- Changes (DB schema changing)
- Remove MODEL_TRANSFORMATION elementary step type
- Additions (backwards compatible):
- Exact type of stored integers in the database is checked before retrieval in case fields have been manipulated with other MongoDB applications
- Projection options are added to almost all internal database queries to reduce the bandwidth requirements.
- Added support for list-of-lists of integers as elements in value collections (calculation settings etc.).
- Changes (DB schema changing):
- Add restart_information field to Calculation
- Add pressure to Model
- Add MODEL_TRANSFORMATION elementary step type
- Change DB version to 1.2.0 and provide update script
- Add additional structure labels for intermediate structures of calculations
- Additions (backwards compatible):
- Python package now includes pure Python code for more complex query utilities. This code is added in the modules
- queries
- energy_query_functions
- compound_and_flask_creation
- concentration_query_functions
- insert_concentration.
All of them are top level modules (import scine_database.energy_query_functions)
Added the possibility to configure the connection based on a custom URI instead of credentials.
- Changes (backwards compatible):
- getAggregate per default recursively looks up the original structure in case the method calling Structure instance is a duplicate. This avoids adding duplicates to aggregates.
- The methods related to duplicates were renamed, the old method calls are now deprecated.
- Important Technical Changes:
- Increase pickle support of Python bindings.
- Bugfixes:
- Corrected the 1.0.0 to 1.1.0 update script.
- Corrected case sensitivity in model completion.
- Corrected temperature setting completion for none case.
- Changes (require updates):
- Structures are now sorted into aggregates which can be Compounds or Flasks
- Update Reactions to connect Flasks and/or Compounds
- lhs and rhs are expanded with a type attribute
- Additions (backwards compatible):
- Add atom index maps to elementary steps
- Add Flasks, a new type of aggregate for stable non-bonded complexes
- Add collection for Flasks
- Add aggregate related functions to the Structure class
- Deprecated:
- All Compound related functions of the Structure class are now deprecated (they point to the new aggregate fields)
- Initial features:
- Connection manager for MongoDB servers
- Definition of specialized classes for data objects that encode chemical reaction networks
- All functionalities present in C++ and Python3 bindings
- Initial classes:
- Structure
- Compound (aggregate of Structures)
- ElementaryStep
- Reaction (aggregate of ElementarySteps)
- Property (Data class attached to Structures)
- BoolProperty (bool/bool)
- NumberProperty (double/float)
- StringProperty (string/str)
- VectorProperty (Eigen::VectorXd/numpy.ndarray)
- DenseMatrixProperty (Eigen::MatrixXd/numpy.ndarray)
- SparseMatrixProperty (Eigen::SparseMatrix/scipy.sparse.csr_matrix)
- Calculation
- Initial collections:
- structures
- compounds
- elementary_steps
- reactions
- properties
- calculations