.
@@ -77,14 +77,14 @@ Many of Foldseek's modules (subprograms) rely on MMseqs2. For more information a
## Quick start
### Search
-The `easy-search` module allows to search single or multiple query structures, formatted in PDB/mmCIF format (flat or gzipped), against a target database, folder or single protein structures. In default it outputs the alignment information as a [tab-separated file](#tab-separated) but we support also [Superposed Cα PDBs](#superpositioned-cα-only-pdb-files) or a [HTML](#interactive-html) output.
+The `easy-search` module allows to query one or more single-chain protein structures, formatted in PDB/mmCIF format (flat or gzipped), against a target database, folder or individual single-chain protein structures (for multi-chain proteins see [complexsearch](#complexsearch)). The default alignment information output is a [tab-separated file](#tab-separated) but Foldseek also supports [Superposed Cα PDBs](#superpositioned-cα-only-pdb-files) and [HTML](#interactive-html).
foldseek easy-search example/d1asha_ example/ aln tmpFolder
#### Output Search
##### Tab-separated
-The default fields are containing the following fields: `query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits` but they can be customized with the `--format-output` option e.g. `--format-output "query,target,qaln,taln"` returns the query and target accession and the pairwise alignments in tab separated format. You can choose many different output columns.
+The default output fields are: `query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits` but they can be customized with the `--format-output` option e.g., `--format-output "query,target,qaln,taln"` returns the query and target accessions and the pairwise alignments in tab-separated format. You can choose many different output columns.
| Code | Description |
| --- | --- |
@@ -101,14 +101,14 @@ The default fields are containing the following fields: `query,target,fident,aln
|lddtfull | LDDT per aligned position |
|prob | Estimated probability for query and target to be homologous (e.g. being within the same SCOPe superfamily) |
-Check out the [MMseqs2 documentation for more format output codes](https://github.com/soedinglab/MMseqs2/wiki#custom-alignment-format-with-convertalis).
+Check out the [MMseqs2 documentation for additional output format codes](https://github.com/soedinglab/MMseqs2/wiki#custom-alignment-format-with-convertalis).
##### Superpositioned Cα only PDB files
-Foldseek's `--format-mode 5` generates PDB files with all Cα atoms superimposed based on the aligned coordinates on to the query structure.
-For each pairwise alignment it will write a single PDB files, so be carefull when using this options for large searches.
+Foldseek's `--format-mode 5` generates PDB files with all target Cα atoms superimposed onto the query structure based on the aligned coordinates.
+For each pairwise alignment it will write its own PDB file, so be careful when using this options for large searches.
##### Interactive HTML
-Foldseek can locally generate a search result HTML similiar to the [webserver](https://search.foldseek.com) by specifying the format mode `--format-mode 3`
+Locally run Foldseek can generate an HTML search result, similar to the one produced by the [webserver](https://search.foldseek.com) by specifying `--format-mode 3`
```
foldseek easy-search example/d1asha_ example/ result.html tmp --format-mode 3
@@ -129,17 +129,17 @@ foldseek easy-search example/d1asha_ example/ result.html tmp --format-mode 3
| --cov-mode | Alignment | 0: coverage of query and target, 1: coverage of target, 2: coverage of query |
#### Alignment Mode
-In default Foldseek uses its local 3Di+AA strutural alignment but it also supports to realign hits using the global TMalign as well as rescoring alignments using TMscore.
+By default, Foldseek uses its local 3Di+AA structural alignment but it also supports realigning hits using the global TMalign as well as rescoring alignments using TMscore.
foldseek easy-search example/d1asha_ example/ aln tmp --alignment-type 1
-In case of the alignment type (`--alignment-type 1`) tmalign, we sort the results by the TMscore normalized by query length. We write the TMscore into the e-value=(qTMscore+tTMscore)/2 as well as into the score(=qTMscore*100) field. All output fields (like pident, fident, and alnlen) are calculated from the TMalign alignment.
+If alignment type is set to tmalign (`--alignment-type 1`), the results will be sorted by the TMscore normalized by query length. The TMscore is used for reporting two fields: the e-value=(qTMscore+tTMscore)/2 and the score=(qTMscore*100). All output fields (e.g., pident, fident, and alnlen) are calculated based on the TMalign alignment.
### Databases
The `databases` command downloads pre-generated databases like PDB or AlphaFoldDB.
# pdb
- foldseek databases PDB100 pdb tmp
+ foldseek databases PDB pdb tmp
# alphafold db
foldseek databases Alphafold/Proteome afdb tmp
@@ -155,14 +155,14 @@ We currently support the following databases:
```
#### Create custom databases and indexes
-The target database can be pre-processed by `createdb`. This make sense if searched multiple times.
+The target database can be pre-processed by `createdb`. This is useful when searching multiple times against the same set of target structures.
foldseek createdb example/ targetDB
foldseek createindex targetDB tmp #OPTIONAL generates and stores the index on disk
foldseek easy-search example/d1asha_ targetDB aln.m8 tmpFolder
### Cluster
-The `easy-cluster` algorithm is designed for structural clustering by assigning structures to a representative protein using structural alignment. It accepts input in either PDB or mmCIF format, with support for both flat and gzipped files. By default, easy-cluster generates three output files with the following prefixes: (1) `_clu.tsv`, (2) `_repseq.fasta`, and (3) `_allseq.fasta`. The first file (1) is a [tab-separated](#tab-separated-cluster) file describing the mapping from representative to member, while the second file (2) contains only [representative sequences](#representative-fasta), and the third file (3) includes all [cluster member sequences](#all-member-fasta).
+The `easy-cluster` algorithm is designed for structural clustering by assigning structures to a representative protein structure using structural alignment. It accepts input in either PDB or mmCIF format, with support for both flat and gzipped files. By default, easy-cluster generates three output files with the following prefixes: (1) `_clu.tsv`, (2) `_repseq.fasta`, and (3) `_allseq.fasta`. The first file (1) is a [tab-separated](#tab-separated-cluster) file describing the mapping from representative to member, while the second file (2) contains only [representative sequences](#representative-fasta), and the third file (3) includes all [cluster member sequences](#all-member-fasta).
foldseek easy-cluster example/ res tmp -c 0.9
@@ -187,7 +187,7 @@ MCAT...Q
```
##### All member fasta
-In `_allseq.fasta` file all sequences of the cluster are present. A new cluster is marked by two identical name lines of the representative sequence, where the first line stands for the cluster and the second is the name line of the first cluster sequence. It is followed by the fasta formatted sequences of all its members.
+In the `_allseq.fasta` file all sequences of the cluster are present. A new cluster is marked by two identical name lines of the representative sequence, where the first line stands for the cluster and the second is the name line of the first cluster sequence. It is followed by the fasta formatted sequences of all its members.
```
>Q0KJ32
@@ -220,23 +220,26 @@ MCAR...Q
### Complexsearch
-The `easy-complexsearch` module is a tool for searching single or multiple query protein complexes (PDB/mmCIF, flat or gzipped) against a target database of protein complexes. It reports the similarity metrices of the complexes like TMscore.
+The `easy-complexsearch` module is designed for querying one or more protein complex (multi-chain) structures (supported input formats: PDB/mmCIF, flat or gzipped) against a target database of protein complex structures. It reports the similarity metrices between the complexes (e.g., the TMscore).
#### Using Complexsearch
-To pairwise compare complexes use `easy-complexsearch`, run the following command:
+The examples below use files that can be found in the `example` directory, which is part of the Foldseek repo, if you clone it.
+If you use the precompiled version of the software, you can download the files directly: [1tim.pdb.gz](https://github.com/steineggerlab/foldseek/raw/master/example/1tim.pdb.gz) and [8tim.pdb.gz](https://github.com/steineggerlab/foldseek/raw/master/example/8tim.pdb.gz).
+
+For a pairwise alignment of complexes using `easy-complexsearch`, run the following command:
```
foldseek easy-complexsearch example/1tim.pdb.gz example/8tim.pdb.gz result tmpFolder
```
-This command searches the specified protein complexe `1tim.pdb.gz` against 8tim.pdb.gz, producing alignment information.
-Foldseek `easy-complexsearch` can also be used to search full databases:
+Foldseek `easy-complexsearch` can also be used for searching one or more query complexes against a target database:
```
-foldseek databases PDB100 pdb tmp
+foldseek databases PDB pdb tmp
foldseek easy-complexsearch example/1tim.pdb.gz pdb result tmpFolder
```
#### Complex Search Output
##### Tab-separated-complex
-By default, `easy-complexsearch` outputs the alignment as a tab-separated file. The standard fields include `query, target, fident, alnlen, mismatch, gapopen, qstart, qend, tstart, tend, evalue, bits, complexassignid`. Customize output with the `--format-output` option. For example, `--format-output "query,target,complexqtmscore,complexttmscore,complexassignid"` alters the output to show specific scores and identifiers.
+By default, `easy-complexsearch` reports the output alignment in a tab-separated file.
+The default output fields are: `query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,complexassignid` but they can be customized with the `--format-output` option e.g., `--format-output "query,target,complexqtmscore,complexttmscore,complexassignid"` alters the output to show specific scores and identifiers.
| Code | Description |
| --- | --- |
@@ -257,34 +260,24 @@ By default, `easy-complexsearch` outputs the alignment as a tab-separated file.
```
##### Complex Report
-`easy-complexsearch` also generates a report format (prefixed `_report`), which provides a summary ot the inter complex chain matching, including identifiers, chains, TM scores, rotation matrices, translation vectors, and assignment IDs. Reports are containing the following fields:
+`easy-complexsearch` also generates a report (prefixed `_report`), which provides a summary of the inter-complex chain matching, including identifiers, chains, TMscores, rotation matrices, translation vectors, and assignment IDs. The report includes the following fields:
| Column | Description |
| --- | --- |
-| 1 | Identifiers for query complex |
-| 2 | Identifiers for query complex |
-| 3 | Matched chains of query complex |
-| 4 | Matched chains of target complex |
-| 5 | TM scores normalized by query length |
-| 6 | TM scores normalized by target length |
-| (8,9) | Rotation matrix (u) and Translation vector(t) |
-| 9 | Complex Assignment Id |
+| 1 | Identifier of the query complex |
+| 2 | Identifier of the target complex |
+| 3 | Comma separated matched chains in the query complex |
+| 4 | Comma separated matched chains in the target complex |
+| 5 | TM score normalized by query length [0-1] |
+| 6 | TM score normalized by target length [0-1] |
+| 7 | Comma separated nine rotation matrix (U) values |
+| 8 | Comma separated three translation vector (T) values |
+| 9 | Complex alignment ID |
**Example Output:**
```
1tim.pdb.gz 8tim.pdb.gz A,B A,B 0.98941 0.98941 0.999983,0.000332,0.005813,-0.000373,0.999976,0.006884,-0.005811,-0.006886,0.999959 0.298992,0.060047,0.565875 0
```
-
-
## Main Modules
- `easy-search` fast protein structure search
- `easy-cluster` fast protein structure clustering
@@ -293,12 +286,12 @@ foldseek easy-search example/d1asha_ example/ result.html tmp --format-mode 3
## Examples
### Rescore aligments using TMscore
-Easiest way to get the alignment TMscore normalized by min(alnLen,qLen,targetLen) as well as a rotation matrix is through the following command:
+The easiest way to get the alignment TMscore normalized by min(alnLen,qLen,targetLen) as well as a rotation matrix is through the following command:
```
foldseek easy-search example/ example/ aln tmp --format-output query,target,alntmscore,u,t
```
-Alternative, it is possible to compute TMscores for the kind of alignment output (e.g. 3Di/AA) using the following commands:
+Alternatively, it is possible to compute TMscores for the kind of alignment output (e.g., 3Di+AA) using the following commands:
```
foldseek createdb example/ targetDB
foldseek createdb example/ queryDB
@@ -307,10 +300,10 @@ foldseek aln2tmscore queryDB targetDB aln aln_tmscore
foldseek createtsv queryDB targetDB aln_tmscore aln_tmscore.tsv
```
-Output format `aln_tmscore.tsv`: query and target identifier, TMscore, translation(3) and rotation vector=(3x3)
+Output format `aln_tmscore.tsv`: query and target identifiers, TMscore, translation(3) and rotation vector=(3x3)
### Cluster search results
-The following command aligns the input structures all-against-all and keeps only alignments with 80% of the sequence covered by the alignment (-c 0.8) (read more about alignment coverage [here](https://github.com/soedinglab/MMseqs2/wiki#how-to-set-the-right-alignment-coverage-to-cluster)). It then clusters the results using greedy set cover algorithm. The clustering mode can be adjusted using --cluster-mode, read more [here](https://github.com/soedinglab/MMseqs2/wiki#clustering-modes). The clustering output format is described [here](https://github.com/soedinglab/MMseqs2/wiki#cluster-tsv-format).
+The following command performs an all-against-all alignments of the input structures and retains only the alignments, which cover 80% of the sequence (-c 0.8) (read more about alignment coverage options [here](https://github.com/soedinglab/MMseqs2/wiki#how-to-set-the-right-alignment-coverage-to-cluster)). It then clusters the results using a greedy set cover algorithm. The clustering mode can be adjusted using --cluster-mode, read more [here](https://github.com/soedinglab/MMseqs2/wiki#clustering-modes). The clustering output format is described [here](https://github.com/soedinglab/MMseqs2/wiki#cluster-tsv-format).
```
foldseek createdb example/ db
@@ -320,8 +313,8 @@ foldseek createtsv db db clu clu.tsv
```
### Query centered multiple sequence alignment
-Foldseek can generate a3m based multiple sequence alignments using the following commands.
-a3m can be converted to fasta format using [reformat.pl](https://raw.githubusercontent.com/soedinglab/hh-suite/master/scripts/reformat.pl) (`reformat.pl in.a3m out.fas`).
+Foldseek can output multiple sequence alignments in a3m format using the following commands.
+To convert a3m to FASTA format, the following script can be used [reformat.pl](https://raw.githubusercontent.com/soedinglab/hh-suite/master/scripts/reformat.pl) (`reformat.pl in.a3m out.fas`).
```
foldseek createdb example/ targetDB
diff --git a/data/CMakeLists.txt b/data/CMakeLists.txt
index 000a2d3..ad4256a 100644
--- a/data/CMakeLists.txt
+++ b/data/CMakeLists.txt
@@ -13,6 +13,7 @@ set(COMPILED_RESOURCES
evalue_nn.kerasify
main.js
vendor.js.zst
+ complexsearch.sh
easycomplexsearch.sh
)
diff --git a/data/complexsearch.sh b/data/complexsearch.sh
new file mode 100644
index 0000000..0ce67fe
--- /dev/null
+++ b/data/complexsearch.sh
@@ -0,0 +1,46 @@
+#!/bin/sh -e
+fail() {
+ echo "Error: $1"
+ exit 1
+}
+
+notExists() {
+ [ ! -f "$1" ]
+}
+
+if notExists "${TMP_PATH}/result.dbtype"; then
+ # shellcheck disable=SC2086
+ "$MMSEQS" search "${QUERYDB}" "${TARGETDB}" "${TMP_PATH}/result" "${TMP_PATH}/search_tmp" ${SEARCH_PAR} \
+ || fail "Search died"
+fi
+
+RESULT="${TMP_PATH}/result"
+if [ "$PREFMODE" != "EXHAUSTIVE" ]; then
+ if notExists "${TMP_PATH}/result_expand_pref.dbtype"; then
+ # shellcheck disable=SC2086
+ "$MMSEQS" expandcomplex "${QUERYDB}" "${TARGETDB}" "${RESULT}" "${TMP_PATH}/result_expand_pref" ${THREADS_PAR} \
+ || fail "Expandcomplex died"
+ fi
+ if notExists "${TMP_PATH}/result_expand_aligned.dbtype"; then
+ # shellcheck disable=SC2086
+ "$MMSEQS" $COMPLEX_ALIGNMENT_ALGO "${QUERYDB}" "${TARGETDB}" "${TMP_PATH}/result_expand_pref" "${TMP_PATH}/result_expand_aligned" ${COMPLEX_ALIGN_PAR} \
+ || fail $COMPLEX_ALIGNMENT_ALGO "died"
+ fi
+ RESULT="${TMP_PATH}/result_expand_aligned"
+fi
+if notExists "${TMP_PATH}/complex_result.dbtype"; then
+ # shellcheck disable=SC2086
+ $MMSEQS scorecomplex "${QUERYDB}" "${TARGETDB}" "${RESULT}" "${OUTPUT}" ${SCORECOMPLEX_PAR} \
+ || fail "ScoreComplex died"
+fi
+
+if [ -n "${REMOVE_TMP}" ]; then
+ # shellcheck disable=SC2086
+ "$MMSEQS" rmdb "${TMP_PATH}/result" ${VERBOSITY}
+ if [ "$PREFMODE" != "EXHAUSTIVE" ]; then
+ # shellcheck disable=SC2086
+ "$MMSEQS" rmdb "${TMP_PATH}/result_expand_aligned" ${VERBOSITY}
+ fi
+ rm -rf "${TMP_PATH}/search_tmp"
+ rm -f "${TMP_PATH}/complexsearch.sh"
+fi
diff --git a/data/easycomplexsearch.sh b/data/easycomplexsearch.sh
index a197805..b914133 100644
--- a/data/easycomplexsearch.sh
+++ b/data/easycomplexsearch.sh
@@ -26,39 +26,31 @@ if notExists "${TARGET}.dbtype"; then
TARGET="${TMP_PATH}/target"
fi
-
-SEARCH_RESULT="${TMP_PATH}/result"
-if notExists "${SEARCH_RESULT}.dbtype"; then
+if notExists "${TMP_PATH}/complex_result.dbtype"; then
# shellcheck disable=SC2086
-
- "$MMSEQS" search "${QUERY}" "${TARGET}" "${SEARCH_RESULT}" "${TMP_PATH}/search_tmp" ${SEARCH_PAR} \
- || fail "Search died"
+ "$MMSEQS" complexsearch "${QUERY}" "${TARGET}" "${TMP_PATH}/complex_result" "${TMP_PATH}/complexsearch_tmp" ${COMPLEXSEARCH_PAR} \
+ || fail "ComplexSearch died"
fi
-SCORECOMPLEX_RESULT="${TMP_PATH}/result2"
-if notExists "${SCORECOMPLEX_RESULT}/.dbtype"; then
- # shellcheck disable=SC2086
- $MMSEQS scorecomplex "${QUERY}" "${TARGET}" "${SEARCH_RESULT}" ${SCORECOMPLEX_RESULT} ${SCORECOMPLEX_PAR} \
- || fail "ScoreComplex died"
-fi
+# shellcheck disable=SC2086
+"$MMSEQS" convertalis "${QUERY}" "${TARGET}" "${TMP_PATH}/complex_result" "${OUTPUT}" ${CONVERT_PAR} \
+ || fail "Convert Alignments died"
-if notExists "${TMP_PATH}/alis.dbtype"; then
+if [ -z "${NO_REPORT}" ]; then
# shellcheck disable=SC2086
- "$MMSEQS" convertalis "${QUERY}" "${TARGET}" "${SCORECOMPLEX_RESULT}" "${OUTPUT}" ${CONVERT_PAR} \
- || fail "Convert Alignments died"
+ "$MMSEQS" createcomplexreport "${QUERY}" "${TARGET}" "${TMP_PATH}/complex_result" "${OUTPUT}_report" ${REPORT_PAR} \
+ || fail "createcomplexreport died"
fi
-# shellcheck disable=SC2086
-"$MMSEQS" createcomplexreport "${QUERY}" "${TARGET}" "${SCORECOMPLEX_RESULT}" "${REPORT}" ${REPORT_PAR}\
- || fail "Createcomplexreport dies"
-
-
-
-
-
if [ -n "${REMOVE_TMP}" ]; then
# shellcheck disable=SC2086
"$MMSEQS" rmdb "${TMP_PATH}/result" ${VERBOSITY}
+ if [ "$PREFMODE" != "EXHAUSTIVE" ]; then
+ # shellcheck disable=SC2086
+ "$MMSEQS" rmdb "${TMP_PATH}/result_expand_aligned" ${VERBOSITY}
+ fi
+ # shellcheck disable=SC2086
+ "$MMSEQS" rmdb "${TMP_PATH}/complex_result" ${VERBOSITY}
if [ -z "${LEAVE_INPUT}" ]; then
if [ -f "${TMP_PATH}/target" ]; then
# shellcheck disable=SC2086
@@ -79,6 +71,6 @@ if [ -n "${REMOVE_TMP}" ]; then
# shellcheck disable=SC2086
"$MMSEQS" rmdb "${TMP_PATH}/query_ss" ${VERBOSITY}
fi
- rm -rf "${TMP_PATH}/search_tmp"
- rm -f "${TMP_PATH}/easyscorecomplex.sh"
-fi
+ rm -rf "${TMP_PATH}/complexsearch_tmp"
+ rm -f "${TMP_PATH}/easycomplexsearch.sh"
+fi
\ No newline at end of file
diff --git a/data/main.js b/data/main.js
index bc9a3ea..d82201e 100644
--- a/data/main.js
+++ b/data/main.js
@@ -2089,8 +2089,8 @@
version: 3,
sources: [ "webpack://./frontend/StructureViewer.vue" ],
names: [],
- mappings: ";AA0mBA;IACA,YAAA;IACA,aAAA;IACA,cAAA;AACA;AAEA;IACA,iCAAA;AACA;AACA;;;;GAIA;AACA;IACA,WAAA;IACA,YAAA;AACA;AACA;IACA,kBAAA;AACA;AACA;IACA,kBAAA;AACA;AACA;IACA,oBAAA;IACA,mBAAA;IACA,kBAAA;IACA,uBAAA;IACA,WAAA;IACA,SAAA;IACA,UAAA;IACA,OAAA;AACA;AACA;IACA,kBAAA;IACA,WAAA;IACA,MAAA;IACA,OAAA;IACA,UAAA;IACA,sBAAA;IACA,wBAAA;AACA;AACA;IACA,iBAAA;IACA,UAAA;AACA;AACA;IACA,gBAAA;IACA,UAAA;IACA,mBAAA;AACA",
- sourcesContent: [ '\n | TM-Score: | \n{{ tmAlignResults.tmScore }} | \n
| RMSD: | \n{{ tmAlignResults.rmsd }} | \n