echo "Do not use this script. Use the python colabfold_search instead"

exit 0

set -x

export OMP_NUM_THREADS=100

MMSEQS="$1"

QUERY="$2"

DBBASE="$3"

BASE="$4"

DB1="$5"

DB2="$6"

DB3="$7"

USE_ENV="$8"

USE_TEMPLATES="$9"

FILTER="${10}"

THREADS="${11}"

SENSITIVITY=8

EXPAND_EVAL=inf

ALIGN_EVAL=10

DIFF=3000

QSC=-20.0

MAX_ACCEPT=1000000

if [ "${FILTER}" = "1" ]; then

ALIGN_EVAL=10

QSC=0.8

MAX_ACCEPT=100000

export MMSEQS_CALL_DEPTH=1

SEARCH_PARAM="--num-iterations 3 --db-load-mode 2 -a -s ${SENSITIVITY} -e 0.1 --max-seqs 10000"

FILTER_PARAM="--filter-msa ${FILTER} --filter-min-enable 1000 --diff ${DIFF} --qid 0.0,0.2,0.4,0.6,0.8,1.0 --qsc 0 --max-seq-id 0.95"

EXPAND_PARAM="--expansion-mode 0 -e ${EXPAND_EVAL} --expand-filter-clusters ${FILTER} --max-seq-id 0.95"

mkdir -p "${BASE}"

"${MMSEQS}" createdb "${QUERY}" "${BASE}/qdb"

"${MMSEQS}" search "${BASE}/qdb" "${DBBASE}/${DB1}" "${BASE}/res" "${BASE}/tmp" $SEARCH_PARAM

"${MMSEQS}" expandaln "${BASE}/qdb" "${DBBASE}/${DB1}.idx" "${BASE}/res" "${DBBASE}/${DB1}.idx" "${BASE}/res_exp" --db-load-mode 2 --threads ${THREADS} ${EXPAND_PARAM}

"${MMSEQS}" mvdb "${BASE}/tmp/latest/profile_1" "${BASE}/prof_res"

"${MMSEQS}" lndb "${BASE}/qdb_h" "${BASE}/prof_res_h"

"${MMSEQS}" align "${BASE}/prof_res" "${DBBASE}/${DB1}.idx" "${BASE}/res_exp" "${BASE}/res_exp_realign" --db-load-mode 2 --threads ${THREADS} -e ${ALIGN_EVAL} --max-accept ${MAX_ACCEPT} --alt-ali 10 -a

"${MMSEQS}" filterresult "${BASE}/qdb" "${DBBASE}/${DB1}.idx" "${BASE}/res_exp_realign" "${BASE}/res_exp_realign_filter" --db-load-mode 2 --threads ${THREADS} --qid 0 --qsc $QSC --diff 0 --max-seq-id 1.0 --filter-min-enable 100

"${MMSEQS}" result2msa "${BASE}/qdb" "${DBBASE}/${DB1}.idx" "${BASE}/res_exp_realign_filter" "${BASE}/uniref.a3m" --msa-format-mode 6 --db-load-mode 2 --threads ${THREADS} ${FILTER_PARAM}

"${MMSEQS}" rmdb "${BASE}/res_exp_realign"

"${MMSEQS}" rmdb "${BASE}/res_exp"

"${MMSEQS}" rmdb "${BASE}/res"

"${MMSEQS}" rmdb "${BASE}/res_exp_realign_filter"

if [ "${USE_TEMPLATES}" = "1" ]; then

"${MMSEQS}" search "${BASE}/prof_res" "${DBBASE}/${DB2}" "${BASE}/res_pdb" "${BASE}/tmp" --db-load-mode 2 --threads ${THREADS} -s 7.5 -a -e 0.1

"${MMSEQS}" convertalis "${BASE}/prof_res" "${DBBASE}/${DB2}.idx" "${BASE}/res_pdb" "${BASE}/${DB2}.m8" --threads ${THREADS} --format-output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,cigar --db-load-mode 2

"${MMSEQS}" rmdb "${BASE}/res_pdb"

if [ "${USE_ENV}" = "1" ]; then

"${MMSEQS}" search "${BASE}/prof_res" "${DBBASE}/${DB3}" "${BASE}/res_env" "${BASE}/tmp" --threads ${THREADS} $SEARCH_PARAM

"${MMSEQS}" expandaln "${BASE}/prof_res" "${DBBASE}/${DB3}.idx" "${BASE}/res_env" "${DBBASE}/${DB3}.idx" "${BASE}/res_env_exp" -e ${EXPAND_EVAL} --threads ${THREADS} --expansion-mode 0 --db-load-mode 2

"${MMSEQS}" align "${BASE}/tmp/latest/profile_1" "${DBBASE}/${DB3}.idx" "${BASE}/res_env_exp" "${BASE}/res_env_exp_realign" --db-load-mode 2 --threads ${THREADS} -e ${ALIGN_EVAL} --max-accept ${MAX_ACCEPT} --alt-ali 10 -a

"${MMSEQS}" filterresult "${BASE}/qdb" "${DBBASE}/${DB3}.idx" "${BASE}/res_env_exp_realign" "${BASE}/res_env_exp_realign_filter" --db-load-mode 2 --threads ${THREADS} --qid 0 --qsc $QSC --diff 0 --max-seq-id 1.0 --filter-min-enable 100

"${MMSEQS}" result2msa "${BASE}/qdb" "${DBBASE}/${DB3}.idx" "${BASE}/res_env_exp_realign_filter" "${BASE}/bfd.mgnify30.metaeuk30.smag30.a3m" --msa-format-mode 6 --db-load-mode 2 --threads ${THREADS} ${FILTER_PARAM}

"${MMSEQS}" rmdb "${BASE}/res_env_exp_realign_filter"

"${MMSEQS}" rmdb "${BASE}/res_env_exp_realign"

"${MMSEQS}" rmdb "${BASE}/res_env_exp"

"${MMSEQS}" rmdb "${BASE}/res_env"

"${MMSEQS}" rmdb "${BASE}/qdb"

"${MMSEQS}" rmdb "${BASE}/qdb_h"

"${MMSEQS}" rmdb "${BASE}/res"

rm -f -- "${BASE}/prof_res"*

rm -rf -- "${BASE}/tmp"