foldseek multimer tmalign update

Author: Woosub-Kim

data/complexsearch.sh

@@ -22,9 +22,19 @@ if [ "$PREFMODE" != "EXHAUSTIVE" ]; then
             || fail "Expandcomplex died"
     fi
     if notExists "${TMP_PATH}/result_expand_aligned.dbtype"; then
+
+        if [ "$COMPLEX_ALIGNMENT_ALGO" == "tmalign" ]; then
+                 # shellcheck disable=SC2086
+                 "$MMSEQS" structurealign "${QUERYDB}" "${TARGETDB}" "${TMP_PATH}/result_expand_pref" "${TMP_PATH}/result_expand_aligned_tmp" -e 100 \
+                     || fail $COMPLEX_ALIGNMENT_ALGO "died"
+                 # shellcheck disable=SC2086
+                 "$MMSEQS" tmalign "${QUERYDB}" "${TARGETDB}" "${TMP_PATH}/result_expand_aligned_tmp" "${TMP_PATH}/result_expand_aligned" ${COMPLEX_ALIGN_PAR} \
+                     || fail $COMPLEX_ALIGNMENT_ALGO "died"
+        else
         # shellcheck disable=SC2086
         "$MMSEQS" $COMPLEX_ALIGNMENT_ALGO "${QUERYDB}" "${TARGETDB}" "${TMP_PATH}/result_expand_pref" "${TMP_PATH}/result_expand_aligned" ${COMPLEX_ALIGN_PAR} \
             || fail $COMPLEX_ALIGNMENT_ALGO "died"
+        fi
     fi
     RESULT="${TMP_PATH}/result_expand_aligned"
 fi