scripts/colabfold_search.sh

#!/bin/bash -e
# Copied from colabfold.mmseqs.com

MMSEQS="$1"
QUERY="$2"
DBBASE="$3"
BASE="$4"
DB1="$5"
DB2="$6"
DB3="$7"
USE_ENV="${8:-1}"
USE_TEMPLATES="${9:-0}"
FILTER="${10:-1}"
INDEX=${11:-1}
DB_LOAD_MODE="${12:-2}"
EXPAND_EVAL=inf
ALIGN_EVAL=10
DIFF=3000
QSC=-20.0
MAX_ACCEPT=1000000
if [ "${FILTER}" = "1" ]; then
# 0.1 was not used in benchmarks due to POSIX shell bug in line above
#  EXPAND_EVAL=0.1
  ALIGN_EVAL=10
  QSC=0.8
  MAX_ACCEPT=100000
fi
if [ "${INDEX}" = "1" ]; then
  SEQ=".idx"
  ALN=".idx"
  IDX=".idx"
else
  SEQ="_seq"
  ALN="_aln"
  IDX=""
  export MMSEQS_IGNORE_INDEX=1
fi
export MMSEQS_CALL_DEPTH=1
SEARCH_PARAM="--num-iterations 3 --db-load-mode ${DB_LOAD_MODE} -a -s 8 -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}/${DB1}${SEQ}" "${BASE}/res" "${DBBASE}/${DB1}${ALN}" "${BASE}/res_exp" --db-load-mode ${DB_LOAD_MODE} ${EXPAND_PARAM}
"${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}/${DB1}${SEQ}" "${BASE}/res_exp" "${BASE}/res_exp_realign" --db-load-mode ${DB_LOAD_MODE} -e ${ALIGN_EVAL} --max-accept ${MAX_ACCEPT} --alt-ali 10 -a
"${MMSEQS}" filterresult "${BASE}/qdb" "${DBBASE}/${DB1}${SEQ}" "${BASE}/res_exp_realign" "${BASE}/res_exp_realign_filter" --db-load-mode ${DB_LOAD_MODE} --qid 0 --qsc $QSC --diff 0 --max-seq-id 1.0 --filter-min-enable 100
"${MMSEQS}" result2msa "${BASE}/qdb" "${DBBASE}/${DB1}${SEQ}" "${BASE}/res_exp_realign_filter" "${BASE}/uniref.a3m" --msa-format-mode 6 --db-load-mode ${DB_LOAD_MODE} ${FILTER_PARAM}
"${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 ${DB_LOAD_MODE} -s 7.5 -a -e 0.1
  "${MMSEQS}" convertalis "${BASE}/prof_res" "${DBBASE}/${DB2}${IDX}" "${BASE}/res_pdb" "${BASE}/${DB2}.m8" --format-output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,cigar --db-load-mode ${DB_LOAD_MODE}
  "${MMSEQS}" rmdb "${BASE}/res_pdb"
fi
if [ "${USE_ENV}" = "1" ]; then
  "${MMSEQS}" search "${BASE}/prof_res" "${DBBASE}/${DB3}" "${BASE}/res_env" "${BASE}/tmp" $SEARCH_PARAM
  "${MMSEQS}" expandaln "${BASE}/prof_res" "${DBBASE}/${DB3}${SEQ}" "${BASE}/res_env" "${DBBASE}/${DB3}${ALN}" "${BASE}/res_env_exp" -e ${EXPAND_EVAL} --expansion-mode 0 --db-load-mode ${DB_LOAD_MODE}
  "${MMSEQS}" align "${BASE}/tmp/latest/profile_1" "${DBBASE}/${DB3}${SEQ}" "${BASE}/res_env_exp" "${BASE}/res_env_exp_realign" --db-load-mode ${DB_LOAD_MODE} -e ${ALIGN_EVAL} --max-accept ${MAX_ACCEPT} --alt-ali 10 -a
  "${MMSEQS}" filterresult "${BASE}/qdb" "${DBBASE}/${DB3}${SEQ}" "${BASE}/res_env_exp_realign" "${BASE}/res_env_exp_realign_filter" --db-load-mode ${DB_LOAD_MODE} --qid 0 --qsc $QSC --diff 0 --max-seq-id 1.0 --filter-min-enable 100
  "${MMSEQS}" result2msa "${BASE}/qdb" "${DBBASE}/${DB3}${SEQ}" "${BASE}/res_env_exp_realign_filter" "${BASE}/bfd.mgnify30.metaeuk30.smag30.a3m" --msa-format-mode 6 --db-load-mode ${DB_LOAD_MODE} ${FILTER_PARAM}
  "${MMSEQS}" rmdb "${BASE}/res_env_exp_realign_filter"
  "${MMSEQS}" rmdb "${BASE}/res_env_exp_realign"
  "${MMSEQS}" rmdb "${BASE}/res_env_exp"
  "${MMSEQS}" rmdb "${BASE}/res_env"
fi
"${MMSEQS}" rmdb "${BASE}/qdb"
"${MMSEQS}" rmdb "${BASE}/qdb_h"
"${MMSEQS}" rmdb "${BASE}/res"
rm -f -- "${BASE}/prof_res"*
rm -rf -- "${BASE}/tmp"