x2pdb

最经典的分子对结软件

#!/bin/sh

# This script converts an extended PDB format file (e.g. DOCK output) 
# to standard PDB format, commonly used by many graphics packages.

# Rewritten in sh 8/26/94 DAG

# Check for proper invocation
if [ $# != 1 ]; then
	echo "Error --> need 1 argument.  Usage:  `basename $0` <xpdb_filename>"
	exit 1
fi

infile=$1


# See if the input file actually exists
if [ ! -f $infile ]; then
	echo "Error --> $infile does not exist!"
	exit 1
fi


# Substitute "xpdb" extension, if it exists, for "pdb", otherwise append.
outfile=`echo $infile | sed -e s/xpdb/pdb/`

if [ $outfile = $infile ]; then
	# the input file did not have an "xpdb" extension, so just append
	# a .pdb to the original name
	outfile=$infile.pdb
fi


# Check to see if the desired output file exists already.
if [ -f $outfile ]; then
	echo "Desired output file $outfile exists.  Overwrite? "
	read ans
	case $ans in
		[Yy]*) 
			# we'll continue and overwrite the file...
			;;
		*)
			# ...otherwise quit now
			echo "Aborting..."
			exit
			;;
	esac
			
fi


# Now process the xpdb file
#	note that there are two alternative print statements
#	the first is for 1,2, or 3 letter pdb atom names, while
#	the second is for 4 letter pdb atom names

nawk '
{
if (($1 == "ATOM") || ($1 ~ /ATM/))
	{
	if (NF == 11)
		{
		if ( length($3) < 4 )
			{
		   printf("%-6s%5d  %-4s%-4s%5d%12.3f%8.3f%8.3f%6.2f%6.2f\n",
				$1,$2,$3,$4,$5,$6,$7,$8,$9,$9*$10)
			}
		else
			{
		   printf("%-6s%5d %-4s %-4s%5d%12.3f%8.3f%8.3f%6.2f%6.2f\n",
				$1,$2,$3,$4,$5,$6,$7,$8,$9,$9*$10)
			}
		}
	else
		{
		print;
		next
		}
	}
else
	{print}
}
' $1 > $outfile

echo "Standard PDB file $outfile created."