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List: relax-commits
Subject: r2698 - in /branches/tensor_pdb: generic_fns/molmol.py prompt/molmol.py
From: edward.dauvergne () domain ! hid
Date: 2006-10-29 6:37:49
Message-ID: E1Ge4In-0003XK-Cm () domain ! hid
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Author: bugman
Date: Sun Oct 29 07:37:48 2006
New Revision: 2698
URL: http://svn.gna.org/viewcvs/relax?rev=2698&view=rev
Log:
Created the user function 'molmol.ribbon()'.
This function applies the Molmol ribbon style and is equivalent to clicking on \
'ribbon' in the Molmol side menu.
Modified:
branches/tensor_pdb/generic_fns/molmol.py
branches/tensor_pdb/prompt/molmol.py
Modified: branches/tensor_pdb/generic_fns/molmol.py
URL: http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/generic_fns/molmol.py?rev=2698&r1=2697&r2=2698&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/molmol.py (original)
+++ branches/tensor_pdb/generic_fns/molmol.py Sun Oct 29 07:37:48 2006
@@ -169,6 +169,27 @@
self.command_history = self.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 self.relax.data.run_names:
+ raise RelaxNoRunError, 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 view(self, run=None):
"""Function for running Molmol."""
Modified: branches/tensor_pdb/prompt/molmol.py
URL: http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/prompt/molmol.py?rev=2698&r1=2697&r2=2698&view=diff
==============================================================================
--- branches/tensor_pdb/prompt/molmol.py (original)
+++ branches/tensor_pdb/prompt/molmol.py Sun Oct 29 07:37:48 2006
@@ -77,7 +77,9 @@
Example
~~~~~~~
- relax> molmol.command("InitAll yes")
+ To reinitialise the Molmol instance for the run 'aic', type:
+
+ relax> molmol.command("aic", "InitAll yes")
"""
# Function intro text.
@@ -197,6 +199,48 @@
# 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.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ run: The name of the run.
+
+
+ Description
+ ~~~~~~~~~~~
+
+ This function applies the Molmol ribbon style. To do this, the following \
commands are + executed:
+
+ CalcAtom 'H'
+ CalcAtom 'HN'
+ CalcSecondary
+ XMacStand ribbon.mac
+
+
+ Example
+ ~~~~~~~
+
+ 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("
+ text = text + "run=" + `run` + ")"
+ print text
+
+ # The run name.
+ if type(run) != str:
+ raise RelaxStrError, ('run', run)
+
+ # Execute the functional code.
+ self.__relax__.generic.molmol.ribbon(run=run)
def view(self, run=None):
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