mysql-q.sh

#! /usr/bin/bash
db_location='/home/common/babel'
export db_location

array_opt=( Pstv Ngtv abonds atoms bonds cansmi cansmiNS dbonds formula HBA1
HBA2 HBD InChI InChIKey logP MP MR MW nF sbonds tbonds TPSA heavya)

help_txt="To search the databases you need:

1. Specify the database(s) by using the --db $(echo -e "\e[4mnameofdb\e[0m") arguement, one or multiple times

2. Optionally use filters with --max-$(echo -e "\e[4mSUFFIX\e[0m") or --min-$(echo -e "\e[4mSUFFIX\e[0m"). Available suffixes:
$(echo ${array_opt[*]} | fold -s -w 80  | sed -e "s|^|\t- |g")

When run without enough valid vina options, you will only receive the results of your query.
Otherwise the script will automatically run the resulting ligands to your specified receptor.

Vina Options:
  --zinc-mode
  --vina-threads
  --vina-log
  --vina-cfg
  --vina-rcp
  --vina-rlt
"

mysql_q() {
echo Searching $I 1>&2
if [ ! "$I" = 'Zinc' ] && [ ! "$I" = 'Ambinter' ]
  then mysql --login-path=local -N -e "use BABEL" -e "
    SELECT IF(Zinc_ext.ID IS NULL,Frog.ID,Zinc_ext.ID)
    FROM ${I}
    LEFT JOIN Zinc_ext ON ${I}.ID = Zinc_ext.EXT_ID
    LEFT JOIN Frog ON ${I}.ID = Frog.EXT_ID
    $(cat -)
  ;
  "
  else mysql --login-path=local -N -e "use BABEL" -e "
    SELECT ID
    FROM ${I}
    $(cat -)
    ;"
fi
}


query_writer() {
line_start=WHERE
for i in ${array_opt[*]}
  do
  max_i=max_$i
  min_i=min_$i
  if [ "${!max_i}" ]
    then if [ "${!min_i}" ]
      then echo $line_start $I.\`$i\` BETWEEN ${!min_i} AND ${!max_i}
      else echo $line_start $I.\`$i\` \<\= ${!max_i}
      fi
      line_start=AND
    elif [ "${!min_i}" ]
      then echo $line_start $I.\`$i\` \>\= ${!min_i}
      line_start=AND
    fi
done
echo $line_start $I.\`Halo\` $halo
}

vina_fun() {
mkdir "$1"
cd "$1"
obabel -ipdbqt "$db_location/pdbqt/$1.pdbqt" -opdbqt -O $1\_out.pdbqt -m &> /dev/null
for i in $(find -name \*pdbqt | sed 's/\.pdbqt//g' )
  do $vina --cpu 4 --config $vina_cfg --ligand "$i.pdbqt" $vina_rcp --out "$i_out.pdbqt" &> /dev/null
  rm "$i.pdbqt"
done
}

score() {
mv "$*" $(sed '2q;d' "$*" | cut -d '-' -f 2 | cut -d ' ' -f1)_$*
}

vina_wrapper() {
export vina_cfg vina_log vina_rcp out_dir vina
export -f vina_fun

(
cd $out_dir
echo Starting Docking:
parallel --eta --progress -j $((threads/4)) --joblog ../vina.job vina_fun {}
)

export -f score
(
cd $out_dir || exit 5
echo Renaming results per score:
find . -type f -printf "%f\n" |
parallel --progress -j $threads score {/}
echo Tarring $results best results.
find . -type f -printf "%f\n" | sort -h |
tail -n $results | tar zcfv ../$vina\-result_$(date +'%s').tar.gz \
--files-from -
)
echo Deleting temporary files
#rm -rf $out_dir #results
echo Results are in vina-result_$(date +'%s').tar.gz
}

results=1000

if [ -z "$*" ] 2> /dev/null
  then echo --help for help
  exit 2
fi

creategetargs() {
echo 'function getargs() {'
  echo '  while true
    do case $1 in'
  for i in $*
    do for I in min max
      do echo -e '      '--$I-$i'  \t'\) $I\_$i=\$2 ';' shift 2 ';;'
    done
  done
  echo '      --help            ) echo "$help_txt" ; exit 2 ;;
      --db              ) DB+=($2) ; shift 2 ;;
      --zinc-mode       ) zinc_mode=1 ; shift 1 ;;
      --vina-threads    ) threads=$2 ; export threads ; shift 2 ;;
      --vina-cfg        ) vina_cfg=$2 ; shift 2 ;;
      --vina-rcp        ) vina_rcp="--receptor $2" ; shift 2 ;;
      --vina-rlt        ) results="$2" ; shift 2 ;;
      '\'\''                ) break ;;
      *                 ) echo error, what is: $1 ; exit 1 ;;
    esac
  done'
echo '}'
}



eval "$(creategetargs ${array_opt[*]})"
getargs $*

db_loop() {

for I in ${DB[*]}
  do halo='= 0'
  query_writer | tee mysql | mysql_q
done > query

for I in ${DB[*]}
  do halo='> 0'
  query_writer | tee hmysql | mysql_q
done > haloquery
}

if [ "$vina_cfg" ]
then findoutput="$(find query -maxdepth 1 2> /dev/null)"
  if [ "$findoutput" ]
    then read -p "$(echo $findoutput) found, do you want to use it?" -n 1 -r
      if [[ $REPLY =~ ^[Nn]$ ]]
        then echo 'Searching - this could take a lot of time (see mysql threads)'
        db_loop
      fi
  else
    echo 'Searching - this could take a lot of time (see mysql threads)'
    db_loop
  fi
    echo
    if [ -e ./query ]
    then
      out_dir=$(mktemp -d -p .)

      vina='vina'
      cat query | vina_wrapper
      vina='vinaSH'
      cat haloquery | vina_wrapper

    fi
else
  echo 'Searching - this could take a lot of time (see mysql threads)'
  db_loop
  read -p "Do you want the resulting pdbqts?" -n 1 -r
  echo
  if [[ $REPLY =~ ^[Yy]$ ]]
  then
    out_dir=$(mktemp -d -p .)
    (
      cd $out_dir || exit 5
      cat ../query | xargs -I{} cp $db_location/pdbqt/{}.pdbqt .
      tar zcfv ../queryresults_$(date +'%s').tar.gz .
    )
    rm -rf $out_dir
  fi
fi