diff --git a/README.md b/README.md index ccafb872..05da2da8 100644 --- a/README.md +++ b/README.md @@ -27,7 +27,7 @@ Foldseek enables fast and sensitive comparisons of large structure sets. - [Output](#output-cluster) - [Important Parameters](#important-cluster-parameters) - [Complexsearch](#complexsearch) - - [Output](#output-complexsearch) + - [Output](#complex-search-output) - [Main Modules](#main-modules) - [Examples](#examples) @@ -218,14 +218,26 @@ MCAR...Q | --tmscore-threshold | Alignment | accept alignments with an alignment TMscore > thr | | --lddt-threshold | Alignment | accept alignments with an alignment LDDT score > thr | -### Complexsearch -The `easy-complexsearch` module allows to search single or multiple query protein complexes, formatted in PDB/mmCIF format (flat or gzipped), against a target database, folder or single protein complexes. In default it outputs the alignment information as a [tab-separated file](#tab-separated-complex) but we support also [report](#report). - foldseek easy-complexsearch example/1tim.pdb.gz example/8tim.pdb.gz aln tmpFolder +### 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. -#### Output Complexsearch +#### Using Complexsearch +To pairwise compare complexes use `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 databases PDB100 pdb tmp +foldseek easy-complexsearch example/1tim.pdb.gz pdb result tmpFolder +``` + +#### Complex Search Output ##### Tab-separated-complex -The default fields are containing the following fields: `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"` returns the query and target accession, the tm scores of complex alignment normalized with query and target lengthes, and assignment id. You can choose many different output columns. +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. + | Code | Description | | --- | --- | | **Commons** | @@ -237,22 +249,31 @@ The default fields are containing the following fields: `query,target,fident,aln |complexu | Rotation matrix of Complex alignment (computed to by TM-score) | |complext | Translation vector of Complex alignment (computed to by TM-score) | |complexassignid| Index of Complex alignment | + +**Example Output:** ``` 1tim.pdb.gz_A 8tim.pdb.gz_A 0.967 247 8 0 1 247 1 247 5.412E-43 1527 0 1tim.pdb.gz_B 8tim.pdb.gz_B 0.967 247 8 0 1 247 1 247 1.050E-43 1551 0 ``` -##### Report -Reports are containing the following fields: + +##### 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: | Column | Description | | --- | --- | -| (1,2) | Identifiers for query and target complex | -| (3,4) | Chains of query complex and target complex | -| (5,6) | TM scores based on query and target residue length | +| 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) | Assignment id | +| 9 | Complex Assignment 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 ``` +