lipyphilicBB package

Submodules

lipyphilicBB.assign_leaflets module

Module containing the Cpptraj Density class and the command line interface.

class lipyphilicBB.assign_leaflets.AssignLeaflets(input_top_path, input_traj_path, output_leaflets_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_mem AssignLeaflets
Wrapper of the Lipyphilic AssignLeaflets module for assigning lipids to leaflets in a bilayer.
LiPyphilic is a Python package for analyzing MD simulations of lipid bilayers. The parameter names and defaults are the same as the ones in the official Lipyphilic documentation.
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:3880), 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_leaflets_path (str) –

    Path to the output leaflet assignments. 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.

    • lipid_sel (str) - (“all”) Selection string for the lipids in a membrane. The selection should cover all residues in the membrane, including cholesterol.

    • midplane_sel (str) - (None) Selection string for residues that may be midplane. Any residues not in this selection will be assigned to a leaflet regardless of its proximity to the midplane. The default is None, in which case all lipids will be assigned to either the upper or lower leaflet.

    • midplane_cutoff (float) - (0) Minimum distance in z an atom must be from the midplane to be assigned to a leaflet rather than the midplane. The default is 0, in which case all lipids will be assigned to either the upper or lower leaflet. Must be non-negative.

    • n_bins (int) - (1) Number of bins in x and y to use to create a grid of membrane patches. Local membrane midpoints are computed for each patch, and lipids assigned a leaflet based on the distance to their local membrane midpoint. The default is 1, which is equivalent to computing a single global midpoint.

    • 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.lipyphilicBB.assign_leaflets import assign_leaflets
prop = {
    'lipid_sel': 'name GL1 GL2 ROH',
}
assign_leaflets(input_top_path='/path/to/myTopology.tpr',
            input_traj_path='/path/to/myTrajectory.xtc',
            output_leaflets_path='/path/to/leaflets.csv',
            properties=prop)
Info:
launch() → int[source]

Execute the AssignLeaflets lipyphilicBB.assign_leaflets.AssignLeaflets object.

lipyphilicBB.assign_leaflets.assign_leaflets(input_top_path: str, input_traj_path: str, output_leaflets_path: str | None = None, properties: dict | None = None, **kwargs) → int[source]

Execute the AssignLeaflets class and execute the launch() method.

lipyphilicBB.assign_leaflets.main()[source]

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