v0.5.0

Version 0.5.0

Important BREAKING CHANGES affecting the entire groan_rs library

• Fields position, velocity, and force in the Atom structure are now of type Option<Vector3D>.
  • Atom::new initializes these values to None. Use Atom::with_position, Atom::with_velocity, or Atom::with_force to set them.
  • Accessor methods (Atom::get_position, etc.) now return Option<&Vector3D>.
  • Distance functions require all atoms to have position information; absence leads to panic.
  • When writing files, undefined positions (and velocities) are output as 0.0 in all dimensions.
  • Reading xtc trajectories sets velocity and force of all atoms to None.
  • Atoms without position are excluded from geometric shape calculations in (Mut)FilterAtomIterator and System::group_create_from_geometry.
  • System::has_forces, System::has_velocities, System::has_positions return true only if all atoms have the respective property.
  • A position with x = 0.0, y = 0.0, z = 0.0 is now considered valid. However, atoms without positions are still written with 0.0 coordinates.

Other changes to the Atom structure

• New optional fields charge and bonded added:
  • charge: Specifies the atom's charge.
  • bonded: Contains indices of atoms bonded to the atom.
  • Methods added to use and access charge and bonded.
  • Atom::wrap method introduced for wrapping the atom into the simulation box.

AtomContainer structure

• Breaking Change: Introduction of AtomContainer:
  • Describes a collection of atoms in the System structure.
  • Group structure and all atom iterators reworked to use AtomContainer.
  • Many methods associated with Group removed/renamed/rewritten.

Reading and writing PDB files

• Breaking Change: System::write_pdb and System::group_write_pdb now require an argument for connectivity information.
• Potentially Breaking Change: Reading of PDB files now stops at ENDMDL or END. END keyword is written correctly at the end of files.
• Connectivity section can now be read with System::add_bonds_from_pdb and written with System::write_pdb/System::group_write_pdb.

Reading systems with non-orthogonal simulation boxes

• Support added for reading/writing systems with non-orthogonal simulation boxes from/to PDB, XTC, and TRR files.

New System connectivity methods

• New methods introduced:
  1. System::add_bond: Adds a bond between atoms.
  2. System::bonded_atoms_iter and System::bonded_atoms_iter_mut: Iterates through bonded atoms.
  3. System::has_bonds: Checks for available connectivity information.
  4. System::molecule_iter and System::molecule_iter_mut: Iterates through atoms in the same molecule.
  5. System::make_molecules_whole: Fixes molecules broken at periodic boundaries.

Quality-of-Life improvements

• ProgressPrinter introduced for trajectory reading progress. Activated via TrajMasterRead::print_progress.

Other changes

• Breaking Change: Atom access methods (System::get_atom_as_ref, etc.) now use index instead of gmx_atom_number.
• Breaking Change: System::from_file returns Result<Self, Box<dyn Error + Send + Sync>> for threading compatibility.
• System::has_duplicate_atom_numbers: Checks for duplicate atom numbers.
• System::residues_renumber: Renumbers residues in the system.
• System::atoms_wrap and System::group_wrap: Wraps atoms into the simulation box.
• System::atoms_distance: Calculates distance between two atoms.
• Panic groan errors now specify the originating function.