From e30649f750271e2a5499f1d1ab3dddc8d5b21ad4 Mon Sep 17 00:00:00 2001 From: Rodrigo Vargas Honorato Date: Wed, 12 Jun 2024 16:49:09 +0200 Subject: [PATCH] Update README.md --- README.md | 179 +++++------------------------------------------------- 1 file changed, 15 insertions(+), 164 deletions(-) diff --git a/README.md b/README.md index ba0a80b..d74ed5f 100644 --- a/README.md +++ b/README.md @@ -9,24 +9,26 @@ A standalone command-line application to generate restraints to be used in HADDOCK. +> Check [bonvinlab.org/haddock-restraints](https://bonvinlab.org/haddock-restraints) for a user guide. + ## Commands -- [`tbl`: Generates a TBL file](#tbl-command) -- [`ti`: Generate true-interface restraints from a PDB file](#ti-command) -- [`restraint`: Generate Unambiguous restraints to keep molecules together during docking](#restraint-command) -- [`interface`: List residues in the interface](#interface-command) +- [`tbl`: Generates a TBL file](https://www.bonvinlab.org/haddock-restraints/tbl.html) +- [`ti`: Generate true-interface restraints from a PDB file](https://www.bonvinlab.org/haddock-restraints/ti.html) +- [`restraint`: Generate Unambiguous restraints to keep molecules together during docking](https://www.bonvinlab.org/haddock-restraints/restraint.html) +- [`interface`: List residues in the interface](https://www.bonvinlab.org/haddock-restraints/interface.html) ## Planned features -- [x] Generate `.tbl` files from an input file -- [x] Define passive residues based on surface accessibility (`surface_as_passive`) -- [x] Define passive residues around active ones (`passive_from_active`) -- [x] Support for N interactors; 2-body, 3-body, 4-body, etc -- [x] Support for multiple interaction sites in the same interactor -- [x] Generate _true-interface_ restraints for benchmarking -- [x] Create unambiguous restraints to keep molecules together during docking -- [x] Filter out buried residues -- [x] List residues in the interface +- [x] Generate `.tbl` files from an input file (tbl command) +- [x] Define passive residues based on surface accessibility (tbl command - `surface_as_passive`) +- [x] Define passive residues around active ones (tbl command - `passive_from_active`) +- [x] Support for N interactors; 2-body, 3-body, 4-body, etc (tbl command) +- [x] Support for multiple interaction sites in the same interactor (tbl command) +- [x] Generate _true-interface_ restraints for benchmarking (ti command) +- [x] Create unambiguous restraints to keep molecules together during docking (restraint command) +- [x] Filter out buried residues (tbl command) +- [x] List residues in the interface (interface command) - [ ] Template based restraints - [ ] Specify atom subsets - [ ] ~Generate random-restraints~ done via CNS @@ -61,157 +63,6 @@ Options: -V, --version Print version ``` -### `ti` command - -```bash -$ ./haddock-restraints ti -h -Generate true-interface restraints from a PDB file - -Usage: haddock-restraints ti - -Arguments: - PDB file - Cutoff distance for interface residues - -Options: - -h, --help Print help -``` - -Example: - -```bash -./haddock-restraints ti examples/2oob.pdb 5.0 > ti.tbl -``` - -### `tbl` command - -```bash -$ ./haddock-restraints tbl -h -Generate TBL file from input file - -Usage: haddock-restraints tbl - -Arguments: - Input file - -Options: - -h, --help Print help -``` - -Example: - -```bash -./haddock-restraints tbl examples/restraints.json > ambig.tbl -``` - -Check the [examples](https://github.com/rvhonorato/haddock-restraints/tree/main/examples) folder for examples of restraint files. - -The mandatory fields are: - -- `id`: an integer that identifies the interactor -- `chain`: the chain of the interactor -- `active`: a list of residues that are active in the interaction -- `passive`: a list of residues that are passive in the interaction -- `target`: a list of integers that identifies the interactors that the current interactor interacts with - -Optional fields are: - -- `structure`: the PDB file that contains the structure of the interactor -- `passive_from_active`: if true, the passive residues are defined based on the active residues (_requires structure_) -- `surface_as_passive`: if true, the passive residues are defined based on the surface accessibility of the residues (_requires structure_) -- `filter_buried`: if true, the buried residues are filtered out (_requires structure_) -- `filter_buried_cutoff`: the cutoff to consider a residue as buried, default = 0.7 (_requires structure_) - -```json -[ - { - "id": 1, - "chain": "A", - "active": [ - 934, - 939 - ], - "passive": [], - "structure": "2oob.pdb", - "target": [ - 2 - ], - "passive_from_active": true, - "filter_buried": true - }, - { - "id": 2, - "chain": "B", - "active": [ - 68 - ], - "passive": [], - "target": [ - 1 - ] - }, - { - "id": 3, - "chain": "B", - "active": [], - "passive": [], - "target": [ - 1 - ], - "structure": "2oob.pdb", - "surface_as_passive": true - } -] -``` - -### `restraint` command - -```bash -$ ./haddock-restraints restraint -h -Generate Unambiguous restraints to keep molecules together during docking - -Usage: haddock-restraints restraint - -Arguments: - PDB file - -Options: - -h, --help Print help -``` - -Example: - -```bash -./haddock-restraints restraint examples/2oob_w_gaps.pdb > unambiguous.tbl -``` - -### `interface` command - -```bash -$ ./haddock-restraints interface -h -List residues in the interface - -Usage: haddock-restraints interface - -Arguments: - PDB file - Cutoff distance for interface residues - -Options: - -h, --help Print help -``` - -Example: - -```bash -./haddock-restraints interface examples/2oob.pdb 5.0 - -Chain A: [931, 933, 934, 936, 937, 938, 940, 941, 946, 950] -Chain B: [6, 8, 42, 44, 45, 46, 47, 48, 49, 66, 68, 69, 70] -``` - -*** - ## Troubleshooting ### `/usr/bin/ld: cannot find -lc++: No such file or directory`