ambpdb package

Submodules

ambpdb.amber_to_pdb module

Module containing the AmberToPDB class and the command line interface.

class ambpdb.amber_to_pdb.AmberToPDB(input_top_path, input_crd_path, output_pdb_path, properties: dict | None = None, **kwargs)

Bases: BiobbObject

biobb_amber AmberToPDB

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

Generates a PDB structure from AMBER topology (parmtop) and coordinates (crd) files, using the ambpdb tool from the AmberTools MD package.

Parameters:

• input_top_path (str) – AMBER topology file. File type: input. Sample file. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881).

• input_crd_path (str) –

  AMBER coordinates file. File type: input. Sample file. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878), rst (edam:format_3886).

• output_pdb_path (str) –

  Structure PDB file. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

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

  • binary_path (str) - (“ambpdb”) Path to the ambpdb 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.ambpdb.amber_to_pdb import amber_to_pdb
prop = {
    'remove_tmp': True
}
amber_to_pdb(input_top_path='/path/to/topology.top',
              input_crd_path='/path/to/coordinates.crd',
              output_pdb_path='/path/to/newStructure.pdb',
              properties=prop)

Info:

• wrapped_software:

  • name: AmberTools ambpdb

  • 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()

ambpdb.amber_to_pdb.amber_to_pdb(input_top_path: str, input_crd_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs) → int

Create AmberToPDB method

ambpdb.amber_to_pdb.main()

Command line execution of this building block. Please check the command line documentation.