HADDOCK2.4 parameter file tools documentation

This document aims to provide some usage and info about the different ways provided by the CSB team to manipulate or visualise HADDOCK2.4 new parameter files. Those new parameter files are associated with all your HADDOCK runs performed with the portal and are named by default job_params.json.

The tools are split in two categories:

  • scripts

Standalone scripts that can be used at the command-line level and piped together to perform actions on a parameter file. They usually take a JSON parameter file as input and output the same file with the change required.

  • API - param_to_json

This API lets you manipulate HADDOCK2.4 parameter files at the Python level. It allows you to perform changes on your parameters within your own Python scripts. It encapsulates the parameter file ito a HADDOCKParam python class that ensures for the validity and integrity of your parameters.

API Reference

The param_to_json Python module

Representation of a HADDOCK parameter file as a Python object.

This library allows to create, load, modify and write HADDOCK parameter files in JSON format.

Several functions are made available and are based on a common structure HADDOCKParam that needs to be initialized prior to doing anything.

class param_to_json.HADDOCKParamError(message)

Exception class related to any error within the HADDOCKParam class

class param_to_json.HADDOCKParamFormatError(message, param=None)

Exception class related to any format error within the HADDOCKParam class

class param_to_json.HADDOCKParam(verbose=True)

Top-level class representing a complete HADDOCK parameter file.

Parameters:verbose (bool) – Get validation details and warnings
check_status()

Check if a HADDOCKParam is loaded and valid

get(param)

Get value of a parameter using its name

Parameters:param – Name of the parameter
load(input, skip_validation=False)

Load the parameter file in a HADDOCKParam object

Parameters:
  • input (str, file) – JSON file path or file-object
  • skip_validation (bool) – Flag to skip or not the validation step
set(param, value)

Get value of a parameter using its name

Parameters:param – Name of the parameter
validate(init=False)

Validation of parameter file format and keys

Param:bool init: Indicate if validation occurs upon loading file
Returns:True/False
Return type:bool
Raise:HADDOCKParamFormatError

Scripts

  • haddock_param_summary.py

Get a quick summary of the job parameter file (JSON)

usage:
$> python haddock_param_summary.py <json file>
example:
$> python haddock_param_summary.py job_params.json
it0 1000
it1 20
itw 20
Partner1: Protein
Partner2: Protein
clust_meth: FCC
clust_cutoff: 0.6

This script is supposed to work with the new parameter files used in HADDOCK2.4 (JSON format).

  • haddock_param_extract_pdb.py

Extract the PDB input files from a job parameter file (JSON) in the current directory

usage:
$> python haddock_param_summary.py <json file>
example:
$> python haddock_param_summary.py job_params.json
partner1.pdb created
partner2.pdb created

This script is supposed to work with the new parameter files used in HADDOCK2.4 (JSON format).

  • haddock_param_validate.py

Validate a HADDOCK parameter file (JSON) and returns any WARNING/ERRORS found.

usage:
$> python haddock_param_validate.py [-v/–verbose] <json file>
example:
$> python haddock_param_validate.py job_params.json
WARNING: No partner detected
ERROR: Wrong type for parameter ‘amb_cool2’
…

This script is supposed to work with the new parameter files used in HADDOCK2.4 (JSON format).

  • haddock_param_replace.py

Replace a parameter in a HADDOCK parameter file (JSON), returns the full parameter file with the modified parameter. Parameter must be int, float, string or boolean

usage:
$> python haddock_param_replace.py <param_name> <param_new_value> <json file>
example:
$> python haddock_param_replace.py amb_cool1 20 job_params.json
{
‘amb_cool1’: 20,
‘amb_cool2’: 50,
…
}

This script is supposed to work with the new parameter files used in HADDOCK2.4 (JSON format).

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