silentfrompdbs

#!/bin/bash


tags=""

tmp_list=$(head /dev/urandom | tr -dc A-Za-z0-9 | head -c 13)
tmp_list="tmp_${tmp_list}.list"
rm $tmp_list > /dev/null 2>&1

#https://stackoverflow.com/questions/19408649/pipe-input-into-a-script
if [ -p /dev/stdin ]; then
    while read tag; do
        echo $tag
        # tags+="$tag\n"
        # tags+="$tag\n"
    done > $tmp_list

fi

silent_dir="$(dirname $(type -p "$0"))"
source "$silent_dir"/_extract_flags.sh


for tag in "$@"; do
    echo $tag
done >> $tmp_list


if [ ! -f $tmp_list ]; then
    echo >&2 ""
    echo >&2 "silentfrompdbs by bcov - a tool to make a silent file from pdbs"
    echo >&2 "Usage:"
    echo >&2 "        cat list_of_tags.list | silentfrompdbs > silent.silent"
    echo >&2 "                             or"
    echo >&2 "        silentfrompdbs tag1 tag2 tag3 > silent.silent"
    echo >&2 "Flags:"
    echo >&2 "        -j cpus"
    echo >&2 "        -p param_file"
    echo >&2 "        @flags_file"
    exit 1
fi

# bakerlab stuff. Appologies to others but this fixes so many problems for us
PATH="$PATH:/software/rosetta/latest/bin"

jd2_program=score_jd2

#https://stackoverflow.com/questions/592620/how-to-check-if-a-program-exists-from-a-bash-script/677212#677212
command -v score_jd2 >/dev/null 2>&1 || { 
    #echo >&2 "You must have extract_pdbs on your path!"; 
    #echo >&2 "Try doing cd silent_tools; ln -s /software/rosetta/latest/bin/extract_pdbs ."
    #exit 1; 
    jd2_program="$silent_dir"/pyjd2
}


if [ -z "${SILENT_J}" ]; then
# Do single-thread generation

    tmp_file=$(head /dev/urandom | tr -dc A-Za-z0-9 | head -c 13)
    tmp_file="tmp_${tmp_file}.silent"

    $jd2_program -l $tmp_list -out:file:silent $tmp_file -out:file:silent_struct_type binary $SILENT_PARAMS $SILENT_AT 1>&2

    "$silent_dir"/silentls $tmp_file | sed 's/_0001$//g' | "$silent_dir"/silentrename $tmp_file

    rm $tmp_list
    rm $tmp_file
    rm $tmp_file.idx

else
# Do multi-thread extraction
    tmp_fol=$(head /dev/urandom | tr -dc A-Za-z0-9 | head -c 13)
    tmp_fol="tmp_${tmp_fol}"

    cpus=${SILENT_J} #$(parallel --number-of-cores)

    splitno=$((( $(wc -l $tmp_list | awk '{print $1}') / $cpus + 1)))

    mkdir $tmp_fol

    split -l $splitno $tmp_list $tmp_fol/x

    ls $tmp_fol/x* | parallel -j$cpus "cat {} | $silent_dir/silentfrompdbs $SILENT_FLAGS_NO_J"

    rm $tmp_list
    rm -r $tmp_fol
fi