# haddock-restraints
A standalone command-line application to generate restraints to be used in HADDOCK.
## 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
- [ ] Specify atom subsets
- [ ] ~Generate random-restraints~ done via CNS
## Usage
### Install
```bash
cargo install haddock-restraints
```
### Execute
```bash
$ haddock-restraints -h
Generate restraints to be used in HADDOCK
Usage: haddock-restraints <COMMAND>
Commands:
tbl Generate TBL file from input file
ti Generate true-interface restraints from a PDB file
restraint Generate Unambiguous restraints to keep molecules together during docking
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
```
### `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
```
***
## Troubleshooting
### `/usr/bin/ld: cannot find -lc++: No such file or directory`
```bash
sudo apt-get install libc++-dev libc++abi-dev
```
### `Unable to find libclang`
```bash
sudo apt-get install libclang-dev
```