#!/bin/sh# a script to perform a QCPE connolly MS calculation (ACG,DAG 1/95)# input:#	receptor pdb file#	exclude.pdb file containing residues which should NOT be surfaced# output:#	receptor.ms surface file#	receptor.dot surface file for sybyl#	an INSPH file for SPHGEN# define the location for dock related programs - users should update thisdock_root=/bert/dock/bin# users should update the location of their copy of QCPE MSMS_executable=$dock_root/qcpe_msexclude_pdb=exclude.pdbsurfdens_default=5.0proberad_default=1.4stars="_______________________________________________________________________"# Check invocationcase $# in    1)  receptor=$1	surfdens=$surfdens_default	proberad=$proberad_default	;;    2)  receptor=$1	surfdens=$2	proberad=$proberad_default	;;    3)  receptor=$1	surfdens=$2	proberad=$3	;;    *)	echo "Usage: `basename $0` <receptor_pdbfile> [<surface_density>] [<probe_size>]"	echo "    where <surface_density defaults to $surfdens_default and probe size to $proberad_default."	exit 1	;;esac# make sure required files existif [ ! -f "$receptor" ]; then	echo "A receptor file named $receptor was not found."	exit 1fi# make sure an exclude file existsif [ ! -f "$exclude_pdb" ]; then	echo "The file $exclude_pdb was not found.  Please create one containing"	echo "residues of the receptor that should NOT be surfaced."	exit 1fiif [ ! -f "$MS_executable" ]; then	echo "Error - could not locate your copy of QCPE MS."	echo "Please update the location of the MS executable you obtained from QCPE"	echo "in the `basename $0` script."	exit 1fi# determine the root name of the receptorreceptor=$1rec_root=`echo $receptor | nawk '{p=index($1,".pdb"); if (p != 0) {print substr($1,1,p-1)} else {print}}'`echo $starsecho Preparing input for surface calculation...echo# convert the pdb file into the required format for ms# unit names are assigned for this conversionln -fs $receptor fort.1 > /dev/null 2>&1ln -fs $exclude_pdb fort.2  > /dev/null 2>&1ln -fs temp.msin fort.3 > /dev/null 2>&1# perform the conversion$dock_root/pdb2ms/bin/rm fort.[12] > /dev/null 2>&1# set up for the surface calculation# set up input unitsecho " "$surfdens"       "$proberad"         0    0" > fort.1cat > fort.2 << EndOfRadii    1      1.20    2      1.90    3      1.50    4      1.40    5      1.35    6      1.90    7      1.85    8      1.80     9      1.95   10      2.15EndOfRadii# remove existing surface files/bin/rm CONTACT REENTRANT > /dev/null 2>&1echo $starsecho Performing QCPE MS calculation...echo$MS_executable# clean up MS outputcat CONTACT REENTRANT | sort -n > temp.msout/bin/rm CONTACT REENTRANT BEFORE > /dev/null 2>&1/bin/rm $rec_root.ms $rec_root.dot > /dev/null 2>&1echo $starsecho Converting output to SPHGEN input format...echocat > reform.in << EOO$receptortemp.msout$rec_root.msEOO$dock_root/reformatms < reform.in# create sybyl dot surface if ms2dot has been compiledif [ -x $dock_root/ms2dot ]; then	echo $stars	echo Creating dot surface for SYBYL...	echo	cat > color.in << EOO$rec_root.ms$rec_root.dot0EOO	$dock_root/ms2dot < color.infiechoecho $starsecho Cleaning up after myself...echo/bin/rm temp.msout reform.in color.in fort.[123] temp.msin > /dev/null 2>&1echo $starsecho Preparing for SPHGEN run...echocat > INSPH << EndOfINSPH$rec_root.msRX0.04.0$proberad$rec_root.sphEndOfINSPH# remove any temp files in preparation for SPHGEN run/bin/rm temp1.{ms,sph} temp2.sph temp3.atc > /dev/null 2>&1echoecho $starsecho Ready to run SPHGEN.either=if [ -f OUTSPH ]; then	echo " I didn't delete your OUTSPH in case you wanted to keep it around."	either=" either"fiif [ -f $rec_root.sph ]; then	echo " I noticed a sphere file already here ($rec_root.sph), but didn't delete it$either."#	echo " didn't delete it$either."fi