joinpdb

#!/bin/sh
# Author: Jurgen F. Doreleijers (modified by Ton Rullmann).
# Make a multi-model PDB file from separate PDB files.
#
# The result appears on stdout or on the file named with the "-o" option.
# The input files are given as arguments, or they are taken to be
# xxx1.pdb, xxx2.pdb etc. where xxx and the number of files are
# retrieved interactively.
#

if [ $# -eq 0 ]
then
    echo "Usage: joinpdb  -o outputfile  [inputfiles]"
    echo "   if no inputfiles are given, their names are assumed to be"
    echo "   xxx1.pdb, xxx2.pdb etc."
    echo "   and you will be prompted to specify xxx and the number of files"
    echo
    echo "Concatenate separate single structure PDB files into a multi-model"
    echo "file."
    echo
    echo "Everything before the first ATOM record will be left out except for the"
    echo "first model."
    echo "An END record MUST be present in every file (therefore it is added by the"
    echo "script when missing)."
    echo "CONECT and MASTER records are discarded."
    exit
fi
if [ "$1" = "-o" ]
then
    outfil=$2
    shift 2
fi
if [ $# -eq 0 ]
then
    echo "Make a multi-model PDB file from separate files, named xxx1.pdb etc."
    echo "Rootname of files (xxx): "
    read xxx
    echo "Number of files: "
    read max_files
else
    max_files=$#
fi

if [ -s join.temp ]
then
    /bin/rm join.temp
fi

number=1
while [ "$number" -le "$max_files" ]
do
    if [ $# -eq 0 ]
    then
        infil=$xxx$number".pdb"
    else
        infil=$1
        shift
    fi
    echo "Concatenate" $infil
    cat $infil >> join.temp
    if [ "`tail -1 $infil | cut -c1-3`" != "END" ]
    then
        echo "END" >> join.temp
    fi
    number=`expr $number + 1`
done

echo "Using a awk script to adjust the result"

awk '
BEGIN {
    ModelNumber = 1
    NewModel    = "yes"
}

# first ATOM card signals start of model
/^ATOM/ {
    if ( NewModel == "yes" ) {
	printf( "MODEL     %4i\n", ModelNumber )
	NewModel = "no"
    }
}

/^CONECT/ { next }

/^MASTER/ { next }

# END card signals end of model
/^END/ {
    ModelNumber++
    NewModel = "yes"
    print "ENDMDL"
    next
}

# print everything else, except things BEFORE start of 2nd, 3rd... model
ModelNumber == 1 || ( ModelNumber > 1 && NewModel == "no" ) { print $0 }

END { print "END" }

' join.temp > $outfil

/bin/rm join.temp