from icolos.utils.enums.step_enums import StepBaseEnum, StepGromacsEnum
from icolos.utils.enums.program_parameters import GromacsEnum
from icolos.core.workflow_steps.gromacs.base import StepGromacsBase
from icolos.utils.execute_external.gromacs import GromacsExecutor
from pydantic import BaseModel
from icolos.core.workflow_steps.step import _LE
import os
_GE = GromacsEnum()
_SGE = StepGromacsEnum()
_SBE = StepBaseEnum
[docs]class StepGMXGenion(StepGromacsBase, BaseModel):
"""
Wrapper for gmx genion
"""
def __init__(self, **data):
super().__init__(**data)
self._initialize_backend(executor=GromacsExecutor)
self._check_backend_availability()
[docs] def execute(self):
tmp_dir = self._make_tmpdir()
topol = self.get_topol()
self.write_input_files(tmp_dir, topol=topol)
arguments = self._parse_arguments(
{
"-o": _SGE.STD_STRUCTURE,
"-p": _SGE.STD_TOPOL,
"-s": _SGE.STD_TPR,
}
)
result = self._backend_executor.execute(
command=_GE.GENION,
arguments=arguments,
location=tmp_dir,
pipe_input=self.construct_pipe_arguments(
tmp_dir, self.settings.additional[_SBE.PIPE_INPUT]
),
)
for line in result.stdout.split("\n"):
self._logger_blank.log(line, _LE.DEBUG)
self._logger.log(
f"Completed execution for {self.step_id} successfully", _LE.INFO
)
# this is the last structural change to the topology in a regular gromacs setup,
# update the index groups here
make_ndx_args = ["-f", _SGE.STD_STRUCTURE, "-o", _SGE.STD_INDEX]
index_files = [f for f in os.listdir(tmp_dir) if f.endswith(".ndx")]
# remove any existing index files
for f in index_files:
self._remove_temporary(os.path.join(tmp_dir, f))
# generate new index file
result = self._backend_executor.execute(
command=_GE.MAKE_NDX,
arguments=make_ndx_args,
location=tmp_dir,
check=True,
pipe_input='echo -e "1 | 12 \nq"',
)
for line in result.stdout.split("\n"):
self._logger_blank.log(line, _LE.DEBUG)
self._logger.log('Added index group to "index.ndx"', _LE.DEBUG)
self._parse_output(tmp_dir)
topol.set_structure(tmp_dir)
topol.parse(tmp_dir)
self._remove_temporary(tmp_dir)