haddock-restraints

A standalone command-line application to generate restraints to be used in HADDOCK.

Check bonvinlab.org/haddock-restraints for a user guide.

Commands

• tbl: Generates a TBL file
• ti: Generate true-interface restraints from a PDB file
• restraint: Generate Unambiguous restraints to keep molecules together during docking
• interface: List residues in the interface
• z: Generate Z-restraints for a protein

Planned features

• Generate .tbl files from an input file (tbl command)
• Define passive residues based on surface accessibility (tbl command - surface_as_passive)
• Define passive residues around active ones (tbl command - passive_from_active)
• Support for N interactors; 2-body, 3-body, 4-body, etc (tbl command)
• Support for multiple interaction sites in the same interactor (tbl command)
• Generate true-interface restraints for benchmarking (ti command)
• Create unambiguous restraints to keep molecules together during docking (restraint command)
• Filter out buried residues (tbl command)
• List residues in the interface (interface command)
• 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

Usage

Install

Install Rust if you don't have it yet - later we will provide the execution binaries 🤓

cargo install haddock-restraints

Execute

$ 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
  interface  List residues in the interface
  z          Generate Z-restraints for a protein
  help       Print this message or the help of the given subcommand(s)

Options:
  -h, --help     Print help
  -V, --version  Print version

Troubleshooting

/usr/bin/ld: cannot find -lc++: No such file or directory

sudo apt-get install libc++-dev libc++abi-dev

Unable to find libclang

sudo apt-get install libclang-dev