76 lines
3.9 KiB
Bash
Executable File
76 lines
3.9 KiB
Bash
Executable File
#!/bin/bash -e
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# Copied from colabfold.mmseqs.com
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MMSEQS="$1"
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QUERY="$2"
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DBBASE="$3"
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BASE="$4"
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DB1="$5"
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DB2="$6"
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DB3="$7"
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USE_ENV="${8:-1}"
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USE_TEMPLATES="${9:-0}"
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FILTER="${10:-1}"
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INDEX=${11:-1}
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DB_LOAD_MODE="${12:-2}"
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EXPAND_EVAL=inf
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ALIGN_EVAL=10
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DIFF=3000
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QSC=-20.0
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MAX_ACCEPT=1000000
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if [ "${FILTER}" = "1" ]; then
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# 0.1 was not used in benchmarks due to POSIX shell bug in line above
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# EXPAND_EVAL=0.1
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ALIGN_EVAL=10
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QSC=0.8
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MAX_ACCEPT=100000
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fi
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if [ "${INDEX}" = "1" ]; then
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SEQ=".idx"
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ALN=".idx"
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IDX=".idx"
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else
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SEQ="_seq"
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ALN="_aln"
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IDX=""
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export MMSEQS_IGNORE_INDEX=1
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fi
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export MMSEQS_CALL_DEPTH=1
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SEARCH_PARAM="--num-iterations 3 --db-load-mode ${DB_LOAD_MODE} -a -s 8 -e 0.1 --max-seqs 10000"
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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"
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EXPAND_PARAM="--expansion-mode 0 -e ${EXPAND_EVAL} --expand-filter-clusters ${FILTER} --max-seq-id 0.95"
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mkdir -p "${BASE}"
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"${MMSEQS}" createdb "${QUERY}" "${BASE}/qdb"
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"${MMSEQS}" search "${BASE}/qdb" "${DBBASE}/${DB1}" "${BASE}/res" "${BASE}/tmp" $SEARCH_PARAM
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"${MMSEQS}" expandaln "${BASE}/qdb" "${DBBASE}/${DB1}${SEQ}" "${BASE}/res" "${DBBASE}/${DB1}${ALN}" "${BASE}/res_exp" --db-load-mode ${DB_LOAD_MODE} ${EXPAND_PARAM}
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"${MMSEQS}" mvdb "${BASE}/tmp/latest/profile_1" "${BASE}/prof_res"
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"${MMSEQS}" lndb "${BASE}/qdb_h" "${BASE}/prof_res_h"
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"${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 ${MAX_ACCEPT} --alt-ali 10 -a
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"${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 $QSC --diff 0 --max-seq-id 1.0 --filter-min-enable 100
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"${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} ${FILTER_PARAM}
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"${MMSEQS}" rmdb "${BASE}/res_exp_realign"
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"${MMSEQS}" rmdb "${BASE}/res_exp"
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"${MMSEQS}" rmdb "${BASE}/res"
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"${MMSEQS}" rmdb "${BASE}/res_exp_realign_filter"
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if [ "${USE_TEMPLATES}" = "1" ]; then
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"${MMSEQS}" search "${BASE}/prof_res" "${DBBASE}/${DB2}" "${BASE}/res_pdb" "${BASE}/tmp" --db-load-mode ${DB_LOAD_MODE} -s 7.5 -a -e 0.1
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"${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 ${DB_LOAD_MODE}
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"${MMSEQS}" rmdb "${BASE}/res_pdb"
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fi
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if [ "${USE_ENV}" = "1" ]; then
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"${MMSEQS}" search "${BASE}/prof_res" "${DBBASE}/${DB3}" "${BASE}/res_env" "${BASE}/tmp" $SEARCH_PARAM
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"${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 ${DB_LOAD_MODE}
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"${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 ${MAX_ACCEPT} --alt-ali 10 -a
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"${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 $QSC --diff 0 --max-seq-id 1.0 --filter-min-enable 100
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"${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} ${FILTER_PARAM}
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"${MMSEQS}" rmdb "${BASE}/res_env_exp_realign_filter"
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"${MMSEQS}" rmdb "${BASE}/res_env_exp_realign"
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"${MMSEQS}" rmdb "${BASE}/res_env_exp"
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"${MMSEQS}" rmdb "${BASE}/res_env"
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fi
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"${MMSEQS}" rmdb "${BASE}/qdb"
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"${MMSEQS}" rmdb "${BASE}/qdb_h"
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"${MMSEQS}" rmdb "${BASE}/res"
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rm -f -- "${BASE}/prof_res"*
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rm -rf -- "${BASE}/tmp"
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