Add backend for environmental pairing

soedinglab · May 2, 2024 · b76b605 · b76b605
1 parent 00f89de
commit b76b605
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Showing 2 changed files with 40 additions and 11 deletions.
diff --git a/backend/config.go b/backend/config.go
@@ -67,6 +67,7 @@ var defaultFileContent = []byte(`{
  "uniref" : "~databases/uniref30_2103",
  "pdb" : "~databases/pdb70",
  "environmental" : "~databases/colabfold_envdb_202108",
+ "environmentalpair" : "~databases/spire_ctg10_2401_db",
  // paths for templates
  "pdb70" : "~databases/pdb70",
  "pdbdivided" : "~databases/pdbdivided",
@@ -151,13 +152,14 @@ var defaultFileContent = []byte(`{
 `)
 
 type ConfigColabFoldPaths struct {
- ParallelStages bool `json:"parallelstages"`
- Uniref string `json:"uniref"`
- Pdb string `json:"pdb"`
- Environmental string `json:"environmental"`
- Pdb70 string `json:"pdb70"`
- PdbDivided string `json:"pdbdivided"`
- PdbObsolete string `json:"pdbobsolete"`
+ ParallelStages bool `json:"parallelstages"`
+ Uniref string `json:"uniref"`
+ Pdb string `json:"pdb"`
+ Environmental string `json:"environmental"`
+ EnvironmentalPair string `json:"environmentalpair"`
+ Pdb70 string `json:"pdb70"`
+ PdbDivided string `json:"pdbdivided"`
+ PdbObsolete string `json:"pdbobsolete"`
 }
 
 type ConfigPaths struct {

diff --git a/backend/worker.go b/backend/worker.go
@@ -900,8 +900,10 @@ MMSEQS="$1"
 QUERY="$2"
 BASE="$4"
 DB1="$5"
-USE_PAIRWISE="$6"
-PAIRING_STRATEGY="$7"
+DB2="$6"
+USE_ENV="$7"
+USE_PAIRWISE="$8"
+PAIRING_STRATEGY="$9"
 SEARCH_PARAM="--num-iterations 3 --db-load-mode 2 -a --k-score 'seq:96,prof:80' -e 0.1 --max-seqs 10000"
 EXPAND_PARAM="--expansion-mode 0 -e inf --expand-filter-clusters 0 --max-seq-id 0.95"
 export MMSEQS_CALL_DEPTH=1
@@ -922,21 +924,44 @@ fi
 "${MMSEQS}" align "${BASE}/qdb" "${DB1}.idx" "${BASE}/res_exp_realign_pair" "${BASE}/res_exp_realign_pair_bt" --db-load-mode 2 -e inf -a
 "${MMSEQS}" pairaln "${BASE}/qdb" "${DB1}.idx" "${BASE}/res_exp_realign_pair_bt" "${BASE}/res_final" --db-load-mode 2 --pairing-mode "${PAIRING_STRATEGY}" --pairing-dummy-mode 1
 "${MMSEQS}" result2msa "${BASE}/qdb" "${DB1}.idx" "${BASE}/res_final" "${BASE}/pair.a3m" --db-load-mode 2 --msa-format-mode 5
-"${MMSEQS}" rmdb "${BASE}/qdb"
-"${MMSEQS}" rmdb "${BASE}/qdb_h"
+
+"${MMSEQS}" rmdb "${BASE}/res"
+"${MMSEQS}" rmdb "${BASE}/res_exp"
+"${MMSEQS}" rmdb "${BASE}/res_exp_realign"
+"${MMSEQS}" rmdb "${BASE}/res_exp_realign_pair"
+"${MMSEQS}" rmdb "${BASE}/res_exp_realign_pair_bt"
+"${MMSEQS}" rmdb "${BASE}/res_final"
+
+if [ "${USE_ENV}" = "1" ]; then
+ "${MMSEQS}" search "${BASE}/qdb" "${DB2}" "${BASE}/res" "${BASE}/tmp" $SEARCH_PARAM
+ "${MMSEQS}" expandaln "${BASE}/qdb" "${DB2}.idx" "${BASE}/res" "${DB2}.idx" "${BASE}/res_exp" --db-load-mode 2 ${EXPAND_PARAM}
+ "${MMSEQS}" align "${BASE}/qdb" "${DB2}.idx" "${BASE}/res_exp" "${BASE}/res_exp_realign" --db-load-mode 2 -e 0.001 --max-accept 1000000 -c 0.5 --cov-mode 1
+ "${MMSEQS}" pairaln "${BASE}/qdb" "${DB2}.idx" "${BASE}/res_exp_realign" "${BASE}/res_exp_realign_pair" --db-load-mode 2 --pairing-mode "${PAIRING_STRATEGY}" --pairing-dummy-mode 0
+ "${MMSEQS}" align "${BASE}/qdb" "${DB2}.idx" "${BASE}/res_exp_realign_pair" "${BASE}/res_exp_realign_pair_bt" --db-load-mode 2 -e inf -a
+ "${MMSEQS}" pairaln "${BASE}/qdb" "${DB2}.idx" "${BASE}/res_exp_realign_pair_bt" "${BASE}/res_final" --db-load-mode 2 --pairing-mode "${PAIRING_STRATEGY}" --pairing-dummy-mode 1
+ "${MMSEQS}" result2msa "${BASE}/qdb" "${DB2}.idx" "${BASE}/res_final" "${BASE}/pair.env.a3m" --db-load-mode 2 --msa-format-mode 5
+ cat "${BASE}/pair.a3m" "${BASE}/pair.env.a3m" > "${BASE}/pair.a3m_tmp"
+ mv -f -- "${BASE}/pair.a3m_tmp" "${BASE}/pair.a3m"
+fi
+
 "${MMSEQS}" rmdb "${BASE}/res"
 "${MMSEQS}" rmdb "${BASE}/res_exp"
 "${MMSEQS}" rmdb "${BASE}/res_exp_realign"
 "${MMSEQS}" rmdb "${BASE}/res_exp_realign_pair"
 "${MMSEQS}" rmdb "${BASE}/res_exp_realign_pair_bt"
 "${MMSEQS}" rmdb "${BASE}/res_final"
+
+"${MMSEQS}" rmdb "${BASE}/qdb"
+"${MMSEQS}" rmdb "${BASE}/qdb_h"
+
 rm -rf -- "${BASE}/tmp"
 `)
  err = script.Close()
  if err != nil {
  return &JobExecutionError{err}
  }
  modes := strings.Split(job.Mode, "-")
+ useEnv := isIn("env", modes) != -1
  usePairwise := isIn("pairwise", modes) != -1
  var b2i = map[bool]int{false: 0, true: 1}
 
@@ -961,6 +986,8 @@ rm -rf -- "${BASE}/tmp"
  config.Paths.Databases,
  resultBase,
  config.Paths.ColabFold.Uniref,
+ config.Paths.ColabFold.EnvironmentalPair,
+ strconv.Itoa(b2i[useEnv]),
  strconv.Itoa(b2i[usePairwise]),
  pairingStrategy,
  }