:::::::: bmrb.py ::::::::

Author   : Nicolas Sapay, Ph.D. student at IBCP - France
Contact  : n.sapay@ibcp.fr
Creation : Sept 2004 - last update Jan 2005
Version  : 1.0
           1.1 * bug on atom deletion during nomenclature translation fixed
               * modification of the atom retrieving procedure 
               * error message added when a file can't be open

SYNOPSIS :
==========
	This Python script is a SPARKY EXTENSION that provides methods to
create a BMRB submission form directly from a SPARKY resonance list (Only 
for amino acids). Methods defined here include :
	- methods to detect possible atom nomenclature mistakes
	- methods to detect redundant assignation in the resonance list
	- methods to detect strong chemical shift Standard Deviation (SD)

	A NMR STAR template file is required to run the extension. The 
template file can be generated on the BMRB web site:
                www.bmrb.wisc.edu/elec_dep/gen_aa.html

INSTALLATION :
==============
	Sparky3.10 or higher and Python2.10 or higher are required to run
the extension. To install the Sparky extension you have to:
	-copy <brmb.py> Python script in the Sparky extension folder. If you
	 have install Sparky </usr/local/bin>, it should be:
		/usr/local/bin/sparky/pyhton/sparky/
	-modify the file sparky_init.py in the Spary extension folder by
	adding those lines:
	
	
     1	def initialize_session(session):
     2		#pass
     3		def bs_command(s = session):
     4			import bmrb
     5			bmrb.show_dialog(s)
     6
     7		session.add_command("bs", "BRMB submission form", bs_command) 

	You can now run Sparky. An entry call "BMRB submission form" have been
added at the end of the Extension menu. You can also run the extension by
using th <bs> shortcut

USAGE :
=======
	The BMRB extension in composed of 4 panel:
	> Panel 1 : used to configure the atom selection to be included in the
	  BMRB submission form : 
		- SD chemical shift threshold is used to detect atoms with a
		  large SD chemical shift. Large SD could potentially
		  correspond to an assignment mistake
		- Atom assignment nomenclature is used to check the atom names
		- BMRB template file is use to create the list of atoms that
		  have to be included in the final BMRB submission form.
		  Template file can be generated using your sequence at :
		      http://www.bmrb.wisc.edu/elec_dep/gen_aa.html
	
	> Panel 2 : used to select the correct chemical shift in the redundant
	  chemical shift assignments.

	> Panel 3 : used to select chemical shift with large SD which have to
	  be included in the BMRB submission form.

	> Panel 4 : used to select the atom not corresponding to atom
	  nomenclature that have to be included in the BMRB submission form.

	The BMRB submission form cna be generated by clicking on the <create>
button. This will show the list of not retrieved atom in the template file and
the assignment list. Concretly, the extension try to fill the submission formm
by retrieving each assigned atoms in the template file. Non retrieved atoms
are then printed out. The BMRB submission form can be save using the <Save>
button.