Update README.md

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 <INPUT> <CUTOFF>
-
-Arguments:
-  <INPUT>   PDB file
-  <CUTOFF>  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 <INPUT>
-
-Arguments:
-  <INPUT>  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 <INPUT>
-
-Arguments:
-  <INPUT>  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 <INPUT> <CUTOFF>
-
-Arguments:
-  <INPUT>   PDB file
-  <CUTOFF>  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`