from icolos.loggers.steplogger import StepLogger
from icolos.utils.execute_external.sdconvert import SDConvertExecutor
from icolos.utils.enums.program_parameters import SchrodingerExecutablesEnum
from icolos.utils.enums.logging_enums import LoggingConfigEnum
from icolos.utils.general.icolos_exceptions import StepFailed
_SEE = SchrodingerExecutablesEnum()
_LE = LoggingConfigEnum()
[docs]class SDConvertUtil:
def __init__(self, prefix_execution: str = None, binary_location: str = None):
self._logger = StepLogger()
# initialize and check executor
self.executor = SDConvertExecutor(
prefix_execution=prefix_execution, binary_location=binary_location
)
if not self.executor.is_available():
raise StepFailed("Cannot initialize sdconvert backend - abort.")
self._logger.log(f"Checked sdconvert availability - valid.", _LE.DEBUG)
[docs] def execute(self, arguments: list):
execution_result = self.executor.execute(
command=_SEE.SDCONVERT, arguments=arguments, check=True
)
if execution_result.returncode != 0:
self._logger.log(
f"Could not execute sdconvert (returncode != 0) with error: {execution_result.stderr}.",
_LE.ERROR,
)
[docs] def mae2sdf(self, mae_file: str, sdf_file: str):
arguments = [
"".join([_SEE.SDCONVERT_I, _SEE.SDCONVERT_FORMAT_MAE]),
mae_file,
"".join([_SEE.SDCONVERT_O, _SEE.SDCONVERT_FORMAT_SD]),
sdf_file,
]
self.execute(arguments=arguments)
[docs] def sdf2mae(self, sdf_file: str, mae_file: str):
arguments = [
"".join([_SEE.SDCONVERT_I, _SEE.SDCONVERT_FORMAT_SD]),
sdf_file,
"".join([_SEE.SDCONVERT_O, _SEE.SDCONVERT_FORMAT_MAE]),
mae_file,
]
self.execute(arguments=arguments)
[docs] def sdf2pdb(self, sdf_file: str, pdb_file: str):
arguments = [
"".join([_SEE.SDCONVERT_I, _SEE.SDCONVERT_FORMAT_SD]),
pdb_file,
"".join([_SEE.SDCONVERT_O, _SEE.SDCONVERT_FORMAT_PDB]),
sdf_file,
]
self.execute(arguments=arguments)