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: Optional[dict] = None, **kwargs)[source]
Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_amber AmberToPDBWrapper 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) –
remove_tmp (bool) - (True) [WF property] Remove temporal files.
restart (bool) - (False) [WF property] Do not execute if output files exist.
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