This is currently mostly just a consolidation of the --help output and 
some error output (flagging that Biopython and rnaview are required, and
where they can be downloaded.)

The modified dtd is provided so that validating xml editors may be used with 
the rnaview output (both copies of the drtd are the modified version.)




This tool requires BioPython and RNAVIEW; installation instructions for which\n" )
may be found (at the time of writing) here: http://www.biopython.org
and here: http://ndbserver.rutgers.edu/services/download/index.html


command format:  python rnaDB.py [options] <identifier1> [<identifier2>...]
<options> MUST include either --audit, --build, --extract,  --inventory or --printHelices
<identifier> : for --build, a pdb filename, or with the -l option a name of a textfile containing a list of pdb files,
			 or a wildcard-glob for either.
<identifier> : for --extract, a pdb ID, or pdbID:chains such as 1A34:BC, or with the -l option a name 
			 of a textfile containing a list of such, or a wildcard-glob for such textfiles.
options:
	--audit: checks existing entries for helix patterns known to need special attention
	--build: new pdb entries will be added to the rnaDB
	--extract:  helical (default) or non-helical RNA portions of specified pdbIDs and chains
			  will be extracted to separate pdb files
	--db=<rna_db_name>: specifies rna_db file name, default "rna_db.dat"
	-h, --help: display this help message.  This tool requires BioPython and RNAVIEW; installation instructions
			 for which are found here: http://www.biopython.org/docs/install/Installation.html
			 and here: http://ndbserver.rutgers.edu/services/download/index.html
	-l : command line identifiers are textfiles containing a whitespace separated list of 
			 identifiers to be processed
	--tmp=<dir_name>: specifies directory for temporary files, default is "rnaDB_tmp"
	--dest=<dir_name>: specifies directory for extracted pdb files, default is "rna_pdbs"
	--helices: deprecated, replaced with intra_helices, below, for clarity.
	--intra_helices: only works with --extract, specifies single-stranded (intra-molecular) helical portions are to be extracted
	--all_helices (default): only works with --extract, specifies all helical portions are to be extracted
	--inter_helices: only works with --extract, specifies only intermolecular helical portions are to be extracted
	--invert: only works with --extract, specifies extraction of the portions not meeting helical and/or other requirements
	--noDL: disables downloading of pdb files from pdb.org
	--printHelices: prints helix descriptors for helices in specified entries
	--basePairs: adds inidividual basePair details to --printHelices output
	--savexml: saves xml files created during build process