Coverage for biobb_mem/lipyphilic_biobb/lpp_flip_flop.py: 74%
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« prev ^ index » next coverage.py v7.6.11, created at 2025-02-10 11:25 +0000
1#!/usr/bin/env python3
3"""Module containing the Lipyphilic FlipFlop class and the command line interface."""
4import argparse
5from biobb_common.generic.biobb_object import BiobbObject
6from biobb_common.configuration import settings
7from biobb_common.tools.file_utils import launchlogger
8import MDAnalysis as mda
9from biobb_mem.lipyphilic_biobb.common import calculate_box
10from lipyphilic.lib.flip_flop import FlipFlop
11import pandas as pd
12import numpy as np
15class LPPFlipFlop(BiobbObject):
16 """
17 | biobb_mem LPPFlipFlop
18 | Wrapper of the LiPyphilic FlipFlop module for finding flip-flop events in a lipid bilayer.
19 | 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/stable/reference/lib/flip_flop.html>`_.
21 Args:
22 input_top_path (str): Path to the input structure or topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/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).
23 input_traj_path (str): Path to the input trajectory to be processed. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/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).
24 input_leaflets_path (str): Path to the input leaflet assignments. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/lipyphilic_biobb/leaflets_data.csv>`_. Accepted formats: csv (edam:format_3752), npy (edam:format_4003).
25 output_flip_flop_path (str): Path to the output flip-flop data. File type: output. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/lipyphilic_biobb/flip_flop.csv>`_. Accepted formats: csv (edam:format_3752).
26 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
27 * **start** (*int*) - (None) Starting frame for slicing.
28 * **stop** (*int*) - (None) Ending frame for slicing.
29 * **steps** (*int*) - (None) Step for slicing.
30 * **lipid_sel** (*str*) - ("all") Selection string for the lipids in a membrane. The selection should cover **all** residues in the membrane, including cholesterol.
31 * **frame_cutoff** (*float*) - (1) To be counted as a successful flip-flop, a molecule must reside in its new leaflet for at least ‘frame_cutoff’ consecutive frames. The default is 1, in which case the molecule only needs to move to the opposing leaflet for a single frame for the flip-flop to be successful.
32 * **ignore_no_box** (*bool*) - (False) Ignore the absence of box information in the trajectory. If the trajectory does not contain box information, the box will be set to the minimum and maximum positions of the atoms in the trajectory.
33 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
34 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
35 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
37 Examples:
38 This is a use example of how to use the building block from Python::
40 from biobb_mem.lipyphilic_biobb.lpp_flip_flop import lpp_flip_flop
41 prop = {
42 'lipid_sel': 'name GL1 GL2 ROH',
43 }
44 lpp_flip_flop(input_top_path='/path/to/myTopology.tpr',
45 input_traj_path='/path/to/myTrajectory.xtc',
46 input_leaflets_path='/path/to/leaflets.csv',
47 output_flip_flop_path='/path/to/flip_flops.csv',
48 properties=prop)
50 Info:
51 * wrapped_software:
52 * name: LiPyphilic
53 * version: 0.10.0
54 * license: GPL-2.0
55 * ontology:
56 * name: EDAM
57 * schema: http://edamontology.org/EDAM.owl
59 """
61 def __init__(self, input_top_path, input_traj_path,
62 input_leaflets_path, output_flip_flop_path,
63 properties=None, **kwargs) -> None:
64 properties = properties or {}
66 # Call parent class constructor
67 super().__init__(properties)
68 self.locals_var_dict = locals().copy()
70 # Input/Output files
71 self.io_dict = {
72 "in": {"input_top_path": input_top_path,
73 "input_traj_path": input_traj_path,
74 "input_leaflets_path": input_leaflets_path},
75 "out": {"output_flip_flop_path": output_flip_flop_path}
76 }
77 self.start = properties.get('start', None)
78 self.stop = properties.get('stop', None)
79 self.steps = properties.get('steps', None)
80 self.lipid_sel = properties.get('lipid_sel', 'all')
81 self.frame_cutoff = properties.get('frame_cutoff', 1)
82 # Properties specific for BB
83 self.ignore_no_box = properties.get('ignore_no_box', True)
84 self.properties = properties
86 # Check the properties
87 self.check_properties(properties)
88 self.check_arguments()
90 @launchlogger
91 def launch(self) -> int:
92 """Execute the :class:`LPPFlipFlop <lipyphilic_biobb.lpp_flip_flop.LPPFlipFlop>` lipyphilic_biobb.lpp_flip_flop.LPPFlipFlop object."""
94 # Setup Biobb
95 if self.check_restart():
96 return 0
97 self.stage_files()
99 # Load the trajectory
100 u = mda.Universe(self.stage_io_dict["in"]["input_top_path"], self.stage_io_dict["in"]["input_traj_path"])
101 if u.dimensions is None:
102 if self.ignore_no_box:
103 calculate_box(u)
104 else:
105 raise ValueError('The trajectory does not contain box information. Please set the ignore_no_box property to True to ignore this error.')
106 # Load the leaflets
107 leaflets_path = self.stage_io_dict["in"]["input_leaflets_path"]
108 if leaflets_path.endswith('.csv'):
109 df = pd.read_csv(leaflets_path)
110 n_frames = len(df['frame'].unique())
111 n_residues = len(df['resindex'].unique())
112 leaflets = df['leaflet_index'].values.reshape(n_frames, n_residues).T
113 else: # .npy file
114 leaflets = np.load(leaflets_path)
115 # Create FlipFlop object
116 flip_flop = FlipFlop(
117 universe=u,
118 lipid_sel=self.lipid_sel,
119 leaflets=leaflets,
120 frame_cutoff=self.frame_cutoff,
121 )
122 # Run the analysis
123 flip_flop.run(
124 start=self.start,
125 stop=self.stop,
126 step=self.steps
127 )
129 # Save the results
130 resnames = []
131 if flip_flop.flip_flops.size > 0:
132 resnames = u.residues.resnames[flip_flop.flip_flops[:, 0]]
133 else:
134 print('No flip-flop events found.')
136 df = pd.DataFrame({
137 'resname': resnames,
138 'resindex': flip_flop.flip_flops[:, 0],
139 'start_frame': flip_flop.flip_flops[:, 1],
140 'end_frame': flip_flop.flip_flops[:, 2],
141 'end_leaflet': flip_flop.flip_flops[:, 3]
142 })
144 # Save the DataFrame to a CSV file
145 df.to_csv(self.stage_io_dict["out"]["output_flip_flop_path"], index=False)
147 # Copy files to host
148 self.copy_to_host()
149 # remove temporary folder(s)
150 self.tmp_files.extend([
151 self.stage_io_dict.get("unique_dir")
152 ])
153 self.remove_tmp_files()
155 self.check_arguments(output_files_created=True, raise_exception=False)
157 return self.return_code
160def lpp_flip_flop(input_top_path: str, input_traj_path: str, input_leaflets_path: str = None,
161 output_flip_flop_path: str = None, properties: dict = None, **kwargs) -> int:
162 """Execute the :class:`LPPFlipFlop <lipyphilic_biobb.lpp_flip_flop.LPPFlipFlop>` class and
163 execute the :meth:`launch() <lipyphilic_biobb.lpp_flip_flop.LPPFlipFlop.launch>` method."""
165 return LPPFlipFlop(input_top_path=input_top_path,
166 input_traj_path=input_traj_path,
167 input_leaflets_path=input_leaflets_path,
168 output_flip_flop_path=output_flip_flop_path,
169 properties=properties, **kwargs).launch()
172def main():
173 """Command line execution of this building block. Please check the command line documentation."""
174 parser = argparse.ArgumentParser(description="Find flip-flop events in a lipid bilayer.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
175 parser.add_argument('--config', required=False, help='Configuration file')
177 # Specific args of each building block
178 required_args = parser.add_argument_group('required arguments')
179 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.')
180 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.')
181 required_args.add_argument('--input_leaflets_path', required=True, help='Path to the input leaflet assignments. Accepted formats: csv, npy.')
182 required_args.add_argument('--output_flip_flop_path', required=True, help='Path to the output processed analysis.')
184 args = parser.parse_args()
185 args.config = args.config or "{}"
186 properties = settings.ConfReader(config=args.config).get_prop_dic()
188 # Specific call of each building block
189 lpp_flip_flop(input_top_path=args.input_top_path,
190 input_traj_path=args.input_traj_path,
191 output_leaflets_path=args.input_leaflets_path,
192 output_flip_flop_path=args.output_flip_flop_path,
193 properties=properties)
196if __name__ == '__main__':
197 main()