#!/usr/bin/env python3
"""Module containing the PMX merge_ff class and the command line interface."""
import glob
import os
import sys
from pathlib import Path
from typing import Optional
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from pmx import ligand_alchemy # type: ignore
[docs]
class Pmxmerge_ff(BiobbObject):
"""
| biobb_pmx Pmxmerge_ff
| Wrapper class for the `PMX merge_ff <https://github.com/deGrootLab/pmx>`_ module.
| Merge ligand topology files.
Args:
input_topology_path (str): Path to the input ligand topologies as a zip file containing a list of itp files. File type: input. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/itps_to_merge.zip>`_. Accepted formats: zip (edam:format_3987).
output_topology_path (str): Path to the merged ligand topology file. File type: output. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_mergedTopology.itp>`_. Accepted formats: itp (edam:format_3883).
properties (dic):
* **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_pmx.pmxbiobb.pmxmerge_ff import pmxmerge_ff
prop = {
'remove_tmp' : True
}
pmxmerge_ff(input_topology_path='/path/to/myTopologies.zip',
output_topology_path='/path/to/myMergedTopology.itp',
properties=prop)
Info:
* wrapped_software:
* name: PMX merge_ff
* version: >=1.0.1
* license: GNU
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(
self,
input_topology_path: str,
output_topology_path: str,
properties: Optional[dict] = 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_topology_path": input_topology_path},
"out": {"output_topology_path": output_topology_path},
}
# Properties specific for BB
# None yet
# Properties common in all PMX BB
self.gmx_lib = properties.get("gmx_lib", None)
if not self.gmx_lib and os.environ.get("CONDA_PREFIX", ""):
python_version = f"{sys.version_info.major}.{sys.version_info.minor}"
self.gmx_lib = str(
Path(os.environ.get("CONDA_PREFIX", "")).joinpath(
f"lib/python{python_version}/site-packages/pmx/data/mutff/"
)
)
if properties.get("container_path"):
self.gmx_lib = str(
Path("/usr/local/").joinpath(
"lib/python3.7/site-packages/pmx/data/mutff/"
)
)
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`Pmxmerge_ff <pmx.pmxmerge_ff.Pmxmerge_ff>` pmx.pmxmerge_ff.Pmxmerge_ff object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Creating temporary folder
tmp_folder = fu.create_unique_dir()
fu.log("Creating %s temporary folder" % tmp_folder, self.out_log)
fu.unzip_list(
self.stage_io_dict["in"]["input_topology_path"],
tmp_folder,
out_log=self.out_log,
)
files = glob.glob(tmp_folder + "/*.itp")
ffsIn_list = []
for itp in files:
ffsIn_list.append(itp)
fu.log("Running merge_FF_files from pmx package...\n", self.out_log)
ligand_alchemy._merge_FF_files(
self.stage_io_dict["out"]["output_topology_path"], ffsIn=ffsIn_list
)
# ffsIn=[self.stage_io_dict["in"]["input_topology1_path"],self.stage_io_dict["in"]["input_topology2_path"]] )
fu.log("Exit code 0\n", self.out_log)
if self.gmx_lib:
self.env_vars_dict["GMXLIB"] = self.gmx_lib
# Run Biobb block
# self.run_biobb()
# Copy files to host
self.copy_to_host()
self.tmp_files.append(tmp_folder)
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]
def pmxmerge_ff(
input_topology_path: str,
output_topology_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create the :class:`Pmxmerge_ff <pmx.pmxmerge_ff.Pmxmerge_ff>` class and
execute the :meth:`launch() <pmx.pmxmerge_ff.Pmxmerge_ff.launch> method."""
return Pmxmerge_ff(**dict(locals())).launch()
pmxmerge_ff.__doc__ = Pmxmerge_ff.__doc__
main = Pmxmerge_ff.get_main(pmxmerge_ff, "Run PMX merge_ff module")
if __name__ == "__main__":
main()