#!/usr/bin/env python3
"""Module containing the gorder united atom class and the command line interface."""
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools.file_utils import launchlogger
import gorder
[docs]
class GorderUA(BiobbObject):
"""
| biobb_mem GorderUA
| Wrapper of the gorder united atom module for computing lipid order parameters per atom for carbon tails.
| `gorder <https://ladme.github.io/gorder-manual/uaorder_basics.html>`_ uses `GSL <https://ladme.github.io/gsl-guide/>`_ for all its selections.
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/A01JD/A01JD.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/A01JD/A01JD.xtc>`_. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), gro (edam:format_2033).
output_order_path (str): Path to results of the order analysis. File type: output. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/gorder/order_ua.yaml>`_. Accepted formats: yaml (edam:format_3570), xvg (edam:format_2330), csv (edam:format_3752).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **saturated** (*str*) - ("@membrane") Selection query specifying the saturated carbons.
* **unsaturated** (*str*) - (None) Selection query specifying the unsaturated carbons.
* **handle_pbc** (*bool*) - (True) If False, ignores periodic boundary conditions (PBC).
* **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.gorder.gorder_ua import gorder_ua
prop = {
'handle_pbc': False
}
gorder_ua(input_top_path='/path/to/myTopology.tpr',
input_traj_path='/path/to/myTrajectory.xtc',
output_order_path='/path/to/orderAnalysis.yaml',
properties=prop)
Info:
* wrapped_software:
* name: gorder
* version: 1.1.0
* license: MIT
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self,
input_top_path,
input_traj_path,
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,
},
"out": {
"output_order_path": output_order_path
}
}
# Properties specific for BB
self.saturated = properties.get('saturated', "@membrane")
self.unsaturated = properties.get('unsaturated', None)
self.handle_pbc = properties.get('handle_pbc', True)
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`GorderUA <gorder.gorder_ua.GorderUA>` object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Run Biobb block
analysis = gorder.Analysis(
structure=self.stage_io_dict["in"]["input_top_path"],
trajectory=self.stage_io_dict["in"]["input_traj_path"],
analysis_type=gorder.analysis_types.UAOrder(self.saturated, self.unsaturated),
output_yaml=self.stage_io_dict["out"]["output_order_path"],
handle_pbc=False,
)
results = analysis.run()
results.write()
# Copy files to host
self.copy_to_host()
self.remove_tmp_files()
return self.return_code
[docs]
def gorder_ua(input_top_path: str,
input_traj_path: str,
output_order_path: str = None,
properties: dict = None,
**kwargs) -> int:
"""Create :class:`GorderUA <gorder.gorder_ua.GorderUA>` class and
execute :meth:`launch() <gorder.gorder_ua.GorderUA.launch>` method"""
return GorderUA(**dict(locals())).launch()
gorder_ua.__doc__ = GorderUA.__doc__
main = GorderUA.get_main(gorder_ua, "Compute united atom lipid order parameters using gorder order tool.")
if __name__ == '__main__':
main()