pdb4amber package

Submodules

pdb4amber.pdb4amber_run module

Module containing the Pdb4amber class and the command line interface.

class pdb4amber.pdb4amber_run.Pdb4amberRun(input_pdb_path: str, output_pdb_path: str, properties: dict, **kwargs)

Bases: BiobbObject

biobb_amber.pdb4amber.pdb4amber_run Pdb4amberRun

Wrapper of the AmberTools (AMBER MD Package) pdb4amber tool module.

Analyse PDB files and clean them for further usage, especially with the LEaP programs of Amber, using pdb4amber tool from the AmberTools MD package.

Parameters:

• input_pdb_path (str) – Input 3D structure PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

• output_pdb_path (str) –

  Output 3D structure PDB file. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • remove_hydrogens (bool) - (False) Remove hydrogen atoms from the PDB file.

  • remove_waters (bool) - (False) Remove water molecules from the PDB file.

  • constant_pH (bool) - (False) Rename ionizable residues e.g. GLU,ASP,HIS for constant pH simulation.

  • binary_path (str) - (“pdb4amber”) Path to the pdb4amber executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Container path definition.

  • container_image (str) - (‘afandiadib/ambertools:serial’) Container image definition.

  • container_volume_path (str) - (‘/tmp’) Container volume path definition.

  • container_working_dir (str) - (None) Container working directory definition.

  • container_user_id (str) - (None) Container user_id definition.

  • container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.

Examples

This is a use example of how to use the building block from Python:

from biobb_amber.pdb4amber.pdb4amber_run import pdb4amber_run
prop = {
    'remove_tmp': True
}
pdb4amber_run(input_pdb_path='/path/to/structure.pdb',
              output_pdb_path='/path/to/newStructure.pdb',
              properties=prop)

Info:

• wrapped_software:

  • name: AmberTools pdb4amber

  • version: >20.9

  • license: LGPL 2.1

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

check_data_params(out_log, err_log)

Checks input/output paths correctness

launch()

Launches the execution of the Pdb4amberRun module.

pdb4amber.pdb4amber_run.main()

pdb4amber.pdb4amber_run.pdb4amber_run(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs) → int

Create Pdb4amberRun method