v0.4.2

• Introduced System::group_create_from_geometries for group creation with multiple geometry constraints.
• Excluded test files from the crates.io crate distribution.
• Removed unnecessary fields from several error variants.
• Added new test for System::group_create_from_geometry.

v0.4.1

• Added new TrajMasterRead trait that is implemented by TrajReader, TrajRangeReader, TrajStepReader, and TrajRangeStepReader allowing easier usage of these structures in generic functions.
• All new traits and structures for trajectory reading are now properly included in the prelude.

v0.4.0

Changes to the Groan selection language

• Breaking Change: Group names can no longer include the characters '<', '>', or '='.
• Atom, residue, and group names can now be specified using regular expressions in the groan selection language.
• Operators (<, >, <=, and =>) have been introduced for open-ended ranges in the groan selection language.
• Added a new @hydrogen macro for automatic hydrogen atom detection.
• Implemented a new tokenizer for atom and residue numbers in the groan selection language.

Changes to reading xtc and trr files

• Breaking Change: Traits for reading xtc and trr files have been completely redone. Most notably, Xdr* methods, traits, and errors have been renamed to Traj*.
• All trajectory readers must now implement TrajRead trait and do not have to be iterable. Trajectory iterator is constructed by wrapping the TrajRead-implementing structure into TrajReader.
• Introduced several structures for efficient partial reading of trajectory files:
  • TrajRangeReader reads frames in a specified time range. Can be constructed for any structure implementing TrajRangeRead using with_range method.
  • TrajStepReader reads every stepth frame of the trajectory. Can be constructed for any structure implementing TrajStepRead using with_step method.
  • TrajRangeStepReader reads every stepth frame of the trajectory in a specified time range. Can be constructed for any structure implementing both TrajRangeRead and TrajStepRead using with_range and with_step methods.

Other changes

• Added Atom::has_position and System::has_positions methods that check whether the atom or all atoms in the system, respectively, have non-zero position(s).
• Added tests for reading double-precision trr files.
• Enhanced documentation for error variants within the errors module.

v0.3.3

• @ion macro should no longer identify any part of proteins as ions.

v0.3.2

• @water macro should no longer identify N-terminal (or any other) protein hydrogens as water hydrogens.

v0.3.1

• Error message for GroupError::AlreadyExistsWarning changed between v0.2.0 and v0.3.0 which caused one test to fail in the 0.3.0 version. This has been now fixed.

v0.3.0

• Breaking Change: Renamed functions System::group_by_resid and System::group_by_resname to System::atoms_split_by_resid and System::atoms_split_by_resname, respectively.
• Breaking Change: Revised the return type of System::group_create from Result<(), Box<dyn Error>> to Result<(), GroupError>. This change simplifies pattern matching when handling the result of the function. Additionally, the error type SelectError, previously returned by the function, is now encapsulated within the new error variant GroupError::InvalidQuery.
• Updated selection macros according to Gromacs definitions, and introduced new macros for identifying DNA (@dna) and RNA (@rna).
• Introduced new functions: System::group_split_by_resid for splitting groups of atoms by their residue ID and System::group_split_by_resname for splitting by residue name.
• Added functions System::group_remove for removing groups and System::group_rename for renaming them.
• Introduced System::group_create_from_geometry which allows to construct groups of atoms that are inside some geometric shape in the current simulation frame.
• Restructured codebase:
  • Split the system.rs file into multiple smaller files.
  • Grouped files related to IO operations into a dedicated directory.
  • Organized files containing System-related methods into a separate directory.
  • Placed files defining fundamental data structures into their own directory.
• Made minor documentation tweaks.

v0.2.0

• Added functionality to write atom groups into xtc and trr files using the XdrGroupWriter trait along with the XtcGroupWriter and TrrGroupWriter structures.
• Introduced an optional property chain to the Atom structure, allowing specification of the chain ID to which the atom belongs. This property is automatically loaded from pdb files containing chain identifiers and it can also be set manually using the Atom::with_chain function.
• When writing pdb files, if the chain property is set for the Atom, it is now written into the pdb file.
• A new keyword chain has been added to the Groan Selection Language (GSL) that allows to select atoms based on the chain they belong to.
• Made the constructors for AtomIterator and MutAtomIterator public.
• Implemented operations for ndx-writable and ndx-nonwritable groups, including System::group_make_writable, System::group_make_nonwritable, and System::group_names_writable.
• Performed small code refactors.
• Made minor documentation fixes.