# $CVSHeader: pal8e/etc/ChangeLog,v 1.6 2005/02/15 01:10:24 indraneel Rel $

2003-03-06  Indraneel Majumdar  <indraneel@sangala.swmed.edu>

	* project: Major modifications to use fork(). Each file is a
	separate process. Bugfix for strand breaking (copy.copy
	used). This version runs on solaris.

2003-02-28  Indraneel Majumdar  <indraneel@sangala.swmed.edu>

	* AddedFiles: Added these files: TODO, BUGS, ruleset(sequence of
	rules), process(overview) PSSDExceptions (exception handling),
	rotateRuns.sh (rotates debug files between runs)

	* PSSD: Major modifications. Bulges are marked and detected using
	special methods (gap between strands, residue distance, quadruplet
	scores). Hairpin bends are treated separately for strand breaking
	and bad interactions. Uses Polypeptide. Single public method
	run(). Start of chain is tagged.  Helix removal modified. Strand
	extension using quadruplet climbing. Modified quadruplet
	generation to use Polypeptide. Does not cleanup structure (delete
	residues etc).

	* PSSDResult: Uses modified conffile. Uses Polypeptide. Outputs
	info associated with any specified tag. Outputs HELIX, SHEET,
	PAIRS lines in pdb format by replacing HELIX, SHEET lines in PDB.

	* PSSDUI: Uses new conffile. Uses run() to enable future
	threading. Handles 'break' command in conffile.

	* Quad: Major changes. Modified to use Polypeptide. Checks for
	wrongly numbered consecutive residues. Previous and next residues are stored.

	* InsightScript: Changed to use new conf file. First residue of chain is CPK. 

	* pssdconf: Does not point to TLD. Makes easier to manage and rotate.

	* reschk: Added new entries to check.

2003-02-14  Indraneel Majumdar  <indraneel@sangala.swmed.edu>

	* ruleset: Made a list of all rules.

	* project converted into python and works ok. Fine tuning remains
	to be done. Helices and strands are broken and extended as
	required. Extended elements still not defined.

2002-08-30  Indraneel Majumdar  <indraneel@sangala.swmed.edu>

	* project imported into cvs now.  this is first entry after
	checkout.  output ad documentation are located outside working
	directory.  lexer and parser are called from makefiles.

2002-07-15  Indraneel Majumdar  <indraneel@YAST_ASK>

	* datain.cpp is scrapped. code rewritten to use multiple files.

2002-06-03  Indraneel Majumdar  <indraneel@sangala>

	* datain.cpp (base): Checking change log mode in emacs. Now
	checking for eof. Now checking for carriage
	return. OK

