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rvhonorato authored Sep 23, 2024
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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](https://www.bonvinlab.org/haddock-restraints/tbl.html)
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- [`interface`: List residues in the interface](https://www.bonvinlab.org/haddock-restraints/interface.html)
- [`z`: Generate Z-restraints for a protein](https://www.bonvinlab.org/haddock-restraints/z.html)

## Planned features
## Usage

- [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)
- [x] Add Z-restraints to keep molecules aligned in the Z-axis (z command)
- [ ] Template based restraints
- [ ] Specify atom subsets
- [ ] ~Generate random-restraints~ done via CNS
Check [bonvinlab.org/haddock-restraints](https://bonvinlab.org/haddock-restraints) for a user guide.

## Usage
## Install

### Install
- Download the [latest binary in the release page](https://github.com/haddocking/haddock-restraints/releases/latest)

> [Install Rust](https://www.rust-lang.org/tools/install) if you don't have it yet - later we will provide the execution binaries 🤓
OR

```bash
cargo install haddock-restraints
```
- Install it with [`cargo`](https://www.rust-lang.org/tools/install)

### Execute
```bash
cargo install haddock-restraints
```

## Execute

```bash
$ haddock-restraints -h
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-V, --version Print version
```

## Troubleshooting
## Planned features

### `/usr/bin/ld: cannot find -lc++: No such file or directory`
- [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)
- [x] Add Z-restraints to keep molecules aligned in the Z-axis (z command)
- [x] Specify atom subsets
- [ ] Template based restraints
- [ ] ~Generate random-restraints~ done via CNS

```bash
sudo apt-get install libc++-dev libc++abi-dev
```
## Troubleshooting

### `Unable to find libclang`

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