fatslim package

Submodules

fatslim.fatslim_membranes module

Module containing the FATSLiM Membranes class and the command line interface.

class fatslim.fatslim_membranes.FatslimMembranes(input_top_path, input_traj_path, output_ndx_path, properties=None, **kwargs)

Bases: BiobbObject

biobb_mem FatslimMembranes

Wrapper of the FATSLiM membranes module for leaflet and membrane identification.

FATSLiM is designed to provide efficient and robust analysis of physical parameters from MD trajectories, with a focus on processing large trajectory files quickly.

Parameters:

• input_top_path (str) – Path to the input topology file. File type: input. Sample file. Accepted formats: tpr (edam:format_2333), gro (edam:format_2033), g96 (edam:format_2033), pdb (edam:format_1476), brk (edam:format_2033), ent (edam:format_1476).

• input_traj_path (str) –

  Path to the GROMACS trajectory file. File type: input. Sample file. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), cpt (edam:format_2333), gro (edam:format_2033), g96 (edam:format_2033), pdb (edam:format_1476), tng (edam:format_3876).

• output_ndx_path (str) –

  Path to the output index NDX file. File type: output. Sample file. Accepted formats: ndx (edam:format_2033).

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

  • selection (str) - (“resname DPPC and element P”) Molecules used in the identification using MDAnalysis selection language.

  • cutoff (float) - (2) Cutoff distance (in nm) to be used when leaflet identification is performed.

  • begin_frame (int) - (-1) First frame index to be used for analysis.

  • end_frame (int) - (-1) Last frame index to be used for analysis.

  • binary_path (str) - (“fatslim”) Path to the fatslim 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.

Examples

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

from biobb_mem.fatslim.fatslim_membranes import fatslim_membranes
prop = {
    'selection': '(resname DPPC and name P8)',
    'cutoff': 2.2
}
fatslim_membranes(input_top_path='/path/to/myTopology.tpr',
                  input_traj_path='/path/to/myTrajectory.xtc',
                  output_ndx_path='/path/to/newIndex.ndx',
                  properties=prop)

Info:

• wrapped_software:

  • name: FATSLiM

  • version: 0.2.2

  • license: GNU

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

launch() → int

Execute the FatslimMembranes fatslim.fatslim_membranes.FatslimMembranes object.

static parse_index(ndx)

Parses a GROMACS index file (.ndx) to extract leaflet groups.

Parameters:

ndx (str) – Path to the GROMACS index file (.ndx).

Returns:

A dictionary where keys are group names and values are lists of integers representing atom indices.

Return type:

dict

fatslim.fatslim_membranes.fatslim_membranes(input_top_path: str, input_traj_path: str, output_ndx_path: str, properties: dict | None = None, **kwargs) → int

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

fatslim.fatslim_membranes.main()

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