HADDOCK3.md

haddock-runner and HADDOCK3

IMPORTANT: HADDOCK v3.0 is still under development and is not ready for production use!! Please use HADDOCK v2.4.

The input file for haddock3 is slightly different than the one for haddock2.4. This is needed to accomodate for the new features of HADDOCK3. More information about its new features and how to use it can be found in the HADDOCK3 repository.

Input file

The input file for haddock3 is also a YAML file; see the example below:

general:
  # ...
  # same as haddock2.4
  # ...

scenarios:
  - name: true-interface

    parameters:
      general:
        # these are the general parameters defined in haddock3's
        #  `run.toml` header - there's currently limited support for this
        mode: local
        ncores: 1

      modules:
        # these are the modules to be executed in the order they are defined
        order:
          [
            topoaa,
            rigidbody,
            caprieval,
            seletop,
            flexref,
            caprieval.1,
            emref,
            caprieval.2,
          ]
        # these are the parameters for each module
        topoaa:
          autohis: true

        rigidbody:
          sampling: 10
          ambig_fname: "_ti.tbl"

        caprieval:

        seletop:
          select: 2

        # if no custom parameters are being used, it can be empty
        flexref:

        caprieval.1:

        emref:

        caprieval.2:

Executable script

Here you also need to create an executable script that will call haddock3, see the example below:

#!/bin/bash
#===============================================================================

source $HOME/software/miniconda3/etc/profile.d/conda.sh
conda activate haddock3

# mind the $@ at the end, it passes all the arguments to haddock3
haddock3 "$@"