Core library

• Improve the selection language to allow selecting multiple atoms at once. For example, "pairs: name($1) H and mass($2) > 5" will select all pairs of atoms where the first atom name is 'H' and the second atom mass is bigger than 5.
  • The implemented modes for selections are one, atoms, two, pairs, three, four, bonds, angles and dihedrals;
  • The Selection class is now directly exposed to the C API, as CHFL_SELECTION*. The chfl_frame_selection function is replaced by the chfl_selection, chfl_selection_size, chfl_selection_evalutate, chfl_selection_matches and chfl_selection_free functions, and the chfl_match_t helper struct.
• Add the chfl_clear_errors function, to cleanup the error state of the C API.
• Molfiles plugins are now incorporated in the chemfiles library, and no longer distributed as shared libraries. The CHEMFILES_PLUGINS environment variable is a no-op.
• The caching of angles and dihedrals is now an implementation detail. That means that Topology::recalculate is gone, and that Frame::guess_topology and chfl_frame_guess_topology do not take a boolean parameter anymore.
• The opening mode is now a char instead of a string in Trajectory constructor, chfl_trajectory_open, and chfl_trajectory_with_format.
• Remove operator<< and operator>> for Trajectory. Users should use Trajectory::read and Trajectory::write
• Users can now specify the format when reading the topology associated with a trajectory from a file. The chfl_trajectory_set_topology_with_format function can be used to do so from the C API.
• The chfl_atom_from_{frame,topology} function now return NULL in case of out-of-bound access.