#!/usr/bin/env python3
"""Module containing the GROMACS order 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
[docs]
class GMXOrder(BiobbObject):
"""
| biobb_mem GMXOrder
| Wrapper of the GROMACS order module for computing lipid order parameters per atom for carbon tails.
| `GROMCAS order <https://manual.gromacs.org/current/onlinehelp/gmx-order.html>`_ only works for saturated carbons and united atom force fields.
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/main/biobb_mem/test/data/ambertools/topology.tpr>`_. Accepted formats: tpr (edam:format_2333).
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/ambertools/trajectory.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)..
input_index_path (str): Path to the GROMACS index file. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/ >`_. Accepted formats: ndx (edam:format_2033).
output_deuter_path (str): Path to deuterium order parameters xvgr/xmgr file. File type: output. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/gromacs/deuter.xvg>`_. Accepted formats: xvg (edam:format_2330).
output_order_path (str) (Optional): Path to order tensor diagonal elements xvgr/xmgr file. File type: output. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/gromacs/order.xvg>`_. Accepted formats: xvg (edam:format_2330).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **d** (*str*) - ("z") Direction of the normal on the membrane: z, x, y.
* **binary_path** (*str*) - ("cpptraj") Path to the cpptraj 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.ambertools.gmx_order import gmx_order
prop = {
'd': 'z'
}
gmx_order(input_top_path='/path/to/myTopology.top',
input_traj_path='/path/to/myTrajectory.xtc',
output_deuter_path='/path/to/deuterAnalysis.xvg',
output_order_path='/path/to/orderAnalysis.xvg',
properties=prop)
Info:
* wrapped_software:
* name: GROMACS order
* version: 2024.2
* license: LGPL 2.1
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_top_path, input_traj_path, input_index_path=None,
output_deuter_path=None, output_order_path=None, 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,
"input_index_path": input_index_path
},
"out": {
"output_deuter_path": output_deuter_path,
"output_order_path": output_order_path
}
}
# Properties specific for BB
self.d = properties.get('d', 'z')
self.binary_path = properties.get('binary_path', 'gmx')
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`GMXOrder <gromacs.gmx_order.GMXOrder>` gromacs.gmx_order.GMXOrder object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Create cmd and launch execution
cmd = [self.binary_path, 'order',
'-s', self.stage_io_dict["in"]["input_top_path"],
'-f', self.stage_io_dict["in"]["input_traj_path"],
'-n', self.stage_io_dict["in"]["input_index_path"],
'-od', self.stage_io_dict["out"]["output_deuter_path"],
'-d', self.d]
if self.stage_io_dict["out"].get("output_order_path"):
cmd.extend(['-o', self.stage_io_dict["out"]["output_order_path"]])
else:
cmd.extend(['-o', str(PurePath(self.stage_io_dict["unique_dir"]).joinpath('order.xvg'))])
self.cmd = cmd
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
# Remove temporary folder(s)
self.tmp_files.append(self.stage_io_dict.get("unique_dir"))
self.remove_tmp_files()
return self.return_code
[docs]
def gmx_order(input_top_path: str, input_traj_path: str, input_index_path: str = None,
output_deuter_path: str = None, output_order_path: str = None,
properties: dict = None, **kwargs) -> int:
"""Create :class:`GMXOrder <gromacs.gmx_order.GMXOrder>` class and
execute :meth:`launch() <gromacs.gmx_order.GMXOrder.launch>` method"""
return GMXOrder(input_top_path=input_top_path,
input_traj_path=input_traj_path,
input_index_path=input_index_path,
output_deuter_path=output_deuter_path,
output_order_path=output_order_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="Compute lipid order parameters using GROMACS order tool.",
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.')
required_args.add_argument('--input_traj_path', required=True, help='Path to the input trajectory to be processed.')
parser.add_argument('--input_index_path', required=False, help='Path to the GROMACS index file.')
parser.add_argument('--output_deuter_path', required=False, help='Path to deuterium order parameters output file.')
parser.add_argument('--output_order_path', required=False, help='Path to order tensor diagonal elements output file.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call of each building block
gmx_order(input_top_path=args.input_top_path,
input_traj_path=args.input_traj_path,
input_index_path=args.input_index_path,
output_deuter_path=args.output_deuter_path,
output_order_path=args.output_order_path,
properties=properties)
if __name__ == '__main__':
main()