#!/usr/bin/env python3
"""Module containing the Cpptraj Density class and the command line interface."""
import argparse
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools.file_utils import launchlogger
import MDAnalysis as mda
from lipyphilic.lib.assign_leaflets import AssignLeaflets
import pandas as pd
import numpy as np
[docs]
class LPPAssignLeaflets(BiobbObject):
"""
| biobb_mem LPPAssignLeaflets
| 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 <https://lipyphilic.readthedocs.io/en/latest/reference/analysis/leaflets.html>`_.
Args:
input_top_path (str): Path to the input structure or topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/A01JD/A01JD.pdb>`_. 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 <https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/A01JD/A01JD.xtc>`_. 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 <https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/reference/lipyphilic_biobb/leaflets.csv>`_. 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.lipyphilic_biobb.lpp_assign_leaflets import lpp_assign_leaflets
prop = {
'lipid_sel': 'name GL1 GL2 ROH',
}
lpp_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:
* wrapped_software:
* name: LiPyphilic
* version: 0.10.0
* license: GPL-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_top_path, input_traj_path, output_leaflets_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_leaflets_path": output_leaflets_path}
}
# Properties specific for BB
self.lipid_sel = properties.get('lipid_sel', 'all')
self.midplane_sel = properties.get('midplane_sel', None)
self.midplane_cutoff = properties.get('midplane_cutoff', None)
self.n_bins = properties.get('n_bins', 1)
self.start = properties.get('start', None)
self.stop = properties.get('stop', None)
self.steps = properties.get('steps', None)
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`LPPAssignLeaflets <lipyphilic_biobb.lpp_assign_leaflets.LPPAssignLeaflets>` lipyphilic_biobb.lpp_assign_leaflets.LPPAssignLeaflets object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Load the trajectory
u = mda.Universe(self.stage_io_dict["in"]["input_top_path"], self.stage_io_dict["in"]["input_traj_path"])
# Create AssignLeaflets object
leaflets = AssignLeaflets(
universe=u,
lipid_sel=self.lipid_sel,
midplane_sel=self.midplane_sel,
midplane_cutoff=self.midplane_cutoff,
n_bins=self.n_bins
)
# Run the analysis
leaflets.run(
start=self.start,
stop=self.stop,
step=self.steps
)
# Save the results
frames = leaflets.leaflets.shape[1]
resnames = np.repeat(leaflets.membrane.resnames, frames)
resindices = np.tile(leaflets.membrane.resnums, frames)
frame_numbers = np.repeat(np.arange(frames), leaflets.membrane.n_residues)
df = pd.DataFrame({
'resname': resnames,
'resindex': resindices,
'frame': frame_numbers,
'leaflet_index': leaflets.leaflets.T.flatten()
})
# Save the DataFrame to a CSV file
df.to_csv(self.stage_io_dict["out"]["output_leaflets_path"], index=False)
# Copy files to host
self.copy_to_host()
# remove temporary folder(s)
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir")
])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]
def lpp_assign_leaflets(input_top_path: str, input_traj_path: str, output_leaflets_path: str = None, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`LPPAssignLeaflets <lipyphilic_biobb.lpp_assign_leaflets.LPPAssignLeaflets>` class and
execute the :meth:`launch() <lipyphilic_biobb.lpp_assign_leaflets.LPPAssignLeaflets.launch>` method."""
return LPPAssignLeaflets(input_top_path=input_top_path,
input_traj_path=input_traj_path,
output_leaflets_path=output_leaflets_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="Assign lipids to leaflets in a bilayer.", 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: crd, gro, mdcrd, mol2, pdb, pdbqt, prmtop, psf, top, tpr, xml, xyz.')
required_args.add_argument('--input_traj_path', required=True, help='Path to the input trajectory to be processed. Accepted formats: arc, crd, dcd, ent, gro, inpcrd, mdcrd, mol2, nc, pdb, pdbqt, restrt, tng, trr, xtc, xyz.')
required_args.add_argument('--output_leaflets_path', required=True, help='Path to the output processed analysis.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call of each building block
lpp_assign_leaflets(input_top_path=args.input_top_path,
input_traj_path=args.input_traj_path,
output_leaflets_path=args.output_leaflets_path,
properties=properties)
if __name__ == '__main__':
main()