chore: update from obsidian

Author: Spelkington

content/private

@@ -0,0 +1,132 @@
+#!/bin/bash -e
+MMSEQS="$1"
+QUERY="$2"
+BASE="$4"
+DB1="$5"
+DB2="$6"
+DB3="$7"
+USE_ENV="$8"
+USE_TEMPLATES="$9"
+FILTER="${10}"
+TAXONOMY="${11}"
+TAXONOMYREPORT="${12}"
+M8OUT="${13}"
+GPU="${14}"
+GPUSERVER="${15}"
+EXPAND_EVAL=inf
+ALIGN_EVAL=10
+DIFF=3000
+QSC=-20.0
+MAX_ACCEPT=1000000
+if [ "${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
+export MMSEQS_CALL_DEPTH=1
+SEARCH_PARAM="--num-iterations 3 --db-load-mode 2 -a --k-score 'seq:96,prof:80' -e 0.1 --max-seqs 10000"
+if [ "${GPU}" = "1" ]; then
+  GPU_PARAM="--gpu 1 --prefilter-mode 1"
+fi
+if [ "${GPUSERVER}" = "1" ]; then
+  GPU_PARAM="${GPU_PARAM} --gpu-server 1"
+fi
+if [ "${GPU_PARAM}" != "" ]; then
+	SEARCH_PARAM="${SEARCH_PARAM} ${GPU_PARAM}"
+fi
+FILTER_PARAM="--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}" "${BASE}/qdb" --dbtype 1
+if [ -n "${ORIG_CUDA_VISIBLE_DEVICES}" ]; then
+	export CUDA_VISIBLE_DEVICES="${ORIG_CUDA_VISIBLE_DEVICES}"
+fi
+if [ -n "$UNIREF_CUDA_VISIBLE_DEVICES" ]; then
+  export CUDA_VISIBLE_DEVICES="${UNIREF_CUDA_VISIBLE_DEVICES}"
+fi
+"${MMSEQS}" search "${BASE}/qdb" "${DB1}" "${BASE}/res" "${BASE}/tmp1" $SEARCH_PARAM
+"${MMSEQS}" mvdb "${BASE}/tmp1/latest/profile_1" "${BASE}/prof_res"
+"${MMSEQS}" lndb "${BASE}/qdb_h" "${BASE}/prof_res_h"
+
+(
+
+"${MMSEQS}" expandaln "${BASE}/qdb" "${DB1}.idx" "${BASE}/res" "${DB1}.idx" "${BASE}/res_exp" --db-load-mode 2 ${EXPAND_PARAM}
+"${MMSEQS}" align "${BASE}/prof_res" "${DB1}.idx" "${BASE}/res_exp" "${BASE}/res_exp_realign" --db-load-mode 2 -e ${ALIGN_EVAL} --max-accept ${MAX_ACCEPT} --alt-ali 10 -a
+"${MMSEQS}" filterresult "${BASE}/qdb" "${DB1}.idx" "${BASE}/res_exp_realign" "${BASE}/res_exp_realign_filter" --db-load-mode 2 --qid 0 --qsc $QSC --diff 0 --max-seq-id 1.0 --filter-min-enable 100
+if [ "${M8OUT}" = "1" ]; then
+  "${MMSEQS}" filterresult "${BASE}/qdb" "${DB1}.idx" "${BASE}/res_exp_realign_filter" "${BASE}/res_exp_realign_filter_filter" --db-load-mode 2 ${FILTER_PARAM}
+  "${MMSEQS}" convertalis "${BASE}/qdb" "${DB1}.idx" "${BASE}/res_exp_realign_filter_filter" "${BASE}/uniref.m8" --db-load-mode 2 --format-output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,tseq
+  "${MMSEQS}" rmdb "${BASE}/res_exp_realign_filter_filter"
+else
+  "${MMSEQS}" result2msa "${BASE}/qdb" "${DB1}.idx" "${BASE}/res_exp_realign_filter" "${BASE}/uniref.a3m" --msa-format-mode 6 --db-load-mode 2 --filter-msa ${FILTER} ${FILTER_PARAM}
+fi
+"${MMSEQS}" rmdb "${BASE}/res_exp_realign"
+"${MMSEQS}" rmdb "${BASE}/res_exp"
+"${MMSEQS}" rmdb "${BASE}/res"
+if [ "${TAXONOMY}" = "1" ] && [ -e "${DB1}_taxonomy" ]; then
+  "${MMSEQS}" convertalis "${BASE}/qdb" "${DB1}.idx" "${BASE}/res_exp_realign_filter" "${BASE}/res_exp_realign_tax" --db-output 1 --format-output "taxid,target,taxlineage" --db-load-mode 2
+  awk 'BEGIN { printf("%c%c%c%c",8,0,0,0); exit; }' > "${BASE}/res_exp_realign_tax.dbtype"
+  MMSEQS_FORCE_MERGE=1 "${MMSEQS}" filtertaxdb "${DB1}" "${BASE}/res_exp_realign_tax" "${BASE}/res_exp_realign_tax_filt" --taxon-list '!12908&&!28384'
+  tr -d '\000' < "${BASE}/res_exp_realign_tax_filt" | sort -u > "${BASE}/uniref_tax.tsv"
+  "${MMSEQS}" rmdb "${BASE}/res_exp_realign_tax_filt"
+  "${MMSEQS}" rmdb "${BASE}/res_exp_realign_tax"
+fi
+if [ "${TAXONOMYREPORT}" = "1" ] && [ -e "${DB1}_taxonomy" ]; then
+  "${MMSEQS}" taxonomyreport "${DB1}.idx" "${BASE}/res_exp_realign_filter" "${BASE}/res_exp_realign_taxreport" --report-mode 3
+  "${MMSEQS}" createtsv "${BASE}/qdb" "${BASE}/res_exp_realign_taxreport" "${BASE}/uniref_taxreport.tsv"
+  "${MMSEQS}" rmdb "${BASE}/res_exp_realign_taxreport"
+fi
+"${MMSEQS}" rmdb "${BASE}/res_exp_realign_filter"
+
+)&
+(
+
+if [ "${USE_TEMPLATES}" = "1" ]; then
+  if [ -n "${ORIG_CUDA_VISIBLE_DEVICES}" ]; then
+    export CUDA_VISIBLE_DEVICES="${ORIG_CUDA_VISIBLE_DEVICES}"
+  fi
+  if [ -n "${PDB_CUDA_VISIBLE_DEVICES}" ]; then
+    export CUDA_VISIBLE_DEVICES="${PDB_CUDA_VISIBLE_DEVICES}"
+  fi
+  "${MMSEQS}" search "${BASE}/prof_res" "${DB2}" "${BASE}/res_pdb" "${BASE}/tmp2" --db-load-mode 2 -s 7.5 -a -e 0.1 ${GPU_PARAM}
+  "${MMSEQS}" convertalis "${BASE}/prof_res" "${DB2}.idx" "${BASE}/res_pdb" "${BASE}/pdb70.m8" --format-output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,cigar --db-load-mode 2
+  "${MMSEQS}" rmdb "${BASE}/res_pdb"
+fi
+
+)&
+(
+
+if [ "${USE_ENV}" = "1" ]; then
+  if [ -n "${ORIG_CUDA_VISIBLE_DEVICES}" ]; then
+    export CUDA_VISIBLE_DEVICES="${ORIG_CUDA_VISIBLE_DEVICES}"
+  fi
+  if [ -n "${ENV_CUDA_VISIBLE_DEVICES}" ]; then
+    export CUDA_VISIBLE_DEVICES="${ENV_CUDA_VISIBLE_DEVICES}"
+  fi
+  "${MMSEQS}" search "${BASE}/prof_res" "${DB3}" "${BASE}/res_env" "${BASE}/tmp3" $SEARCH_PARAM
+  "${MMSEQS}" expandaln "${BASE}/prof_res" "${DB3}.idx" "${BASE}/res_env" "${DB3}.idx" "${BASE}/res_env_exp" -e ${EXPAND_EVAL} --expansion-mode 0 --db-load-mode 2
+  "${MMSEQS}" align "${BASE}/tmp3/latest/profile_1" "${DB3}.idx" "${BASE}/res_env_exp" "${BASE}/res_env_exp_realign" --db-load-mode 2 -e ${ALIGN_EVAL} --max-accept ${MAX_ACCEPT} --alt-ali 10 -a
+  "${MMSEQS}" filterresult "${BASE}/qdb" "${DB3}.idx" "${BASE}/res_env_exp_realign" "${BASE}/res_env_exp_realign_filter" --db-load-mode 2 --qid 0 --qsc $QSC --diff 0 --max-seq-id 1.0 --filter-min-enable 100
+  if [ "${M8OUT}" = "1" ]; then
+    "${MMSEQS}" filterresult "${BASE}/qdb" "${DB3}.idx" "${BASE}/res_env_exp_realign_filter" "${BASE}/res_env_exp_realign_filter_filter" --db-load-mode 2 ${FILTER_PARAM}
+    "${MMSEQS}" convertalis "${BASE}/qdb" "${DB3}.idx" "${BASE}/res_env_exp_realign_filter_filter" "${BASE}/bfd.mgnify30.metaeuk30.smag30.m8" --db-load-mode 2 --format-output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,tseq
+    "${MMSEQS}" rmdb "${BASE}/res_env_exp_realign_filter_filter"
+  else
+	"${MMSEQS}" result2msa "${BASE}/qdb" "${DB3}.idx" "${BASE}/res_env_exp_realign_filter" "${BASE}/bfd.mgnify30.metaeuk30.smag30.a3m" --msa-format-mode 6 --db-load-mode 2 --filter-msa ${FILTER} ${FILTER_PARAM}
+  fi
+  "${MMSEQS}" rmdb "${BASE}/res_env_exp_realign_filter"
+  "${MMSEQS}" rmdb "${BASE}/res_env_exp_realign"
+  "${MMSEQS}" rmdb "${BASE}/res_env_exp"
+  "${MMSEQS}" rmdb "${BASE}/res_env"
+fi
+
+)&
+wait
+
+"${MMSEQS}" rmdb "${BASE}/qdb"
+"${MMSEQS}" rmdb "${BASE}/qdb_h"
+"${MMSEQS}" rmdb "${BASE}/res"
+rm -f -- "${BASE}/prof_res"*
+rm -rf -- "${BASE}/tmp1" "${BASE}/tmp2" "${BASE}/tmp3"

content/public/assets/3UJZ/3UJZ_1_Chain_A_Metalloprotease_stcE_Escherichia_coli__83334_.a3m

@@ -0,0 +1,5 @@
+101	3ujz_A	0.701	860	1	4	10	869	1	604	1.983E-246	781	99M110I329M100I41M35I15M11I120M
+101	4dny_A	1.000	109	0	0	111	219	1	109	2.157E-35	149	109M
+101	6o38_C	0.205	68	46	4	577	638	153	218	2.498E-02	41	15M2I21M3D5M1D8M2D11M
+101	6o38_F	0.205	68	46	4	577	638	200	265	2.498E-02	41	15M2I21M3D5M1D8M2D11M
+101	6o38_B	0.205	68	46	4	577	638	212	277	2.498E-02	41	15M2I21M3D5M1D8M2D11M