Author: bugman
Date: Fri Apr 7 08:00:21 2006
New Revision: 2454
URL: http://svn.gna.org/viewcvs/relax?rev=2454&view=rev
Log:
The creation of a framework for the generation of Molmol macros.
A large number of changes and additions have been made including:
The user function 'molmol.write()' has been created.
A number of functions in the generic molmol code have been renamed. These
are 'open_pipe' to
'pipe_open', 'pipe_open' to 'pipe_open_test', and 'write' to 'pipe_write'.
The functions 'self.write()' and 'self.create_macro()' have been added to
'generic_fns/molmol.py'.
The first function calls the second which returns an array of Molmol
commands. The point of
splitting the functions is so in the future 'self.exec_macro()' can be added
to pipe the command
directly into Molmol.
The two functions 'self.molmol_macro()' and 'self.molmol_macro_classic()'
have been added to the
model-free specific code. The second function currently returns a dummy
array so that the resultant
macro is useless. The first function is returned by the specific_setup.py
code.
A new error class called 'RelaxStyleError' has been created. This error is
to be called anytime an
argument called 'style' is unrecognised.
Modified:
1.2/errors.py
1.2/generic_fns/molmol.py
1.2/prompt/molmol.py
1.2/specific_fns/model_free.py
1.2/specific_fns/specific_setup.py
Modified: 1.2/errors.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/errors.py?rev=2454&r1=2453&r2=2454&view=diff
==============================================================================
--- 1.2/errors.py (original)
+++ 1.2/errors.py Fri Apr 7 08:00:21 2006
@@ -432,3 +432,11 @@
def __init__(self, run):
self.text = "Simulations for the run " + `run` + " have not been
setup."
+
+ # Style errors.
+ ###############
+
+ # Unknown style.
+ class RelaxStyleError(BaseError):
+ def __init__(self, style):
+ self.text = "The style " + `style` + " is unknown."
Modified: 1.2/generic_fns/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/generic_fns/molmol.py?rev=2454&r1=2453&r2=2454&view=diff
==============================================================================
--- 1.2/generic_fns/molmol.py (original)
+++ 1.2/generic_fns/molmol.py Fri Apr 7 08:00:21 2006
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004 Edward d'Auvergne
#
+# Copyright (C) 2004, 2006 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -39,24 +39,17 @@
self.command_history = ""
- def open_pipe(self):
- """Function for opening a Molmol pipe."""
+ def create_macro(self):
+ """Function for creating an array of Molmol commands."""
- # Open the Molmol pipe.
- self.relax.data.molmol = popen("molmol -f -", 'w', 0)
+ # Function type.
+ self.function_type =
self.relax.data.run_types[self.relax.data.run_names.index(self.run)]
- # Execute the command history.
- if len(self.command_history) > 0:
- self.write(self.command_history, store_command=0)
- return
+ # Specific Molmol macro creation function.
+ molmol_macro = self.relax.specific_setup.setup('molmol_macro',
self.function_type)
- # Test if the PDB file has been loaded.
- if hasattr(self.relax.data, 'pdb'):
- self.open_pdb()
-
- # Run InitAll to remove everything from molmol.
- else:
- self.write("InitAll yes")
+ # Get the macro.
+ self.commands = molmol_macro(self.run, self.data_type, self.style)
def open_pdb(self, run=None):
@@ -67,17 +60,37 @@
self.run = run
# Test if the pipe is open.
- if not self.pipe_open():
+ if not self.pipe_open_test():
return
# Run InitAll to remove everything from molmol.
- self.write("InitAll yes")
+ self.pipe_write("InitAll yes")
# Open the PDB.
- self.write("ReadPdb " + self.relax.data.pdb[self.run].file_name)
+ self.pipe_write("ReadPdb " + self.relax.data.pdb[self.run].file_name)
def pipe_open(self):
+ """Function for opening a Molmol pipe."""
+
+ # Open the Molmol pipe.
+ self.relax.data.molmol = popen("molmol -f -", '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(self.relax.data, 'pdb'):
+ 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.
@@ -86,12 +99,30 @@
# Test if the pipe has been broken.
try:
- self.relax.data.molmol.write('\n')
+ self.relax.data.molmol.pipe_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.
+ self.relax.data.molmol.pipe_write(command + '\n')
+
+ # Place the command in the command history.
+ if store_command:
+ self.command_history = self.command_history + command + "\n"
def view(self, run=None):
@@ -101,25 +132,43 @@
self.run = run
# Open a Molmol pipe.
- if self.pipe_open():
+ if self.pipe_open_test():
raise RelaxError, "The Molmol pipe already exists."
else:
- self.open_pipe()
+ self.pipe_open()
- def write(self, command=None, store_command=1):
- """Function for writing to the Molmol pipe.
+ def write(self, run=None, data_type=None, style="classic", file=None,
dir=None, force=0):
+ """Function for creating a Molmol macro."""
- This function is also used to execute a user supplied Molmol command.
- """
+ # Arguments.
+ self.run = run
+ self.data_type = data_type
+ self.style = style
- # Reopen the pipe if needed.
- if not self.pipe_open():
- self.open_pipe()
+ # Test if the run exists.
+ if not self.run in self.relax.data.run_names:
+ raise RelaxNoRunError, self.run
- # Write the command to the pipe.
- self.relax.data.molmol.write(command + '\n')
+ # Test if the sequence data is loaded.
+ if not self.relax.data.res.has_key(self.run):
+ raise RelaxNoSequenceError, self.run
- # Place the command in the command history.
- if store_command:
- self.command_history = self.command_history + command + "\n"
+ # 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()
+
+
Modified: 1.2/prompt/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/prompt/molmol.py?rev=2454&r1=2453&r2=2454&view=diff
==============================================================================
--- 1.2/prompt/molmol.py (original)
+++ 1.2/prompt/molmol.py Fri Apr 7 08:00:21 2006
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004 Edward d'Auvergne
#
+# Copyright (C) 2004, 2006 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -22,7 +22,12 @@
import sys
+from doc_string import regexp_doc
import help
+from generic_fns.minimise import Minimise
+from specific_fns.model_free import Model_free
+from specific_fns.jw_mapping import Jw_mapping
+from specific_fns.noe import Noe
class Molmol:
@@ -101,3 +106,109 @@
# Execute the functional code.
self.__relax__.generic.molmol.view(run=run)
+
+
+ def write(self, run=None, data_type=None, style="classic", file=None,
dir='molmol', force=0):
+ """Function for creating Molmol macros.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ run: The name of the run.
+
+ data_type: The data type to map to the structure.
+
+ style: The style of the macro.
+
+ file: The name of the file.
+
+ dir: The directory name.
+
+ force: A flag which, if set to 1, will cause the file to be
overwritten.
+
+
+ Description
+ ~~~~~~~~~~~
+
+ This function allows residues specific values to be mapped to a
structure through the
+ creation of a Molmol '*.mac' macro which can be executed in Molmol
by clicking on 'File,
+ Macro, Execute User...'. Currently only the 'classic' style, which
is described below, is
+ availible.
+
+
+ Classic style
+ ~~~~~~~~~~~~~
+
+ Creator: Edward d'Auvergne
+
+ Argument string: "classic"
+
+ Description: The classic style draws the backbone of the protein in
'neon' style. Rather
+ than colouring the amino acids to which the NH bond belongs, the
three covalent bonds of the
+ petide bond from Ca to Ca to which the NH bond belongs is coloured.
+
+ Supported data types:
+ Model-free: S2, te, Rex.
+
+
+
+ Examples
+ ~~~~~~~~
+
+ 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("
+ text = text + "run=" + `run`
+ text = text + ", data_type=" + `data_type`
+ text = text + ", style=" + `style`
+ text = text + ", file=" + `file`
+ text = text + ", dir=" + `dir`
+ text = text + ", force=" + `force` + ")"
+ print text
+
+ # The run name.
+ if type(run) != str:
+ raise RelaxStrError, ('run', run)
+
+ # Data type for mapping to the structure.
+ if type(data_type) != str:
+ raise RelaxStrError, ('data type', data_type)
+
+ # The style.
+ if type(style) != str:
+ raise RelaxStrError, ('style', style)
+
+ # File.
+ if file != None and type(file) != str:
+ raise RelaxStrError, ('file name', file)
+
+ # Directory.
+ if dir != None and type(dir) != str:
+ raise RelaxNoneStrError, ('directory name', dir)
+
+ # The force flag.
+ if type(force) != int or (force != 0 and force != 1):
+ raise RelaxBinError, ('force flag', force)
+
+ # Execute the functional code.
+ self.__relax__.generic.molmol.write(run=run, data_type=data_type,
style=style, file=file, dir=dir, force=force)
+
+
+
+ # Docstring modification.
+ #########################
+
+ # Write function.
+ write.__doc__ = write.__doc__ + "\n\n" + regexp_doc() + "\n"
+ write.__doc__ = write.__doc__ + Minimise.return_data_name.__doc__ +
"\n\n"
+ write.__doc__ = write.__doc__ + Model_free.return_data_name.__doc__ +
"\n\n"
+ write.__doc__ = write.__doc__ + Jw_mapping.return_data_name.__doc__ +
"\n\n"
+ write.__doc__ = write.__doc__ + Noe.return_data_name.__doc__ + "\n"
Modified: 1.2/specific_fns/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/specific_fns/model_free.py?rev=2454&r1=2453&r2=2454&view=diff
==============================================================================
--- 1.2/specific_fns/model_free.py (original)
+++ 1.2/specific_fns/model_free.py Fri Apr 7 08:00:21 2006
@@ -2598,6 +2598,28 @@
return 1
+ def molmol_macro(self, run, data_type, style):
+ """Function for creating Molmol macros of the model-free
parameters."""
+
+ # Arguments.
+ self.run = run
+
+ # The classic style.
+ if style == 'classic':
+ return self.molmol_macro_classic(data_type)
+
+ # Unknown style.
+ else:
+ raise RelaxStyleError, style
+
+
+ def molmol_macro_classic(self, data_type):
+ """Create and return an array of Molmol commands in the classic
style."""
+
+ # Dummy array.
+ return ["InitAll yes"]
+
+
def read_columnar_col_numbers(self, header):
"""Function for sorting the column numbers from the columnar
formatted results file."""
@@ -4283,7 +4305,7 @@
# Create the data structure.
self.relax.data.res[run][i].relax_sim_data = sim_data
-
+
def sim_return_chi2(self, run, instance):
"""Function for returning the array of simulation chi-squared
values."""
Modified: 1.2/specific_fns/specific_setup.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/specific_fns/specific_setup.py?rev=2454&r1=2453&r2=2454&view=diff
==============================================================================
--- 1.2/specific_fns/specific_setup.py (original)
+++ 1.2/specific_fns/specific_setup.py Fri Apr 7 08:00:21 2006
@@ -233,6 +233,10 @@
# Model statistics.
if self.eqi == 'model_stats':
return self.relax.specific.model_free.model_statistics
+
+ # Molmol macro creation.
+ if self.eqi == 'molmol_macro':
+ return self.relax.specific.model_free.molmol_macro
# Number of instances.
if self.eqi == 'num_instances':
r2454 - in /1.2: errors.py generic_fns/molmol.py prompt/molmol.py specific_fns/model_free.py specific_fns/specific_setup.py