+ 1#!/usr/bin/env python3
+ 2
+ 3"""Module containing the FATSLiM Membranes class and the command line interface."""
+ 4import argparse
+ 5from pathlib import PurePath
+ 6from biobb_common.generic.biobb_object import BiobbObject
+ 7from biobb_common.configuration import settings
+ 8from biobb_common.tools.file_utils import launchlogger
+ 9from biobb_common.tools import file_utils as fu
+ 10import MDAnalysis as mda
+ 11import os
+ 12
+ 13
+ 14class FatslimMembranes(BiobbObject):
+ 15 """
+ 16 | biobb_mem FatslimMembranes
+ 17 | Wrapper of the `FATSLiM membranes <https://pythonhosted.org/fatslim/documentation/leaflets.html>`_ module for leaflet and membrane identification.
+ 18 | FATSLiM is designed to provide efficient and robust analysis of physical parameters from MD trajectories, with a focus on processing large trajectory files quickly.
+ 19
+ 20 Args:
+ 21 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).
+ 22 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).
+ 23 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).
+ 24 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
+ 25 * **selection** (*str*) - ("resname DPPC and element P") Molecules used in the identification using MDAnalysis selection language.
+ 26 * **cutoff** (*float*) - (2) Cutoff distance (in nm) to be used when leaflet identification is performed.
+ 27 * **binary_path** (*str*) - ("fatslim") Path to the fatslim executable binary.
+ 28 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
+ 29 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+ 30 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
+ 31
+ 32 Examples:
+ 33 This is a use example of how to use the building block from Python::
+ 34
+ 35 from biobb_mem.fatslim.fatslim_membranes import fatslim_membranes
+ 36 prop = {
+ 37 'selection': '(resname DPPC and name P8)',
+ 38 'cutoff': 2.2
+ 39 }
+ 40 fatslim_membranes(input_top_path='/path/to/myTopology.tpr',
+ 41 input_traj_path='/path/to/myTrajectory.xtc',
+ 42 output_ndx_path='/path/to/newIndex.ndx',
+ 43 properties=prop)
+ 44
+ 45 Info:
+ 46 * wrapped_software:
+ 47 * name: FATSLiM
+ 48 * version: 0.2.2
+ 49 * license: GNU
+ 50 * ontology:
+ 51 * name: EDAM
+ 52 * schema: http://edamontology.org/EDAM.owl
+ 53
+ 54 """
+ 55
+ 56 def __init__(self, input_top_path, input_traj_path, output_ndx_path, properties=None, **kwargs) -> None:
+ 57 properties = properties or {}
+ 58
+ 59 # Call parent class constructor
+ 60 super().__init__(properties)
+ 61 self.locals_var_dict = locals().copy()
+ 62
+ 63 # Input/Output files
+ 64 self.io_dict = {
+ 65 "in": {"input_top_path": input_top_path,
+ 66 "input_traj_path": input_traj_path},
+ 67 "out": {"output_ndx_path": output_ndx_path}
+ 68 }
+ 69
+ 70 # Properties specific for BB
+ 71 self.selection = properties.get('selection', "resname DPPC or resname POPC) and element P")
+ 72 self.cutoff = properties.get('cutoff', 2.2)
+ 73 self.binary_path = properties.get('binary_path', 'fatslim')
+ 74 self.properties = properties
+ 75
+ 76 # Check the properties
+ 77 self.check_properties(properties)
+ 78 self.check_arguments()
+ 79
+ 80 @launchlogger
+ 81 def launch(self) -> int:
+ 82 """Execute the :class:`FatslimMembranes <fatslim.fatslim_membranes.FatslimMembranes>` fatslim.fatslim_membranes.FatslimMembranes object."""
+ 83
+ 84 # Setup Biobb
+ 85 if self.check_restart():
+ 86 return 0
+ 87 self.stage_files()
+ 88
+ 89 # Create index file using MDAnalysis
+ 90 u = mda.Universe(self.stage_io_dict["in"]["input_top_path"],
+ 91 self.stage_io_dict["in"]["input_traj_path"])
+ 92 # Build the index to select the atoms from the membrane
+ 93 self.tmp_ndx = str(PurePath(fu.create_unique_dir()).joinpath('headgroups.ndx'))
+ 94 with mda.selections.gromacs.SelectionWriter(self.tmp_ndx, mode='w') as ndx:
+ 95 ndx.write(u.select_atoms(self.selection), name='headgroups')
+ 96 # Convert topology .gro and add box dimensions if not available in the topology
+ 97 self.tmp_cfg = str(PurePath(fu.create_unique_dir()).joinpath('output.gro'))
+ 98 self.cmd = ['gmx', 'editconf',
+ 99 '-f', self.stage_io_dict["in"]["input_top_path"],
+ 100 '-o ', self.tmp_cfg,
+ 101 '-box', ' '.join(map(str, u.dimensions[:3]))
+ 102 ]
+ 103 self.tmp_out = str(PurePath(fu.create_unique_dir()).joinpath('output.ndx'))
+ 104 # Build command
+ 105 self.cmd.extend([
+ 106 ';',
+ 107 self.binary_path, "membranes",
+ 108 "-c", self.tmp_cfg,
+ 109 "-n", self.tmp_ndx,
+ 110 "--output-index", self.tmp_out,
+ 111 "--cutoff", str(self.cutoff)
+ 112 ])
+ 113
+ 114 # Run Biobb block
+ 115 self.run_biobb()
+ 116 os.rename(self.tmp_out[:-4]+'_0000.ndx', self.stage_io_dict["out"]["output_ndx_path"])
+ 117 # Copy files to host
+ 118 self.copy_to_host()
+ 119
+ 120 # Remove temporary files
+ 121 self.tmp_files.extend([
+ 122 self.stage_io_dict.get("unique_dir"),
+ 123 PurePath(self.tmp_ndx).parent,
+ 124 PurePath(self.tmp_cfg).parent,
+ 125 PurePath(self.tmp_out).parent
+ 126 ])
+ 127 self.remove_tmp_files()
+ 128
+ 129 self.check_arguments(output_files_created=True, raise_exception=False)
+ 130
+ 131 return self.return_code
+ 132
+ 133 @staticmethod
+ 134 def parse_index(ndx):
+ 135 """
+ 136 Parses a GROMACS index file (.ndx) to extract leaflet groups.
+ 137 Args:
+ 138 ndx (str): Path to the GROMACS index file (.ndx).
+ 139 Returns:
+ 140 dict: A dictionary where keys are group names and values are lists of integers representing atom indices.
+ 141 """
+ 142
+ 143 # Read the leaflet.ndx file
+ 144 with open(ndx, 'r') as file:
+ 145 leaflet_data = file.readlines()
+ 146
+ 147 # Initialize dictionaries to store leaflet groups
+ 148 leaflet_groups = {}
+ 149 current_group = None
+ 150
+ 151 # Parse the leaflet.ndx file
+ 152 for line in leaflet_data:
+ 153 line = line.strip()
+ 154 if line.startswith('[') and line.endswith(']'):
+ 155 current_group = line[1:-1].strip()
+ 156 leaflet_groups[current_group] = []
+ 157 elif current_group is not None:
+ 158 leaflet_groups[current_group].extend(map(int, line.split()))
+ 159 return leaflet_groups
+ 160
+ 161
+ 162def fatslim_membranes(input_top_path: str, input_traj_path: str, output_ndx_path: str, properties: dict = None, **kwargs) -> int:
+ 163 """Execute the :class:`FatslimMembranes <fatslim.fatslim_membranes.FatslimMembranes>` class and
+ 164 execute the :meth:`launch() <fatslim.fatslim_membranes.FatslimMembranes.launch>` method."""
+ 165
+ 166 return FatslimMembranes(input_top_path=input_top_path,
+ 167 input_traj_path=input_traj_path,
+ 168 output_ndx_path=output_ndx_path,
+ 169 properties=properties, **kwargs).launch()
+ 170
+ 171
+ 172def main():
+ 173 """Command line execution of this building block. Please check the command line documentation."""
+ 174 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))
+ 175 parser.add_argument('--config', required=False, help='Configuration file')
+ 176
+ 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: ent, gro, pdb, tpr.')
+ 180 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.')
+ 181 required_args.add_argument('--output_ndx_path', required=True, help='Path to the GROMACS index file. Accepted formats: ndx')
+ 182
+ 183 args = parser.parse_args()
+ 184 args.config = args.config or "{}"
+ 185 properties = settings.ConfReader(config=args.config).get_prop_dic()
+ 186
+ 187 # Specific call of each building block
+ 188 fatslim_membranes(input_top_path=args.input_top_path,
+ 189 output_ndx_path=args.output_ndx_path,
+ 190 properties=properties)
+ 191
+ 192
+ 193if __name__ == '__main__':
+ 194 main()
+
+