chunks

来自「最经典的分子对结软件」· 代码 · 共 129 行

#!/bin/sh

# This is a script designed to feed sybdb smaller pieces to avoid 
# memory limitations.  Use no arguments to get usage instructions.  DAG 3/95
# Modified to improve space requirements throughout chunking process DAG 8/95.

# Please customize the location of the DOCK bin directory at your site
dock_bin=/idk2/private/dock/bin

# Check for proper invocation
if [ $# -ne 3 ]; then
	echo "Usage:  `basename $0` <input> <output> <chunk_size>"
	echo "   where <input> is generally the output from sdf2mol2,"
	echo "         <output> is the desired output file name, and"
	echo "         <chunk_size> is the number of molecules to process at a time."
	exit 1
fi

input=$1
output=$2
chunksize=$3

output_sybout=$output.sybout
output_syblog=$output.syblog

tmp=chunk
postfix=processed
splitmol=$dock_bin/splitmol
sybdb=$dock_bin/sybdb
sybdbout=sybdb.out
sybdblog=sybdb.log
executables="$splitmol $sybdb"
newfiles="$output $output_sybout $output_syblog"

# Make sure the executables are there
for exe in $executables
do
	if [ ! -x $exe ]; then
		echo "Can not locate/execute $dock_bin/$exe."
		echo "Please update the location of the DOCK root within the `basename $0` script."
		exit 1
	fi
done

# Make sure the input is readable
if [ ! -r $input ]; then
	echo "Can not read from input: $input."
	exit 1
fi

# Check to see if the parameter file is present and alert user
if [ ! -f gastpar.tab ]; then
	echo "WARNING - no gastpar.tab Gasteiger Marsili parameter file"
	echo "was found in this directory.  Unless you have modified the"
	echo "Tripos-distributed version of this file in"
	echo "       \$TA_ROOT/sybylbase/tables/gastpar.tab"
	echo "sulfoxides and sulfones will be assigned zero charges!"
	echo "Proceed? \c"
	read ans
	case $ans in
		[yY])
			;;
		*)
			echo "Aborting..."
			exit 1
			;;
	esac
fi

# Remove any existing chunks
/bin/rm -f $tmp.*

# Remove any existing log files and databases
for new in $newfiles
do
	if [ -f $new ]; then
		echo "Desired output file exists: $new."
		echo "Remove it? \c"
		read ans
		case $ans in
			[yY])
				/bin/rm -f $new
				;;
			*)
				echo "Aborting..."
				exit 1
				;;
		esac
	fi
done


startat=1
stopat=$chunksize

# Now process the database in chunks with sybdb
while :
do
	echo "\n===============================> Processing chunk at #$startat."

	# extract this chunk from the database - note that since we do this
	# within the loop, this is slower than splitting the entire database
	# prior to beginning the processing as the whole database needs to be
	# scanned for the appropriate chunk every time
	$splitmol -mol2 $input -splitby $chunksize -start $startat -stop $stopat -rel -out $tmp

	echo ""

	# if there were no molecules in the range, we are done
	if [ ! -f $tmp.00001 ]; then 
		echo " Last chunk was empty - we are finished!"
		break
	fi

	# process the current chunk with sybdb
	echo "Processing with sybdb..."
	$sybdb $tmp.00001 $tmp.$postfix > /dev/null
	cat $sybdbout >> $output_sybout
	cat $sybdblog >> $output_syblog
	cat $tmp.$postfix >> $output
	/bin/rm -f $tmp.*

	# determine starting and stopping points for extraction
	startat=`expr $stopat + 1`
	stopat=`expr $stopat + $chunksize`
	
done