automs

最经典的分子对结软件

#!/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 this
dock_root=/bert/dock/bin

# users should update the location of their copy of QCPE MS
MS_executable=$dock_root/qcpe_ms

exclude_pdb=exclude.pdb
surfdens_default=5.0
proberad_default=1.4
stars="_______________________________________________________________________"


# Check invocation
case $# 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 exist
if [ ! -f "$receptor" ]; then
	echo "A receptor file named $receptor was not found."
	exit 1
fi

# make sure an exclude file exists
if [ ! -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 1
fi

if [ ! -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 1
fi



# determine the root name of the receptor
receptor=$1
rec_root=`echo $receptor | nawk '{p=index($1,".pdb"); if (p != 0) {print substr($1,1,p-1)} else {print}}'`


echo $stars
echo Preparing input for surface calculation...
echo
# convert the pdb file into the required format for ms
# unit names are assigned for this conversion
ln -fs $receptor fort.1 > /dev/null 2>&1
ln -fs $exclude_pdb fort.2  > /dev/null 2>&1
ln -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 units
echo " "$surfdens"       "$proberad"         0    0" > fort.1
cat > 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      2.15
EndOfRadii

# remove existing surface files
/bin/rm CONTACT REENTRANT > /dev/null 2>&1

echo $stars
echo Performing QCPE MS calculation...
echo
$MS_executable


# clean up MS output
cat 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>&1



echo $stars
echo Converting output to SPHGEN input format...
echo
cat > reform.in << EOO
$receptor
temp.msout
$rec_root.ms
EOO
$dock_root/reformatms < reform.in



# create sybyl dot surface if ms2dot has been compiled
if [ -x $dock_root/ms2dot ]; then
	echo $stars
	echo Creating dot surface for SYBYL...
	echo
	cat > color.in << EOO
$rec_root.ms
$rec_root.dot
0
EOO
	$dock_root/ms2dot < color.in
fi


echo
echo $stars
echo Cleaning up after myself...
echo
/bin/rm temp.msout reform.in color.in fort.[123] temp.msin > /dev/null 2>&1


echo $stars
echo Preparing for SPHGEN run...
echo
cat > INSPH << EndOfINSPH
$rec_root.ms
R
X
0.0
4.0
$proberad
$rec_root.sph
EndOfINSPH

# remove any temp files in preparation for SPHGEN run
/bin/rm temp1.{ms,sph} temp2.sph temp3.atc > /dev/null 2>&1


echo
echo $stars
echo 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"
fi

if [ -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