To map the order parameter values, S2, of the run 'final' onto the
structure using the
classic style, type:
- relax> molmol.macro_exec('final', 'S2')
- relax> molmol.macro_exec('final', data_type='S2')
- relax> molmol.macro_exec('final', data_type='S2', style="classic")
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "molmol.macro_exec("
+ relax> pymol.macro_exec('final', 'S2')
+ relax> pymol.macro_exec('final', data_type='S2')
+ relax> pymol.macro_exec('final', 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 + ", style=" + `style`
@@ -197,11 +192,11 @@
raise RelaxListNumError, ('ending colour of the linear
gradient', colour_end)
# Execute the functional code.
- self.__relax__.generic.molmol.macro_exec(run=run,
data_type=data_type, style=style, colour_start=colour_start,
colour_end=colour_end, colour_list=colour_list)
-
-
- def ribbon(self, run=None):
- """Apply the Molmol ribbon style.
+ 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.
Keyword Arguments
~~~~~~~~~~~~~~~~~
@@ -226,12 +221,12 @@
To apply the ribbon style to the PDB file loaded for the run
'final', type:
- relax> molmol.ribbon("final")
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "molmol.ribbon("
+ relax> pymol.ribbon("final")
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "pymol.ribbon("
text = text + "run=" + `run` + ")"
print text
@@ -240,7 +235,7 @@
raise RelaxStrError, ('run', run)
# Execute the functional code.
- self.__relax__.generic.molmol.ribbon(run=run)
+ self.__relax__.generic.pymol.ribbon(run=run)
def tensor_pdb(self, run=None, file=None):
@@ -300,7 +295,7 @@
# Function intro text.
if self.__relax__.interpreter.intro:
- text = sys.ps3 + "molmol.tensor_pdb("
+ text = sys.ps3 + "pymol.tensor_pdb("
text = text + "run=" + `run`
text = text + ", file=" + `file` + ")"
print text
@@ -314,7 +309,7 @@
raise RelaxStrError, ('file name', file)
# Execute the functional code.
- self.__relax__.generic.molmol.tensor_pdb(run=run, file=file)
+ self.__relax__.generic.pymol.tensor_pdb(run=run, file=file)
def view(self, run=None):
@@ -329,13 +324,13 @@
Example
~~~~~~~
- relax> molmol.view('m1')
- relax> molmol.view(run='pdb')
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "molmol.view("
+ 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
@@ -344,11 +339,11 @@
raise RelaxStrError, ('run', run)
# Execute the functional code.
- self.__relax__.generic.molmol.view(run=run)
+ 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):
- """Function for creating Molmol macros.
+ """Function for creating PyMOL macros.
Keyword Arguments
~~~~~~~~~~~~~~~~~
@@ -406,14 +401,14 @@
To create a Molmol macro mapping the order parameter values, S2, of
the run 'final' onto the
structure using the classic style, type:
- relax> molmol.write('final', 'S2')
- relax> molmol.write('final', data_type='S2')
- relax> molmol.write('final', data_type='S2', style="classic",
file='s2.mac', dir='molmol')
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "molmol.write("
+ 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')
+ """
+
+ # 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 + ", style=" + `style`
@@ -466,7 +461,7 @@
raise RelaxBinError, ('force flag', force)
# Execute the functional code.
- self.__relax__.generic.molmol.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)
+ 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)
@@ -474,7 +469,7 @@
#########################
# Write function.
- write.__doc__ = write.__doc__ + "\n\n" + Molmol.classic.__doc__ + "\n\n"
+ #write.__doc__ = write.__doc__ + "\n\n" + Molmol.classic.__doc__ + "\n\n"
# Molmol RGB colour list.
write.__doc__ = write.__doc__ + "\n\n" + Colour.molmol_colours.__doc__ +
"\n\n"
r2702 - in /branches/tensor_pdb: generic_fns/ prompt/