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)

Deprecation and removals

• Remove support for configuration files (chemfiles.toml) and associated functions.

New features

• properties are now sorted, and iterating over properties will always yield them sorted by the associated key.
• added chemfiles::guess_format and chfl_guess_format to get the format chemfiles would use for a given file based on its filename
• Added read support for GROMACS TPR format.

Changes in supported formats

• Added read and write support for Amber Restart (.ncrst) files.
• Added native read and write support for LAMMPS trajectory (.lammpstrj) files, replacing the VMD molfile implementation.
• Added read support for PSF files using VMD molfile plugin.
• Amber NetCDF files are now read/written with a custom netcdf parser (#443)
• TRR and XTC files are now read/written with a custom XDR files parser (#451)
• DCD files are now read/written with a custom parser (#453)
• Support TPR files up to version 2023 without a warning. Files from future versions are tried to be read but emit a warning
• Improved reading speed of XTC files by implementing a decoding routine proposed by libxtc

Changes to the C++ API

• Per-atom properties are optional, i.e. Atom::properties returns an optional property map.

0.10.0 (14 Feb 2021)

Changes in supported formats

• Added read and write support for CIF format.
• Added read and write support for extended XYZ. The XYZ format now default to extended output, and read extended files. Extended XYZ allow storing unit cell and arbitrary atomic properties.

New features

• Added ability to read and write files directly in-memory. See Trajectory::memory_reader; Trajectory::memory_writer; Trajectory::memory_buffer; chfl_trajectory_memory_reader; chfl_trajectory_memory_writer and chfl_trajectory_memory_buffer.
• Added support for appending to gzip (.gz) compressed trajectories.
• Added support for sub-selection in numerical functions, for example distance(#1, name O).
• Changed the UnitCell representation to the full cell matrix instead of a/b/c/alpha/beta/gamma
• Added chemfiles::formats_list function to get a list of formats and associated metadata.

Changes to the C API

• Added missing chfl_frame_clear_bonds and chfl_topology_clear_bonds.
• Added chfl_cell_from_matrix and changed parameters to chfl_cell, removed chfl_cell_triclinic.
• Added chfl_formats_list function to get a list of formats and associated metadata.

0.9.3 (5 Feb 2020)

• Fix a bug in the PDB format where no atomic name/type was read from short ATOM/HETATM records.
• Fix a few bugs related to UnitCell Matrix and infinite UnitCell construction

0.9.2 (18 Dec 2019)

• 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 evaluation time by a huge margin.

Changes in supported formats

• Added read and write support for CML (Chemical Markup Language) files, a XML based format.
• Added a native implementation of XTC and TRR formats, replacing the VMD molfile version. The new code supports reading and writing files, should be faster and use less memory.
• Remove the ability to read frames from a trajectory that was opened in append mode. This mode is now write only.
• Added support for bzip2 (.bz2) compressed files when reading and writing

0.9.1 (13 Mar 2019)

• 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.

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.

Changes to the C API

• 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.

Changes to the C API

• 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.

Changes to the C API

• 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;