#!/usr/bin/env python3
"""Module containing the Editconf class and the command line interface."""
import os
import shutil
import argparse
from pathlib import Path
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_md.gromacs.common import get_gromacs_version
from biobb_md.gromacs.common import GromacsVersionError
[docs]class Solvate(BiobbObject):
"""
| biobb_md Solvate
| Wrapper of the `GROMACS solvate <http://manual.gromacs.org/current/onlinehelp/gmx-solvate.html>`_ module.
| The GROMACS solvate module, generates a box of solvent around the selected structure.
Args:
input_solute_gro_path (str): Path to the input GRO file. File type: input. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/data/gromacs/solvate.gro>`_. Accepted formats: gro (edam:format_2033), pdb (edam:format_1476).
output_gro_path (str): Path to the output GRO file. File type: output. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/reference/gromacs/ref_solvate.gro>`_. Accepted formats: gro (edam:format_2033), pdb (edam:format_1476).
input_top_zip_path (str): Path the input TOP topology in zip format. File type: input. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/data/gromacs/solvate.zip>`_. Accepted formats: zip (edam:format_3987).
output_top_zip_path (str): Path the output topology in zip format. File type: output. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/reference/gromacs/ref_solvate.zip>`_. Accepted formats: zip (edam:format_3987).
input_solvent_gro_path (str) (Optional): (spc216.gro) Path to the GRO file containing the structure of the solvent. File type: input. Accepted formats: gro (edam:format_2033).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **shell** (*float*) - (0.0) [0~100|0.1] Thickness in nanometers of optional water layer around solute.
* **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable.
* **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
* **container_path** (*str*) - (None) Path to the binary executable of your container.
* **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
* **container_volume_path** (*str*) - ("/data") 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_md.gromacs.solvate import Solvate
prop = { 'shell': 1.0 }
solvate(input_solute_gro_path='/path/to/myStructure.gro',
output_gro_path='/path/to/newStructure.gro',
input_top_zip_path='/path/to/myTopology.zip',
output_top_zip_path='/path/to/newTopology.zip',
properties=prop)
Info:
* wrapped_software:
* name: GROMACS Solvate
* version: >5.1
* license: LGPL 2.1
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_solute_gro_path: str, output_gro_path: str, input_top_zip_path: str,
output_top_zip_path: str, input_solvent_gro_path: str = None, properties: dict = None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
# Input/Output files
self.io_dict = {
"in": {"input_solute_gro_path": input_solute_gro_path, "input_solvent_gro_path": input_solvent_gro_path},
"out": {"output_gro_path": output_gro_path, "output_top_zip_path": output_top_zip_path}
}
# Should not be copied inside container
self.input_top_zip_path = input_top_zip_path
# Properties specific for BB
self.shell = properties.get('shell')
if not self.io_dict["in"].get('input_solvent_gro_path'):
self.io_dict["in"]['input_solvent_gro_path'] = 'spc216.gro'
# Properties common in all GROMACS BB
self.gmx_lib = properties.get('gmx_lib', None)
self.gmx_path = properties.get('gmx_path', 'gmx')
self.gmx_nobackup = properties.get('gmx_nobackup', True)
self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
if self.gmx_nobackup:
self.gmx_path += ' -nobackup'
if self.gmx_nocopyright:
self.gmx_path += ' -nocopyright'
if not self.container_path:
self.gmx_version = get_gromacs_version(self.gmx_path)
# Check the properties
self.check_properties(properties)
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`Solvate <gromacs.solvate.Solvate>` object."""
# Setup Biobb
if self.check_restart(): return 0
self.stage_files()
# Unzip topology to topology_out
top_file = fu.unzip_top(zip_file=self.input_top_zip_path, out_log=self.out_log)
top_dir = str(Path(top_file).parent)
if self.container_path:
shutil.copytree(top_dir, str(Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(top_dir).name)))
top_file = str(Path(self.container_volume_path).joinpath(Path(top_dir).name, Path(top_file).name))
self.cmd = [self.gmx_path, 'solvate',
'-cp', self.stage_io_dict["in"]["input_solute_gro_path"],
'-cs', self.stage_io_dict["in"]["input_solvent_gro_path"],
'-o', self.stage_io_dict["out"]["output_gro_path"],
'-p', top_file]
if self.shell:
self.cmd.append("-shell")
self.cmd.append(str(self.shell))
if self.gmx_lib:
self.environment = os.environ.copy()
self.environment['GMXLIB'] = self.gmx_lib
# Check GROMACS version
if not self.container_path:
if self.gmx_version < 512:
raise GromacsVersionError("Gromacs version should be 5.1.2 or newer %d detected" % self.gmx_version)
fu.log("GROMACS %s %d version detected" % (self.__class__.__name__, self.gmx_version), self.out_log)
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
if self.container_path:
top_file = str(Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(top_dir).name, Path(top_file).name))
# zip topology
fu.log('Compressing topology to: %s' % self.stage_io_dict["out"]["output_top_zip_path"], self.out_log,
self.global_log)
fu.zip_top(zip_file=self.io_dict["out"]["output_top_zip_path"], top_file=top_file, out_log=self.out_log)
# Remove temporal files
self.tmp_files.extend([self.stage_io_dict.get("unique_dir"), top_dir])
self.remove_tmp_files()
return self.return_code
[docs]def solvate(input_solute_gro_path: str, output_gro_path: str, input_top_zip_path: str,
output_top_zip_path: str, input_solvent_gro_path: str = None, properties: dict = None, **kwargs) -> int:
"""Create :class:`Solvate <gromacs.solvate.Solvate>` class and
execute the :meth:`launch() <gromacs.solvate.Solvate.launch>` method."""
return Solvate(input_solute_gro_path=input_solute_gro_path, output_gro_path=output_gro_path,
input_top_zip_path=input_top_zip_path, output_top_zip_path=output_top_zip_path,
input_solvent_gro_path=input_solvent_gro_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="Wrapper for the GROMACS solvate module.",
formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
# Specific args of each building block
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('--input_solute_gro_path', required=True)
required_args.add_argument('--output_gro_path', required=True)
required_args.add_argument('--input_top_zip_path', required=True)
required_args.add_argument('--output_top_zip_path', required=True)
parser.add_argument('--input_solvent_gro_path', required=False)
args = parser.parse_args()
config = args.config if args.config else None
properties = settings.ConfReader(config=config).get_prop_dic()
# Specific call of each building block
solvate(input_solute_gro_path=args.input_solute_gro_path, output_gro_path=args.output_gro_path,
input_top_zip_path=args.input_top_zip_path, output_top_zip_path=args.output_top_zip_path,
input_solvent_gro_path=args.input_solvent_gro_path, properties=properties)
if __name__ == '__main__':
main()