pdb2syb

来自「最经典的分子对结软件」· 代码 · 共 92 行

#!/bin/sh

# this script simplifies the interface to E.Meng's idtosyb program,
# designed to make better approximations to connectivity and atom
# typing than SYBYL, which does an atrocious job
#

idtosyb_dir=/usr/dock/source/database/idtosyb
idtosyb_exe=/usr/dock/bin/idtosyb
curdir=`pwd`

# check for valid invocation
if [ $# -ne 1 ]; then
	echo "Need 1 argument.  Usage:  `basename $0` <pdb_filename>"
	exit 1
fi

# check for valid file
if [ ! -f $1 ]; then
	echo "Error!  $1 does not exist."
	exit 1
fi


# check for existence of idtosyb directory
if [ ! -d $idtosyb_dir ]; then
	echo Error! idtosyb directory $idtosyb_dir not found.
	echo Please update the variable idtosyb_dir in `basename $0` to point 
	echo to the proper location.
	exit 1
fi

# check for existence of idtosyb executable
if [ ! -x $idtosyb_exe ]; then
	echo Error! idtosyb executable $idtosyb_exe not found.
	echo Please update the variable idtosyb_exe in `basename $0` to point 
	echo to the proper location.
	exit 1
fi

# check for existence of conversion tools
tools="attyps params"
for tool in $tools
do
	if [ ! -f $idtosyb_dir/$tool ]; then
		echo Error! $tool not found in $idtosyb_dir.
		echo Please put a copy in this directory.
		exit 1
	fi
done


pdbin=$1
sybout=`echo $pdbin | nawk '{p=index($1,".pdb"); if (p != 0) {print substr($1,1,p-1)} else {print}}'`.mol2

if [ -f $sybout ]; then
	echo Desired output file exists.  Overwrite?
	read ans
	case $ans in
		[yY]*)
			;;
		*)
			echo Aborting...
			exit
			;;
	esac
fi

# acquire parameter files
if [ "$curdir" != "$idtosyb_dir" ]; then
	/bin/cp $idtosyb_dir/params .
	/bin/cp $idtosyb_dir/attyps .
fi

# set up links
ln -fs $pdbin pdbfil > /dev/null 2>&1
if [ -f sybfil ]; then /bin/rm sybfil; fi

# run the program
$idtosyb_exe

# remove files and clean up
if [ "$curdir" != "$idtosyb_dir" ]; then
	/bin/rm params
	/bin/rm attyps
fi

/bin/rm pdbfil > /dev/null 2>&1
/bin/mv sybfil $sybout

echo "SYBYL mol2 file $sybout created."