v0.7.0

Version 0.7.0

Reading TPR files

• Implemented basic reading of TPR files using the minitpr crate. The System::from_file function can now recognize and parse TPR files.
• TPR files can also be explicitly read using the tpr_io::read_tpr function (import with use groan_rs::io::tpr_io).
• Currently, only the system name, simulation box dimensions, and the topology of the system (atoms and bonds) are being parsed.
• Atom positions, velocities, and forces are not read from the TPR file by groan_rs. All atoms in a system created by parsing a TPR file will have undefined positions and velocities.
• Reading intermolecular bonds and groups from TPR files is not currently supported.

Reading and writing PQR files

• The System::from_file function now supports reading whitespace-delimited PQR files.
• PQR files can also be explicitly read using the pqr_io::read_pqr function (import with use groan_rs::io::pqr_io).
• PQR files can be written with user-specified precision using the System::write_pqr and System::group_write_pqr functions.

TrajConcatenator structure

• All trajectory readers implementing certain traits (refer to trajectory_readers.md for more information) can now be concatenated using the System::traj_cat_iter.
• During concatenation, duplicate frames from trajectory boundaries are removed, allowing for simple iteration through simulation trajectories that directly follow each other.
• The System::xtc_cat_iter and System::trr_cat_iter functions are provided for direct concatenation of XTC and TRR files, respectively.
• Basic methods associated with trajectory readers, such as with_range, with_step, or print_progress, can be applied to the concatenation iterator.
• The TrajConcatenator structure ensures that the trajectory range is correctly identified even if it spans multiple trajectory files and that step iteration properly handles trajectory boundaries.

Replaced custom Vector3D implementation with faster Vector3 from nalgebra crate

• Breaking change: When Vector3D::to_unit is applied to a vector with a length (magnitude) of zero, its fields are now set to NaN instead of the previously used 0.0.

Restructuring of the module system

• Breaking change: The Select structure is now located directly in the groan_rs::select module, not in groan_rs::selections::select.
• Breaking change: The System structure is now located directly in the groan_rs::system module, not in groan_rs::system::general. This change does not affec users who utilize groan_rs::prelude.

serde feature

• Added a new feature, serde, which provides serialization and deserialization for several groan_rs structures, namely Vector3D, SimBox, Atom, AtomContainer, AtomBlock, Group, System, and Select.
• Select can be deserialized from a valid Groan Selection Language (GSL) query and serialized into a valid GSL query.
• This feature is not enabled by default and must be activated by using cargo add groan_rs --features serde or by adding groan_rs = { version = "0.7.0", features = ["serde"] } to your Cargo.toml file.
• Note that automated tests for serialization and deserialization currently only use the YAML file format, but other formats supported by the serde crate should also work.

parallel feature

• Introduced a new feature, parallel, which contains functions that can run on multiple threads.
• Activate with cargo add groan_rs --features parallel or by adding groan_rs = { version = "0.7.0", features = ["parallel"] }.
• Currently, only a parallelized version of System::guess_bonds, called System::guess_bonds_parallel, has been introduced.

Other changes

• Breaking change: The parse_query function from crate::selections::select has been transformed into an associated function of the Select structure and should now be called as Select::parse_query.
• Added a basic implementation of the TriangularPrism shape, which implements the Shape trait.
• Added a method, System::group_create_from_select, allowing groups to be created directly from Select structures.
• Clarified changes in the order of groups when removing or renaming a group from the System.