"""
MDSuite: A Zincwarecode package.
License
-------
This program and the accompanying materials are made available under the terms
of the Eclipse Public License v2.0 which accompanies this distribution, and is
available at https://www.eclipse.org/legal/epl-v20.html
SPDX-License-Identifier: EPL-2.0
Copyright Contributors to the Zincwarecode Project.
Contact Information
-------------------
email: zincwarecode@gmail.com
github: https://github.com/zincware
web: https://zincwarecode.com/
Citation
--------
If you use this module please cite us with:
Summary
-------
"""
from __future__ import annotations
import abc
import typing
from mdsuite.database.simulation_database import TrajectoryChunkData, TrajectoryMetadata
[docs]class FileProcessor(abc.ABC):
"""
Class to handle reading from trajectory files.
Output is supposed to be used by the experiment class for building and populating
trajectory database.
"""
_metadata: TrajectoryMetadata = None
@abc.abstractmethod
def __str__(self):
"""
Return a unique string representing this FileProcessor. (
The absolute file path, for example).
"""
raise NotImplementedError("File Processors must implement a string")
@abc.abstractmethod
def _get_metadata(self) -> TrajectoryMetadata:
"""
Return the metadata required to build a database.
See mdsuite.database.simulation_database.TrajectoryMetadata to see the details of
which values must be extracted from the file.
"""
raise NotImplementedError("File Processors must implement metadata extraction")
@property
def metadata(self):
if self._metadata is None:
self._metadata = self._get_metadata()
return self._metadata
[docs] @abc.abstractmethod
def get_configurations_generator(self) -> typing.Iterator[TrajectoryChunkData]:
"""
Yield configurations as chunks. Batch size must be determined by the
FileProcessor. See mdsuite.database.simulation_database.TrajectoryChunkData for
the format in which to provide the trajectory chunk.
Returns
-------
generator that yields TrajectoryChunkData
"""
raise NotImplementedError("File Processors must implement data loading")
[docs]def assert_species_list_consistent(sp_list_0, sp_list_1):
for sp_info_data, sp_info_mdata in zip(sp_list_0, sp_list_1):
if sp_info_data != sp_info_mdata:
raise ValueError("Species information in the two lists is inconsistent")