mdanalysis_biobb package

Submodules

mdanalysis_biobb.mda_hole module

Module containing the MDAnalysis HOLE class and the command line interface.

class mdanalysis_biobb.mda_hole.MDAHole(input_top_path, input_traj_path, output_hole_path, output_csv_path=None, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_mem MDAHole
Wrapper of the MDAnalysis HOLE module for analyzing ion channel pores or transporter pathways.
MDAnalysis HOLE provides an interface to the HOLE suite of tools to analyze pore dimensions and properties along a channel or transporter pathway. The parameter names and defaults follow the MDAnalysis HOLE implementation.
Parameters:

  • input_top_path (str) – Path to the input structure or topology file. File type: input. Sample file. Accepted formats: crd (edam:3878), gro (edam:2033), mdcrd (edam:3878), mol2 (edam:3816), pdb (edam:1476), pdbqt (edam:1476), prmtop (edam:3881), psf (edam:3882), top (edam:3881), tpr (edam:2333), xml (edam:2332), xyz (edam:3887).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: arc (edam:2333), crd (edam:3878), dcd (edam:3878), ent (edam:1476), gro (edam:2033), inpcrd (edam:3878), mdcrd (edam:3878), mol2 (edam:3816), nc (edam:3650), pdb (edam:1476), pdbqt (edam:1476), restrt (edam:3886), tng (edam:3876), trr (edam:3910), xtc (edam:3875), xyz (edam:3887).

  • output_hole_path (str) –

    Path to the output HOLE analysis results. File type: output. Sample file. Accepted formats: vmd (edam:format_2330).

  • output_csv_path (str) –

    Path to the output CSV file containing the radius and coordinates of the pore. File type: output. Sample file. Accepted formats: csv (edam:format_3752).

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

    • start (int) - (None) Starting frame for slicing.

    • stop (int) - (None) Ending frame for slicing.

    • steps (int) - (None) Step for slicing.

    • executable (str) - (“hole”) Path to the HOLE executable.

    • select (str) - (“protein”) The selection string to create an atom selection that the HOLE analysis is applied to.

    • cpoint (list) - (None) Coordinates of a point inside the pore (Å). If None, tries to guess based on the geometry.

    • cvect (list) - (None) Search direction vector. If None, tries to guess based on the geometry.

    • sample (float) - (0.2) Distance of sample points in Å. This value determines how many points in the pore profile are calculated.

    • end_radius (float) - (22) Radius in Å, which is considered to be the end of the pore.

    • dot_density (int) - (15) [5~35] Density of facets for generating a 3D pore representation.

    • 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.

Examples

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

from biobb_mem.mdanalysis_biobb.mda_hole import mda_hole
prop = {
    'select': 'protein',
    'executable': 'hole'
}
mda_hole(input_top_path='/path/to/myTopology.pdb',
        input_traj_path='/path/to/myTrajectory.xtc',
        output_hole_path='/path/to/hole_analysis.vmd',
        output_csv_path='/path/to/hole_profile.csv',
        properties=prop)
Info:
launch() → int[source]

Execute the MDAHole object.

mdanalysis_biobb.mda_hole.display_hole(input_top_path: str, input_traj_path: str, output_hole_path: str = 'hole.vmd', frame: int = 0, opacity: float = 0.9)[source]

Visualize a channel using NGLView from a VMD file.

Parameters:

  • input_top_path (str) – Path to the input topology file.

  • output_hole_path (str, optional) – Path to the VMD file containing the channel data. Default is ‘hole.vmd’.

  • frame (int, optional) – Frame index to visualize. Default is 0.

  • opacity (float, optional) – Opacity of the visualization. Default is 0.9.

Returns:

NGLView widget for visualizing the channel.

Return type:

nglview.NGLWidget

mdanalysis_biobb.mda_hole.mda_hole(input_top_path: str, input_traj_path: str, output_hole_path: str, output_csv_path: str, properties: dict = None, **kwargs) → int[source]
biobb_mem MDAHole
Wrapper of the MDAnalysis HOLE module for analyzing ion channel pores or transporter pathways.
MDAnalysis HOLE provides an interface to the HOLE suite of tools to analyze pore dimensions and properties along a channel or transporter pathway. The parameter names and defaults follow the MDAnalysis HOLE implementation.
Parameters:

  • input_top_path (str) –

    Path to the input structure or topology file. File type: input. Sample file. Accepted formats: crd (edam:3878), gro (edam:2033), mdcrd (edam:3878), mol2 (edam:3816), pdb (edam:1476), pdbqt (edam:1476), prmtop (edam:3881), psf (edam:3882), top (edam:3881), tpr (edam:2333), xml (edam:2332), xyz (edam:3887).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: arc (edam:2333), crd (edam:3878), dcd (edam:3878), ent (edam:1476), gro (edam:2033), inpcrd (edam:3878), mdcrd (edam:3878), mol2 (edam:3816), nc (edam:3650), pdb (edam:1476), pdbqt (edam:1476), restrt (edam:3886), tng (edam:3876), trr (edam:3910), xtc (edam:3875), xyz (edam:3887).

  • output_hole_path (str) –

    Path to the output HOLE analysis results. File type: output. Sample file. Accepted formats: vmd (edam:format_2330).

  • output_csv_path (str) –

    Path to the output CSV file containing the radius and coordinates of the pore. File type: output. Sample file. Accepted formats: csv (edam:format_3752).

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

    • start (int) - (None) Starting frame for slicing.

    • stop (int) - (None) Ending frame for slicing.

    • steps (int) - (None) Step for slicing.

    • executable (str) - (“hole”) Path to the HOLE executable.

    • select (str) - (“protein”) The selection string to create an atom selection that the HOLE analysis is applied to.

    • cpoint (list) - (None) Coordinates of a point inside the pore (Å). If None, tries to guess based on the geometry.

    • cvect (list) - (None) Search direction vector. If None, tries to guess based on the geometry.

    • sample (float) - (0.2) Distance of sample points in Å. This value determines how many points in the pore profile are calculated.

    • end_radius (float) - (22) Radius in Å, which is considered to be the end of the pore.

    • dot_density (int) - (15) [5~35] Density of facets for generating a 3D pore representation.

    • 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.

Examples

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

from biobb_mem.mdanalysis_biobb.mda_hole import mda_hole
prop = {
    'select': 'protein',
    'executable': 'hole'
}
mda_hole(input_top_path='/path/to/myTopology.pdb',
        input_traj_path='/path/to/myTrajectory.xtc',
        output_hole_path='/path/to/hole_analysis.vmd',
        output_csv_path='/path/to/hole_profile.csv',
        properties=prop)
Info: