CHANGELOG.md

Change Log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning.

Next Release (current master)

• When compiling chemfiles as a shared library, the dependencies symbols are now hidden. This should prevent clashes between say chemfiles's zlib and the system zlib.
• Cache sub-selection (the 'name O' in 'is_bonded(#1, name O)'), reducing selection evaluationg time by a huge margin.
• Fix a bug with memory allocation in the C API. The allocator did not remove pointers as soon as chfl_free was called, which leaded to an error when the system allocator re-used the pointers.

Changes in supported formats

• Added read and write support for CML (Chemical Markup Language) files, a XML based format.

0.9.0 (18 Nov 2018)

• Direct reading and writing of compressed files. gzip and lzma (.xz) formats are supported.
• GROMACS .gro files now supported through custom implementation.
• Properties are now supported in the Residue class. They are accessed using Residue::set and Residue::get.
• The topology of residues is now automatically set using a lookup table for the PDB format.
• Frame::guess_topology was renamed to Frame::guess_bonds.
• The selection engine has been rewritten to add support for more complex selections:
  • it is now possible to use mathematical expressions in selections such as x^2 - y ^2 < sqrt(z^2 + 25);
  • it is now possible to access geometrical properties in such mathematical expressions: distance(#1, #2), angle(#1, #2, #3), dihedral(#1, #2, #3, #4), and out_of_plane(#1, #2, #3, #4) are supported;
  • it is now possible to add constrains on the topology of the system: bonded(#1, #2), is_angle(#1, #2, #3), is_dihedral(#1, #2, #3, #4), and improper(#1, #2, #3, #4) are supported;
  • the topology constrains support sub-selections: instead of checking is #1 and #2 are bonded, one can check if #1 is bonded to any atom matching a selection, for example name O with bonded(#1, name O).
  • When using numbers as atomic names/types, they must now be inside double quotes (name "45"). This also allows for more exotic atomic names (name "名").
  • Atomic properties can be checked, using the [property] == Ow syntax for string properties, [property] == 2.3 for numeric properties and [property] for boolean properties.
• There is only one constructor for the Frame class: Frame(UnitCell cell = UnitCell()). The constructor taking a topology can be replaced with calls to Frame::add_atom and Frame::add_bond.
• Chemfiles will now read configuration from .chemfiles.toml or chemfiles.toml instead of .chemfilesrc
• Added Trajectory::path to get the file path used to create a trajectory
• Renamed Property::get_kind to Property::kind
• Added Atom::properties; Frame::properties; and Residue::properties to allow iteration over all the properties in an Atom/Frame/Residue.

Changes in supported formats

• Added MarcoMolecule Transmission Format (MMTF) support, reading via mmtf-cpp.
• Added Structure-Data File (SDF) support, reading and writing.
• Added Cambridge Structure Search and Retrieval (CSSR) support, reading and writing.
• LAMMPS Data format now support triclinic unit cells.

C API changes

• Added chfl_residue_get_property and chfl_residue_set_property to provide access to residue properties.
• chfl_frame_guess_topology was renamed to chfl_frame_guess_bonds.
• Function accessing atoms/cell/residue/topology inside a frame/topology no longer make a copy. This allows for direct reading and writing inside the containing frame/topology.
• Added chfl_trajectory_path to get the file path used to create a trajectory
• Added chfl_{atom,frame,residue}_properties_count and chfl_{atom,frame,residue}_list_properties to list all properties in an Atom/Frame/Residue
• Replaced chfl_*_free by an unique chfl_free function

0.8 (14 Dec 2017)

New features

• Change the license to the 3-clauses BSD license.
• Chemfiles will now read configuration files (by default in .chemfilesrc), and use the configuration data to rename atomic types to make sure they match element names. The chemfiles::add_configuration function can be used to add additional configuration files.
• Reading a Frame (with Trajectory::read or Trajectory::read_step) will now set the frame step.
• The Atom faillible methods (atomic_number, vdw_radius, covalent_radius and full_name) returns optional<T> instead of T.
• Functions taking an atomic index parameter can now throw OutOfBounds errors if the index is out of bounds.
• Topology::append is now called Topology::add_atom
• Topology::natoms and Frame::natoms are now called Topology::size and Frame::size
• Topology::residue is now called Topology::residue_for_atom
• Added Frame::distance, Frame::angle, Frame::dihedral and Frame::out_of_plane to get geometric information on the system, accounting for periodic boundary conditions.
• Added a Property class to store arbitrary properties in Frame and Atom.
• Added support for improper dihedral angles in Topology.
• chemfiles::add_configuration and chemfiles::set_warning_callback are now thread safe, and will block upon concurrent usage.
• UnitCell::matricial is renamed to UnitCell::matrix.
• The UnitCell::shape setter is renamed to UnitCell::set_shape.
• The Trajectory::close function can be used to close a trajectory and synchronize any buffered content with the storage.
• Some of the topology functions are now accsible directly on the frame: Frame::add_bond, Frame::remove_bond, Frame::clear_bonds, Frame::add_residue and operator[]. The non const version of Frame::topology is removed.

Changes in supported formats

• Amber NetCDF format is now activated by default, by embedding the netcdf library in chemfiles.
• Added LAMMPS Data format, reading and writing LAMMPS data files.
• Added Tinker format, reading and writing Tinker XYZ file format.
• Added MOL2 format, reading mol2 files using VMD molfiles plugin.
• Added Molden format, reading molden files using VMD molfiles plugin.

C API changes

• Added chfl_add_configuration to add more configuration files.
• Renamed chfl_vector_t to chfl_vector3d, chfl_match_t to cfl_match; and chfl_cell_shape_t to chfl_cellshape.
• chfl_atom_atomic_number, chfl_atom_vdw_radius and chfl_atom_covalent_radius all returns 0 instead of -1 if the atom does not have a known value for this property. This allow chfl_atom_atomic_number to take a uint64_t* parameter instead of an int64_t*, following all the other functions in the C API.
• Added CHFL_OUT_OF_BOUNDS and CHFL_PROPERTY_ERROR variants to chfl_status
• Added chfl_frame_distance, chfl_frame_angle, chfl_frame_dihedral, chfl_frame_out_of_plane and chfl_cell_wrap to work with periodic boundary conditions.
• chfl_residue does not take the optional residue id as parameter, instead you should use chfl_residue_with_id.
• Added chfl_residue_atoms to get the list of atoms in a residue.
• Added chfl_topology_impropers and chfl_topology_impropers_count functions.
• Added CHFL_PROPERTY and related functions.
• chfl_add_configuration and chfl_set_warning_callback are now thread safe, and will block upon concurrent usage.
• Added chfl_frame_add_bond, chfl_frame_remove_bond, and chfl_frame_add_residue.

Deprecation and removals

• Topology::isbond, Topology::isangle, Topology::isdihedral, and the corresponding C functions chfl_topology_isbond, chfl_topology_isangle chfl_topology_isdihedral are removed.

0.7 (25 Feb 2017)

New features

• Add a public Residue class to C++ and C API to represent residue data. Residues are groups of atoms bonded together, which may or may not correspond to molecules; and are often used for bio-molecules.
• Add the resname and resid selector, to select atoms based on their residue.
• Account for the difference between the atom name ("H1") and atom type ("H") in some formats (PDB, TNG, ...). This introduces the Atom::type member function and the chfl_atom_type C API function.
• Add the type selector, to select atoms based on their type.
• Add "Frame::add_atom" function to add an atom and the corresponding position (and velocity) data to a frame, and the C API chfl_frame_add_atom function.
• Rename UnitCell::type to UnitCell::shape. This also affect chfl_cell_shape_t, chfl_cell_shape, and chfl_cell_set_shape.
• All the floating point data uses doubles instead of floats. This concerns atomic data, positions and velocities.
• Add "Selection::string" function and the corresponding chfl_selection_string to get the string used to build a selection.
• Selection variables uses the #3 syntax instead of the $3 syntax to allow passing selection string as shell arguments.
• Add Frame::remove and chfl_frame_remove to remove an atom in a frame.
• Allow to use chemfiles with Cmake find_package.

Changes in supported formats

• Add read support for TNG files, an new portable and compressed binary format used by GROMACS.

C API changes

• All the integers at C boundary have a fixed size, most of the time using uint64_t.
• Add missing chfl_topology_resize function to C API.
• C API functions taking three lengths/angles now take a double[3] parameter instead.
• Rename chfl_topology_are_linked to chfl_topology_residues_linked.
• Rename chfl_topology_append to chfl_topology_add_atom.
• Remove chfl_strerror, as it is redundant with chfl_last_error.
• Merge chfl_trajectory_set_topology_file and chfl_trajectory_set_topology_with_format into chfl_trajectory_topology_file.
• The chfl_frame function no longer take the frame size as argument. It always creates an empty frame, that you can resize using chfl_frame_resize.
• chfl_selection_evalutate was a typo, it is renamed to chfl_selection_evaluate.

Deprecation and removals

• Remove the Atom::type enum from C and C++ API.
• Remove the Trajectory::sync and the chfl_trajectory_sync functions. To ensure that all content of a file is written to the disk, the user need to close it.
• Remove the Logger and all the chfl_log* functions. Instead, the users can use chemfiles::set_warning_callback or chfl_set_warning_callback to set a global callback to call on warnings events.

0.6 (1 July 2016)

• 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.

0.5 (19 Feb 2016)

• The C API now provide a direct view into the positions and velocities arrays. This remove the need for copy and separated getter (chfl_frame_{position,velocities}) and setter (chfl_frame_{position,velocities}_set) function. This also force usage of chfl_frame_add_velocities to add velocity data to a frame, and chfl_frame_resize to change the size of the frame.
• Add constants for error codes in C API. The following macro are defined: CHFL_SUCCESS, CHFL_MEMORY_ERROR, CHFL_FILE_ERROR, CHFL_FORMAT_ERROR, CHFL_GENERIC_ERROR, CHFL_CXX_ERROR.
• Add the chfl_version function in C API.
• Add a small selection language a la VMD, allowing to select atoms matching a selection string like "name H and x > 4". This is exposed to C++ with the public Selection class, and to C with the chfl_frame_selection function.
• Remove the periodicity handling from UnitCell. It was not implemented in boundaries conditions. The corresponding function where removed from the C API.
• Rename all setter function from void xxx(const XXX& value) to void set_xxx(const XXX& value) in C++ API.
• It is now possible to provide a callback for logging from the C API. The chfl_log_stdout, chfl_log_silent and chfl_log_callback function where added to the C API.

0.4 (30 Oct 2015)

• Chemharp can now be compiled as a static library! This should allow for easier embedding in external code, and easier distribution of binaries.
• Add a chemfiles::Trajectory::sync method to sync any buffered operation with the disk. The chfl_trajectory_sync function exposes it to the C API.
• Add a Rust binding
• Rewrite the Python binding to use ctypes. The same code can be used with Python 2 & 3, and with all numpy versions.
• Easier Python and Julia binding installation, using conda binary packaging.
• All the bindings now live on their own repository: - Fortran - Python - Julia - Rust
• The library is now continuously tested on Visual Studio
• Various bug fixes and code improvements
• Renamed the library to Chemfiles.

0.3 (3 Aug 2015)

• Julia binding
• Initial Windows support, with both MSVC and mingw
• Add a binary frontend called chrp, implementing some analysis algorithms. For more information, see the specific repository.

0.2 (31 May 2015)

• Add basic geometrical operations on vectors and implement basic periodic boundaries condition with the UnitCell::wrap function;
• Use VMD Molfiles plugins as a format provider to read trajectories. The following formats are added through Molfiles:
  • PDB;
  • GROMACS gro;
  • GROMACS xtc;
  • GROMACS trj;
  • GROMACS trr;
  • CHARMM dcd;

0.1 (16 May 2015)

Initial release. See the documentation for the full API.

Chemharp is usable from four languages:

• C++;
• C;
• Fortran;
• Python;

The following formats are supported:

• XYZ;
• AMBER NetCDF;