Author: bugman
Date: Tue Apr 8 10:37:54 2008
New Revision: 5404
URL: http://svn.gna.org/viewcvs/relax?rev=5404&view=rev
Log:
Updated the macro_exec() function to the new relax design.
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=5404&r1=5403&r2=5404&view=diff
==============================================================================
--- 1.3/generic_fns/pymol.py (original)
+++ 1.3/generic_fns/pymol.py Tue Apr 8 10:37:54 2008
@@ -191,8 +191,147 @@
return commands
-def macro_exec(run=None, data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None):
- """Function for executing a PyMOL macro."""
+def macro_exec(data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None):
+ """Execute a PyMOL macro.
+
+ @keyword data_type: The data type ot map to the structure.
+ @type data_type: str
+ @keyword style: The style of the macro.
+ @type style: str
+ @keyword colour_start: The starting colour of the linear gradient.
+ @type colour_start: str or RBG colour array (len 3 with vals from 0
to 1)
+ @keyword colour_end: The ending colour of the linear gradient.
+ @type colour_end: str or RBG colour array (len 3 with vals from 0
to 1)
+ @keyword colour_list: The colour list to search for the colour names.
Can be either 'molmol'
+ or 'x11'.
+ @type colour_list: str or None
+ """
+
+ # Test if the current data pipe exists.
+ if not relax_data_store.current_pipe:
+ raise RelaxNoPipeError
+
+ # Test if sequence data exists.
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
+
+ # Create the macro.
+ commands = create_macro(data_type=data_type, style=style,
colour_start=colour_start, colour_end=colour_end, colour_list=colour_list)
+
+ # Loop over the commands and execute them.
+ for command in commands:
+ pymol.pipe_write(command)
+
+
+def tensor_pdb(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
+
+ # Read in the tensor PDB file.
+ self.pipe_write("load " + file)
+
+
+ # Centre of mass.
+ #################
+
+ # Select the COM residue.
+ self.pipe_write("select resn COM")
+
+ # Show the centre of mass as the dots representation.
+ self.pipe_write("show dots, 'sele'")
+
+ # Colour it blue.
+ self.pipe_write("color blue, 'sele'")
+
+
+ # The diffusion tensor axes.
+ ############################
+
+ # Select the AXS residue.
+ self.pipe_write("select resn AXS")
+
+ # Hide everything.
+ self.pipe_write("hide ('sele')")
+
+ # Show as 'sticks'.
+ self.pipe_write("show sticks, 'sele'")
+
+ # Colour it cyan.
+ self.pipe_write("color cyan, 'sele'")
+
+ # Select the N atoms of the AXS residue (used to display the axis
labels).
+ self.pipe_write("select (resn AXS and elem N)")
+
+ # Label the atoms.
+ self.pipe_write("label 'sele', name")
+
+
+
+ # Monte Carlo simulations.
+ ##########################
+
+ # Select the SIM residue.
+ self.pipe_write("select resn SIM")
+
+ # Colour it.
+ self.pipe_write("colour cyan, 'sele'")
+
+
+ # Clean up.
+ ###########
+
+ # Remove the selection.
+ self.pipe_write("cmd.delete('sele')")
+
+
+def vector_dist(run=None, file=None):
+ """Display the XH bond vector distribution.
+
+ @param run: The run
+ @type run: str
+ @param file: The vector distribution PDB file.
+ @type file: str
+ """
+
+ # Arguments.
+ self.run = run
+
+ # Test if the run exists.
+ if not self.run in relax_data_store.run_names:
+ raise RelaxNoPipeError, self.run
+
+ # The file root.
+ id = file_root(file)
+
+ # Read in the vector distribution PDB file.
+ self.pipe_write("load " + file)
+
+
+ # Create a surface.
+ ###################
+
+ # Select the vector distribution.
+ self.pipe_write("cmd.show('surface', " + `id` + ")")
+
+
+def view():
+ """Function for running PyMOL."""
+
+ # Open a PyMOL pipe.
+ if pymol.pipe_open_test():
+ raise RelaxError, "The PyMOL pipe already exists."
+ else:
+ pymol.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 PyMOL macro."""
# Arguments.
self.run = run
@@ -216,143 +355,6 @@
# Create the macro.
self.create_macro()
- # Loop over the commands and execute them.
- for command in self.commands:
- self.pipe_write(command)
-
-
-def tensor_pdb(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
-
- # Read in the tensor PDB file.
- self.pipe_write("load " + file)
-
-
- # Centre of mass.
- #################
-
- # Select the COM residue.
- self.pipe_write("select resn COM")
-
- # Show the centre of mass as the dots representation.
- self.pipe_write("show dots, 'sele'")
-
- # Colour it blue.
- self.pipe_write("color blue, 'sele'")
-
-
- # The diffusion tensor axes.
- ############################
-
- # Select the AXS residue.
- self.pipe_write("select resn AXS")
-
- # Hide everything.
- self.pipe_write("hide ('sele')")
-
- # Show as 'sticks'.
- self.pipe_write("show sticks, 'sele'")
-
- # Colour it cyan.
- self.pipe_write("color cyan, 'sele'")
-
- # Select the N atoms of the AXS residue (used to display the axis
labels).
- self.pipe_write("select (resn AXS and elem N)")
-
- # Label the atoms.
- self.pipe_write("label 'sele', name")
-
-
-
- # Monte Carlo simulations.
- ##########################
-
- # Select the SIM residue.
- self.pipe_write("select resn SIM")
-
- # Colour it.
- self.pipe_write("colour cyan, 'sele'")
-
-
- # Clean up.
- ###########
-
- # Remove the selection.
- self.pipe_write("cmd.delete('sele')")
-
-
-def vector_dist(run=None, file=None):
- """Display the XH bond vector distribution.
-
- @param run: The run
- @type run: str
- @param file: The vector distribution PDB file.
- @type file: str
- """
-
- # Arguments.
- self.run = run
-
- # Test if the run exists.
- if not self.run in relax_data_store.run_names:
- raise RelaxNoPipeError, self.run
-
- # The file root.
- id = file_root(file)
-
- # Read in the vector distribution PDB file.
- self.pipe_write("load " + file)
-
-
- # Create a surface.
- ###################
-
- # Select the vector distribution.
- self.pipe_write("cmd.show('surface', " + `id` + ")")
-
-
-def view():
- """Function for running PyMOL."""
-
- # Open a PyMOL pipe.
- if pymol.pipe_open_test():
- raise RelaxError, "The PyMOL pipe already exists."
- else:
- pymol.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 PyMOL 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
-
- # No coded yet.
- raise RelaxImplementError
-
- # 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'
r5404 - /1.3/generic_fns/pymol.py