Author: bugman
Date: Thu Feb 7 10:35:21 2008
New Revision: 4912
URL: http://svn.gna.org/viewcvs/relax?rev=4912&view=rev
Log:
Converted all the Molmol class methods into module functions.
Modified:
1.3/generic_fns/molmol.py
Modified: 1.3/generic_fns/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/molmol.py?rev=4912&r1=4911&r2=4912&view=diff
==============================================================================
--- 1.3/generic_fns/molmol.py (original)
+++ 1.3/generic_fns/molmol.py Thu Feb 7 10:35:21 2008
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004, 2006-2007 Edward d'Auvergne
#
+# Copyright (C) 2004, 2006-2008 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -33,254 +33,246 @@
"""Variable for storing the Molmol command history."""
-
-class Molmol:
- def __init__(self, relax):
- """Class containing the functions for viewing molecules."""
-
- self.relax = relax
-
-
- def clear_history(self):
- """Function for clearing the Molmol command history."""
-
- 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 relax_data_store.run_names:
- raise RelaxNoPipeError, self.run
-
- # Pass the command to Molmol.
- self.pipe_write(command)
-
-
- def create_macro(self):
- """Function for creating an array of Molmol commands."""
-
- # Function type.
- self.function_type =
relax_data_store.run_types[relax_data_store.run_names.index(self.run)]
-
- # Specific Molmol macro creation function.
- molmol_macro = self.relax.specific_setup.setup('molmol_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)
-
-
- 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."""
-
- # 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
-
- # 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 Molmol."""
-
- # Argument.
- if run:
- self.run = run
-
- # Test if the pipe is open.
- if not self.pipe_open_test():
- return
-
- # Run InitAll to remove everything from molmol.
- self.pipe_write("InitAll yes")
-
- # Open the PDB.
- self.pipe_write("ReadPdb " +
relax_data_store.pdb[self.run].file_name)
-
-
- 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.
- relax_data_store.molmol = popen("molmol -f -", 'w', 0)
-
- # Execute the command history.
- if len(command_history) > 0:
- self.pipe_write(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()
-
- # 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."""
-
- # Test if a pipe has been opened.
- if not hasattr(relax_data_store, 'molmol'):
- return 0
-
- # Test if the pipe has been broken.
- try:
- relax_data_store.molmol.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 Molmol pipe.
-
- This function is also used to execute a user supplied Molmol command.
- """
-
- # Reopen the pipe if needed.
- if not self.pipe_open_test():
- self.pipe_open()
-
- # Write the command to the pipe.
- relax_data_store.molmol.write(command + '\n')
-
- # Place the command in the command history.
- if store_command:
- command_history = command_history + command + "\n"
-
-
- def ribbon(self, run=None):
- """Apply the Molmol ribbon style."""
-
- # Arguments.
- self.run = run
-
- # Test if the run exists.
- if not self.run in relax_data_store.run_names:
- raise RelaxNoPipeError, self.run
-
- # Calculate the protons.
- self.pipe_write("CalcAtom 'H'")
- self.pipe_write("CalcAtom 'HN'")
-
- # Calculate the secondary structure.
- self.pipe_write("CalcSecondary")
-
- # Execute the ribbon macro.
- self.pipe_write("XMacStand ribbon.mac")
-
-
- 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
-
- # To overlay the structure with the diffusion tensor, select all and
reorient to the PDB frame.
- self.pipe_write("SelectAtom ''")
- self.pipe_write("SelectBond ''")
- self.pipe_write("SelectAngle ''")
- self.pipe_write("SelectDist ''")
- self.pipe_write("SelectPrim ''")
- self.pipe_write("RotateInit")
- self.pipe_write("MoveInit")
-
- # Read in the tensor PDB file and force Molmol to recognise the
CONECT records (not that it will show the bonds)!
- self.pipe_write("ReadPdb " + file)
- file_parts = split(file, '.')
- self.pipe_write("SelectMol '@" + file_parts[0] + "'")
- self.pipe_write("CalcBond 1 1 1")
-
- # Apply the 'ball/stick' style to the tensor.
- self.pipe_write("SelectAtom '0'")
- self.pipe_write("SelectBond '0'")
- self.pipe_write("SelectAtom ':TNS'")
- self.pipe_write("SelectBond ':TNS'")
- self.pipe_write("XMacStand ball_stick.mac")
-
- # Touch up.
- self.pipe_write("RadiusAtom 1")
- self.pipe_write("SelectAtom ':TNS@C*'")
- self.pipe_write("RadiusAtom 1.5")
-
-
- def view(self, run=None):
- """Function for running Molmol."""
-
- # Arguments.
- self.run = run
-
- # Open a Molmol pipe.
- if self.pipe_open_test():
- raise RelaxError, "The Molmol 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 Molmol 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
-
- # 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()
+def clear_history():
+ """Function for clearing the Molmol command history."""
+
+ command_history = ""
+
+
+def command(run, command):
+ """Function for sending Molmol commands to the program pipe."""
+
+ # Arguments.
+ run = run
+
+ # Test if the run exists.
+ if not run in relax_data_store.run_names:
+ raise RelaxNoPipeError, run
+
+ # Pass the command to Molmol.
+ pipe_write(command)
+
+
+def create_macro():
+ """Function for creating an array of Molmol commands."""
+
+ # Function type.
+ function_type =
relax_data_store.run_types[relax_data_store.run_names.index(run)]
+
+ # Specific Molmol macro creation function.
+ molmol_macro = relax.specific_setup.setup('molmol_macro', function_type)
+
+ # Get the macro.
+ commands = molmol_macro(run, data_type, style, colour_start, colour_end,
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 Molmol macro."""
+
+ # Arguments.
+ run = run
+ data_type = data_type
+ style = style
+ colour_start = colour_start
+ colour_end = colour_end
+ colour_list = colour_list
+
+ # Test if the run exists.
+ if not run in relax_data_store.run_names:
+ raise RelaxNoPipeError, run
+
+ # Test if the sequence data is loaded.
+ if not relax_data_store.res.has_key(run):
+ raise RelaxNoSequenceError, run
+
+ # Create the macro.
+ create_macro()
+
+ # Loop over the commands and execute them.
+ for command in commands:
+ pipe_write(command)
+
+
+def open_pdb(run=None):
+ """Function for opening the PDB file in Molmol."""
+
+ # Argument.
+ if run:
+ run = run
+
+ # Test if the pipe is open.
+ if not pipe_open_test():
+ return
+
+ # Run InitAll to remove everything from molmol.
+ pipe_write("InitAll yes")
+
+ # Open the PDB.
+ pipe_write("ReadPdb " + relax_data_store.pdb[run].file_name)
+
+
+def pipe_open():
+ """Function for opening a Molmol pipe."""
+
+ # Test that the Molmol binary exists.
+ relax.IO.test_binary('molmol')
+
+ # Open the Molmol pipe.
+ relax_data_store.molmol = popen("molmol -f -", 'w', 0)
+
+ # Execute the command history.
+ if len(command_history) > 0:
+ pipe_write(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(run):
+ open_pdb()
+
+ # Run InitAll to remove everything from molmol.
+ else:
+ pipe_write("InitAll yes")
+
+
+def pipe_open_test():
+ """Function for testing if the Molmol pipe is open."""
+
+ # Test if a pipe has been opened.
+ if not hasattr(relax_data_store, 'molmol'):
+ return 0
+
+ # Test if the pipe has been broken.
+ try:
+ relax_data_store.molmol.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 Molmol pipe.
+
+ This function is also used to execute a user supplied Molmol command.
+ """
+
+ # Reopen the pipe if needed.
+ if not pipe_open_test():
+ pipe_open()
+
+ # Write the command to the pipe.
+ relax_data_store.molmol.write(command + '\n')
+
+ # Place the command in the command history.
+ if store_command:
+ command_history = command_history + command + "\n"
+
+
+def ribbon(run=None):
+ """Apply the Molmol ribbon style."""
+
+ # Arguments.
+ run = run
+
+ # Test if the run exists.
+ if not run in relax_data_store.run_names:
+ raise RelaxNoPipeError, run
+
+ # Calculate the protons.
+ pipe_write("CalcAtom 'H'")
+ pipe_write("CalcAtom 'HN'")
+
+ # Calculate the secondary structure.
+ pipe_write("CalcSecondary")
+
+ # Execute the ribbon macro.
+ pipe_write("XMacStand ribbon.mac")
+
+
+def tensor_pdb(run=None, file=None):
+ """Display the diffusion tensor geometric structure."""
+
+ # Arguments.
+ run = run
+
+ # Test if the run exists.
+ if not run in relax_data_store.run_names:
+ raise RelaxNoPipeError, run
+
+ # To overlay the structure with the diffusion tensor, select all and
reorient to the PDB frame.
+ pipe_write("SelectAtom ''")
+ pipe_write("SelectBond ''")
+ pipe_write("SelectAngle ''")
+ pipe_write("SelectDist ''")
+ pipe_write("SelectPrim ''")
+ pipe_write("RotateInit")
+ pipe_write("MoveInit")
+
+ # Read in the tensor PDB file and force Molmol to recognise the CONECT
records (not that it will show the bonds)!
+ pipe_write("ReadPdb " + file)
+ file_parts = split(file, '.')
+ pipe_write("SelectMol '@" + file_parts[0] + "'")
+ pipe_write("CalcBond 1 1 1")
+
+ # Apply the 'ball/stick' style to the tensor.
+ pipe_write("SelectAtom '0'")
+ pipe_write("SelectBond '0'")
+ pipe_write("SelectAtom ':TNS'")
+ pipe_write("SelectBond ':TNS'")
+ pipe_write("XMacStand ball_stick.mac")
+
+ # Touch up.
+ pipe_write("RadiusAtom 1")
+ pipe_write("SelectAtom ':TNS@C*'")
+ pipe_write("RadiusAtom 1.5")
+
+
+def view(run=None):
+ """Function for running Molmol."""
+
+ # Arguments.
+ run = run
+
+ # Open a Molmol pipe.
+ if pipe_open_test():
+ raise RelaxError, "The Molmol pipe already exists."
+ else:
+ 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 Molmol macro."""
+
+ # Arguments.
+ run = run
+ data_type = data_type
+ style = style
+ colour_start = colour_start
+ colour_end = colour_end
+ colour_list = colour_list
+
+ # Test if the run exists.
+ if not run in relax_data_store.run_names:
+ raise RelaxNoPipeError, run
+
+ # Test if the sequence data is loaded.
+ if not relax_data_store.res.has_key(run):
+ raise RelaxNoSequenceError, run
+
+ # Create the macro.
+ create_macro()
+
+ # File name.
+ if file == None:
+ file = data_type + '.mac'
+
+ # Open the file for writing.
+ file = relax.IO.open_write_file(file, dir, force)
+
+ # Loop over the commands and write them.
+ for command in commands:
+ file.write(command + "\n")
+
+ # Close the file.
+ file.close()
r4912 - /1.3/generic_fns/molmol.py