#!/bin/csh -f
#    make a bounds database for a nucleic acid type
#
#    Assumes all files of a given sequence type in the coords directory
#    have the prefix type shown below (i.e., all bdna pdb files start
#    with "bd" ).  
#
#    To make a bounds database for a particular nucleic acid type
#    include the type as a command line argument (i.e., "mkdb bdna").
#    These files result:
#
#	bdna.nucleotide.db - 	distance information between atoms in a 
#				single residue participating in helical
#				stacking and basepairing.
#	watsoncrick.basepair.db-distance information between atoms forming
#				a hydrogen-bonded basepair from a helix,
#				assuming a standard W-C basepair
#	bdna.stack.db - 	distance information between atoms in
#				a stacked geometry exhibited by successive
#				residues in a strand of helical bDNA,
#				assuming standard W-C pairing in each plane.
#	
foreach i ( `ls $NABHOME/coords/*.pdbs` )
	set $newname = `echo $i | sed 's/.pdbs//'`
	echo $newname
	mv ${i}.pdbs ${newname}s.pdb
end 
foreach i (`grep -l HOH $NABHOME/coords/?d*.pdb`)
	cat $i | awk ' { if (($4 !~ /HOH/) && ($1 ~ /ATOM/)) {print} }' > $$.TEMP
        mv $$.TEMP $i
end 
if ( (!( -e $NABHOME/dgdb/functions/getwcdist )) || (!( -e $NABHOME/dgdb/functions/getbackbonedist )) || (!( -e $NABHOME/dgdb/functions/getstackdist )) ) $NABHOME/dgdb/functions/install
foreach natype ( $argv[*] )
	echo making $natype databases...
	if ( $natype == "bdna" ) set prefix = "bd"
	if ( $natype == "adna" ) set prefix = "ad"
	if ( $natype == "zdna" ) set prefix = "zd"
	if ( $natype == "arna" ) set prefix = "ar"
	if ( $natype == "trna" ) set prefix = "tr"
	( $NABHOME/dgdb/functions/getbackbonedist coords/${prefix}*.pdb | sed -f $NABHOME/dgdb/functions/filter.sed | sort | $NABHOME/dgdb/functions/stats.awk ) >! $NABHOME/dgdb/${natype}.nucleotide.db
	echo made $NABHOME/dgdb/${natype}.nucleotide.db
	( $NABHOME/dgdb/functions/getstackdist coords/${prefix}*.pdb | sed -f $NABHOME/dgdb/functions/filter.sed | sort | $NABHOME/dgdb/functions/stats.awk ) >! $NABHOME/dgdb/${natype}.stack.db
	echo made $NABHOME/dgdb/${natype}.stack.db
	( $NABHOME/dgdb/functions/getwcdist coords/${prefix}*.pdb | sed -f $NABHOME/dgdb/functions/filter.sed | sort | $NABHOME/dgdb/functions/stats.awk ) >! $NABHOME/dgdb/${natype}.basepair.db
	echo made $NABHOME/dgdb/${natype}.basepair.db