v0.9.0

Version 0.9.0

Atom Index

• Introduced a new Atom field index, which corresponds to the index of the atom in the system (starting from 0). This field can be accessed using Atom::get_index and is only valid if the atom is part of a system.
• Several functions have been reworked to improve efficiency by utilizing the new index field.
• Breaking change: The keyword atomid in the Groan Selection Language has been removed to avoid confusion with the new index field. Use atomnum instead.
• PositionError and MassError now report the atom index instead of the atom number.

Reworked Trajectory Writing

• Breaking changes:
  • Trajectory writing has been completely reworked.
  • Trajectory writers are now attached to System structures, making them memory safe.
  • A trajectory writer can be initialized and attached to a System using System::traj_writer_init (or System::traj_group_writer_init to write information about a specific group).
  • Multiple trajectory writers can be attached to a single System.
  • The system state can be written into all open output trajectory files using System::traj_write_frame or to a specific file using System::traj_write_frame_to_file.

RMSD Calculation

• Introduced System::calc_rmsd to calculate RMSD between the current and a reference structure.
• RMSD-fitting of a structure to a reference structure can be performed using System::calc_rmsd_and_fit.
• Calculating RMSD and RMSD-fitting for trajectories is more efficient with RMSDTrajRead::calc_rmsd and RMSDTrajRead::calc_rmsd_and_fit, implemented for all trajectory readers.

Reading GRO Trajectories

• Trajectories in 'gro' format can now be read using System::gro_iter.
• The with_step method can be used with the 'gro' iterator, but the with_range method is unavailable since 'gro' trajectories do not guarantee simulation time information.
• A System can now be constructed by calling System::from_file on a trajectory in 'gro' format. Only the first frame is read, and the system is constructed based on the atoms in this frame.

Getters and Setters

• Breaking changes:
  • Many 'setter' and 'getter' methods have been renamed:
    • get_atoms_as_ref -> get_atoms
    • get_atoms_as_mut -> get_atoms_mut
    • get_groups_as_ref -> get_groups
    • get_box_as_ref -> get_box
    • get_box_as_mut -> get_box_mut
    • get_atom_as_ref -> get_atom
    • get_atom_as_mut -> get_atom_mut
    • get_atom_unchecked_as_ref -> get_atom_unchecked
    • get_atom_unchecked_as_mut -> get_atom_unchecked_mut
    • get_labeled_atom_as_ref -> get_labeled_atom
    • get_labeled_atom_as_mut -> get_labeled_atom_mut
  • get_atoms_mut now returns a mutable slice &mut [Atom] instead of a mutable vector &mut Vec<Atom>, preventing users from adding or removing atoms.
  • Signatures of several 'getter' methods originally returning &str or Option<&str> have been changed to return &String or Option<&String>, which may cause minor compatibility issues, for instance when comparing strings.

Changes to System::traj_iter_map_reduce

• Breaking change: System::traj_iter_map_reduce now requires the user to provide the initial Data structure. The Data structure no longer needs to implement Default but must implement Clone.
• System::traj_iter_map_reduce now properly propagates errors and failures from individual threads to the master thread's ProgressPrinter.

Changes to Atom Iterators

• Breaking change: Renamed MasterAtomIterator and MasterMutAtomIterator to AtomIterable.
• Introduced new traits: AtomIteratorWithBox and MutAtomIteratorWithBox implemented by all (im)mutable atom iterators containing information about the simulation box.
• Added a new trait OrderedAtomIterator, implemented by all immutable and mutable iterators yielding atoms in the order they appear in the molecular system.
• Iterator unions and intersections can be constructed for iterators implementing OrderedAtomIterator using OrderedAtomIterator::union and OrderedAtomIterator::intersection.
• Added AtomPairIterator and MutAtomPairIterator for iterating over pairs of atoms. These iterators currently support iterating over molecule bonds and can be created using System::molecule_bonds_iter and System::molecule_bonds_iter_mut for immutable and mutable access, respectively.
• Note: The design of these iterators and the structure of atom pairs are subject to future refinement and potential expansion.

Bug Fixes and Other Changes

• Introduced System::make_group_whole to make a group "whole" in the system (similar to System::make_molecules_whole).
• Breaking change: System::group_all_distances now returns ndarray's Array2 instead of a vector of vectors.
• FileType is now part of the prelude.
• Properly implemented Deref and DerefMut for Vector3D, simplifying access to methods from nalgebra::Vector3.
• Improved the performance of AtomContainer::isin (and consequently System::group_isin).
• Vector3D now implements the Display trait.
• Introduced Vector3D::average for calculating the average 3D vector from a collection of vectors.
• Introduced System::groups_member to return a vector of all group names an atom with a specified index is a member of.
• Values in GridMap can now be cleared using GridMap::clear.
• Reworked the loading of GridMaps from files, ensuring invalid coordinates cannot be loaded.
• Introduced System::guess_elements_unknown to assign elements only to atoms without an assigned element.
• ProgressPrinter now uses a mutex only if the parallel feature is enabled.
• Introduced Vector3D::rotate, Atom::rotate, and Atom::rotate_nopbc for performing rotations using rotation matrices.
• Added trajectory converters and analyzers, which are trajectory readers that modify and/or analyze the current simulation frame. See TrajConverter, TrajAnalyzer, and TrajConverterAnalyzer for more details. These structures are primarily for internal use in the groan_rs crate.
• Introduced center of geometry/mass calculation not taking PBC into consideration (System::group_get_center_naive, System::group_get_com_naive, AtomIterable::get_center_naive, AtomIterable::get_com_naive).
• Bug fix: Regex operators can now be used in regular expression blocks without raising an InvalidOperator error.
• Bug fix: Bonds are now properly loaded for TIP3P and similar water models from TPR files.
• Breaking change: XdrFile::open_xdr is no longer public.