#!/usr/bin/env python3
"""Module containing the FATSLiM Membranes class and the command line interface."""
import argparse
from pathlib import PurePath
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools.file_utils import launchlogger
from biobb_common.tools import file_utils as fu
import MDAnalysis as mda
import shutil
[docs]
class FatslimMembranes(BiobbObject):
"""
| biobb_mem FatslimMembranes
| Wrapper of the `FATSLiM membranes <https://pythonhosted.org/fatslim/documentation/leaflets.html>`_ 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.
Args:
input_top_path (str): Path to the input topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/A01JD/A01JD.pdb>`_. 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 <https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/A01JD/A01JD.xtc>`_. 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 <https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/A01JD/A01JD.ndx>`_. 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 <https://docs.mdanalysis.org/stable/documentation_pages/selections.html>`_.
* **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
"""
def __init__(self, input_top_path, input_traj_path, output_ndx_path, properties=None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"in": {"input_top_path": input_top_path,
"input_traj_path": input_traj_path},
"out": {"output_ndx_path": output_ndx_path}
}
# Properties specific for BB
self.selection = properties.get('selection', "resname DPPC or resname POPC) and element P")
self.cutoff = properties.get('cutoff', 2.2)
self.begin_frame = properties.get('begin_frame', -1)
self.end_frame = properties.get('end_frame', -1)
self.binary_path = properties.get('binary_path', 'fatslim')
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`FatslimMembranes <fatslim.fatslim_membranes.FatslimMembranes>` fatslim.fatslim_membranes.FatslimMembranes object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Create index file using MDAnalysis
u = mda.Universe(self.stage_io_dict["in"]["input_top_path"],
self.stage_io_dict["in"]["input_traj_path"])
# Build the index to select the atoms from the membrane
self.tmp_ndx = str(PurePath(fu.create_unique_dir()).joinpath('headgroups.ndx'))
with mda.selections.gromacs.SelectionWriter(self.tmp_ndx, mode='w') as ndx:
ndx.write(u.select_atoms(self.selection), name='headgroups')
# Convert topology .gro and add box dimensions if not available in the topology
self.tmp_cfg = str(PurePath(fu.create_unique_dir()).joinpath('output.gro'))
self.cmd = ['gmx', 'editconf',
'-f', self.stage_io_dict["in"]["input_top_path"],
'-o', self.tmp_cfg,
'-box', ' '.join(map(str, u.dimensions[:3]))
]
self.tmp_out = str(PurePath(fu.create_unique_dir()).joinpath('output.ndx'))
# Build command
self.cmd.extend([
';',
self.binary_path, "membranes",
"-n", self.tmp_ndx,
"-c", self.tmp_cfg,
"--output-index", self.tmp_out,
"--cutoff", str(self.cutoff),
"--begin-frame", str(self.begin_frame),
"--end-frame", str(self.end_frame)
])
# Run Biobb block
self.run_biobb()
shutil.move(self.tmp_out[:-4]+'_0000.ndx', self.stage_io_dict["out"]["output_ndx_path"])
# Copy files to host
self.copy_to_host()
# Remove temporary files
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir"),
PurePath(self.tmp_ndx).parent,
PurePath(self.tmp_cfg).parent,
PurePath(self.tmp_out).parent
])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]
@staticmethod
def parse_index(ndx):
"""
Parses a GROMACS index file (.ndx) to extract leaflet groups.
Args:
ndx (str): Path to the GROMACS index file (.ndx).
Returns:
dict: A dictionary where keys are group names and values are lists of integers representing atom indices.
"""
# Read the leaflet.ndx file
with open(ndx, 'r') as file:
leaflet_data = file.readlines()
# Initialize dictionaries to store leaflet groups
leaflet_groups = {}
current_group = None
# Parse the leaflet.ndx file
for line in leaflet_data:
line = line.strip()
if line.startswith('[') and line.endswith(']'):
current_group = line[1:-1].strip()
leaflet_groups[current_group] = []
elif current_group is not None:
leaflet_groups[current_group].extend(map(int, line.split()))
return leaflet_groups
[docs]
def fatslim_membranes(input_top_path: str, input_traj_path: str, output_ndx_path: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`FatslimMembranes <fatslim.fatslim_membranes.FatslimMembranes>` class and
execute the :meth:`launch() <fatslim.fatslim_membranes.FatslimMembranes.launch>` method."""
return FatslimMembranes(input_top_path=input_top_path,
input_traj_path=input_traj_path,
output_ndx_path=output_ndx_path,
properties=properties, **kwargs).launch()
[docs]
def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description="Calculates the density along an axis of a given cpptraj compatible trajectory.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('--config', required=False, help='Configuration file')
# Specific args of each building block
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('--input_top_path', required=True, help='Path to the input structure or topology file. Accepted formats: ent, gro, pdb, tpr.')
required_args.add_argument('--input_traj_path', required=True, help='Path to the input trajectory to be processed. Accepted formats: gro, pdb, tng, trr, xtc.')
required_args.add_argument('--output_ndx_path', required=True, help='Path to the GROMACS index file. Accepted formats: ndx')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call of each building block
fatslim_membranes(input_top_path=args.input_top_path,
output_ndx_path=args.output_ndx_path,
properties=properties)
if __name__ == '__main__':
main()