#!/usr/bin/env python3
"""Module containing the PMX create_top class and the command line interface."""
import os
import shutil
import sys
from pathlib import Path, PurePath
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
[docs]
class Pmxcreate_top(BiobbObject):
"""
| biobb_pmx Pmxcreate_top
| Wrapper class for the `PMX create_top <https://github.com/deGrootLab/pmx>`_ module.
| Create a complete ligand topology file from two input topology files.
Args:
input_topology1_path (str): Path to the input topology file 1. File type: input. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/topo1.itp>`_. Accepted formats: itp (edam:format_3883).
input_topology2_path (str): Path to the input topology file 2. File type: input. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/topo2.itp>`_. Accepted formats: itp (edam:format_3883).
output_topology_path (str): Path to the complete ligand topology file. File type: output. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_hybridTopo.zip>`_. Accepted formats: zip (edam:format_3987).
properties (dic):
* **force_field** (*str*) - ("amber99sb-star-ildn-mut.ff") Force-field to be included in the generated topology.
* **water** (*str*) - ("tip3p") Water model to be included in the generated topology.
* **system_name** (*str*) - ("Pmx topology") System name to be included in the generated topology.
* **mols** (*list*) - ([['Protein',1],['Ligand',1]]) Molecules to be included in the generated topology.
* **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.
* **container_path** (*str*) - (None) Path to the binary executable of your container.
* **container_image** (*str*) - (None) Container Image identifier.
* **container_volume_path** (*str*) - ("/inout") Path to an internal directory in the container.
* **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
* **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
* **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
Examples:
This is a use example of how to use the building block from Python::
from biobb_pmx.pmxbiobb.pmxcreate_top import pmxcreate_top
prop = {
'remove_tmp' : True
}
pmxcreate_top(input_topology1_path='/path/to/myTopology1.itp',
input_topology2_path='/path/to/myTopology2.itp',
output_topology_path='/path/to/myMergedTopology.zip',
properties=prop)
Info:
* wrapped_software:
* name: PMX create_top
* version: >=1.0.1
* license: GNU
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(
self,
input_topology1_path: str,
input_topology2_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_topology1_path": input_topology1_path,
"input_topology2_path": input_topology2_path,
},
"out": {"output_topology_path": output_topology_path},
}
# Properties specific for BB
self.force_field = properties.get("force_field", "amber99sb-star-ildn-mut.ff")
self.water = properties.get("water", "tip3p")
self.system_name = properties.get("system_name", "Pmx topology")
self.mols = properties.get("mols", [["Protein", 1], ["Ligand", 1]])
# 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/"
)
)
self.binary_path = properties.get("binary_path", "pmx")
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`Pmxcreate_top <pmx.pmxcreate_top.Pmxcreate_top>` pmx.pmxcreate_top.Pmxcreate_top object."""
# os.chdir("/Users/hospital/BioBB/Notebooks_dev/biobb_wf_pmx_tutorial_ligands/biobb_wf_pmx_tutorial/notebooks")
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
fu.log("Running create_top from pmx package...\n", self.out_log)
# Creating temporary folder
tmp_folder = fu.create_unique_dir()
fu.log("Creating %s temporary folder" % tmp_folder, self.out_log)
itp = os.path.basename(
os.path.normpath(self.stage_io_dict["in"]["input_topology1_path"])
)
fu.log("Creating %s itp file in temporary folder" % itp, self.out_log)
itp_local = str(PurePath(tmp_folder).joinpath(itp))
shutil.copyfile(self.io_dict["in"]["input_topology1_path"], itp_local)
itp2 = os.path.basename(
os.path.normpath(self.stage_io_dict["in"]["input_topology2_path"])
)
fu.log("Creating %s itp file in temporary folder" % itp2, self.out_log)
itp2_local = str(PurePath(tmp_folder).joinpath(itp2))
shutil.copyfile(self.io_dict["in"]["input_topology2_path"], itp2_local)
top_local = str(PurePath(tmp_folder).joinpath("topology.top"))
# _create_top function, taken from the pmx AZ tutorial:
# https://github.com/deGrootLab/pmx/blob/develop/tutorials/AZtutorial.py
fp = open(top_local, "w")
# BioBB signature
fp.write("; Topology generated by the BioBB pmxcreate_top building block\n\n")
# ff itp
fp.write('#include "%s/forcefield.itp"\n\n' % self.force_field)
# additional itp
# for i in self.itps:
# fp.write('#include "%s"\n' % i)
fp.write('#include "%s"\n' % itp)
fp.write('#include "%s"\n\n' % itp2)
# water itp
fp.write('#include "%s/%s.itp"\n' % (self.force_field, self.water))
# ions
fp.write('#include "%s/ions.itp"\n\n' % self.force_field)
# system
fp.write("[ system ]\n")
fp.write("{0}\n\n".format(self.system_name))
# molecules
fp.write("[ molecules ]\n")
for mol in self.mols:
fp.write("%s %s\n" % (mol[0], mol[1]))
fp.close()
# zip topology
current_cwd = os.getcwd()
top_final = str(
PurePath(current_cwd).joinpath(self.io_dict["out"]["output_topology_path"])
)
os.chdir(tmp_folder)
fu.log("Compressing topology to: %s" % top_final, self.out_log, self.global_log)
fu.zip_top(zip_file=top_final, top_file="topology.top", out_log=self.out_log, remove_original_files=self.remove_tmp)
os.chdir(current_cwd)
fu.log("Exit code 0\n", self.out_log)
# 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 pmxcreate_top(
input_topology1_path: str,
input_topology2_path: str,
output_topology_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create the :class:`Pmxcreate_top <pmx.pmxcreate_top.Pmxcreate_top>` class and
execute the :meth:`launch() <pmx.pmxmcreate_top.Pmxmcreate_top.launch> method."""
return Pmxcreate_top(**dict(locals())).launch()
pmxcreate_top.__doc__ = Pmxcreate_top.__doc__
main = Pmxcreate_top.get_main(pmxcreate_top, "Run PMX create_top module")
if __name__ == "__main__":
main()