cpptraj package
Submodules
cpptraj.cpptraj_randomize_ions module
Module containing the CpptrajRandomizeIons class and the command line interface.
- class cpptraj.cpptraj_randomize_ions.CpptrajRandomizeIons(input_top_path: str, input_crd_path: str, output_pdb_path: str, output_crd_path: str, properties, **kwargs)[source]
Bases:
BiobbObject
biobb_amber.cpptraj.cpptraj_randomize_ions CpptrajRandomizeIonsWrapper of the AmberTools (AMBER MD Package) cpptraj tool module.Swap specified ions with randomly selected solvent molecules using cpptraj tool from the AmberTools MD package.- Parameters:
input_top_path (str) – Input topology file (AMBER ParmTop). File type: input. Sample file. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881).
input_crd_path (str) –
Input coordinates file (AMBER crd). File type: input. Sample file. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878).
output_pdb_path (str) –
Structure PDB file with randomized ions. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).
output_crd_path (str) –
Structure CRD file with coordinates including randomized ions. File type: output. Sample file. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878).
properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
ion_mask (str) - (“:K+,Cl-,Na+”) Ions to be randomized. Cpptraj mask syntax can be found at the official Cpptraj manual.
solute_mask (str) - (“:DA,DC,DG,DT,D?3,D?5”) Solute (or set of atoms) around which the ions can get no closer than the distance specified. Cpptraj mask syntax can be found at the official Cpptraj manual.
distance (float) - (5.0) Minimum distance cutoff for the ions around the defined solute.
overlap (float) - (3.5) Minimum distance between ions.
binary_path (str) - (“cpptraj”) Path to the cpptraj 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.cpptraj.cpptraj_randomize_ions import cpptraj_randomize_ions prop = { 'remove_tmp': True } cpptraj_randomize_ions(input_top_path='/path/to/topology.top', input_crd_path='/path/to/coordinates.crd', output_pdb_path='/path/to/newStructure.pdb', output_crd_path='/path/to/newCoordinates.crd', properties=prop)
- Info:
- wrapped_software:
name: AmberTools cpptraj
version: >20.9
license: LGPL 2.1
- ontology:
name: EDAM
schema: http://edamontology.org/EDAM.owl