Change Log

1.6.0 - 2023-12-14

• RPM packages for RMF for RedHat Linux (and clones such as Alma or Rocky) and for Fedora are now provided by the COPR project.
• RMF::decorator::Chain can now store a per-chain sequence offset and UniProt accession. The offset, which defaults to zero, maps from the sequence index (which always starts at 1) to the residue index (which may not).

1.5.1 - 2023-06-08

• Any String or Strings attributes containing filesystem paths are now rewritten when the RMF static frame is cloned (e.g. during rmf_slice or rmf_cat) so that they are relative to the new file, not the old one. This relies on the convention that path attributes have names ending in "filename" or "filenames".
• Bugfix: particles without Cartesian coordinates are now handled correctly by the get_all_global_coordinates() Python function.
• Bugfix: relative paths should now be set correctly when the path to the RMF file itself contains one or more '..' components.

1.5.0 - 2023-03-22

• Windows builds now require MS Visual Studio 2015 or later (for full C++11 support). The following macros for pre-C++11 environments are no longer needed and are deprecated: RMF_NOEXCEPT, RMF_CANEXCEPT.
• All RMF binaries now report the full version (including micro version) when the –version flag is used (e.g. "1.4.1", not "1.4").
• If built with NumPy, some Python-specific functions are now provided to allow direct access to RMF data via NumPy arrays.
• File handles can now be explicitly closed (via a close method). Most IO operations on a closed handle will now raise an error. In Python file handles now support the context manager protocol so can be used in 'with' blocks.

1.4.1 - 2022-11-21

• Build fixes to work with SWIG 4.1.
• Various internal build scripts now use 'python3' rather than unversioned 'python'.

1.4 - 2022-03-10

• RMF now requires a C++11 compiler and SWIG 3 (or later) to build. Most recent compilers should support C++11, such as gcc, clang or MS Visual Studio 2012 or later. Various macro and header workarounds for pre-C++11 environments are thus no longer needed and are deprecated: RMF_FINAL, RMF_OVERRIDE, and RMF_FOREACH.
• Build fixes for latest log4cxx, in C++17 mode, or with newer versions of gcc.

1.3.1 - 2021-12-01

• Various build fixes for newer versions of gcc and clang.
• Build fixes for Fedora 33 or later.
• Add support for Python 3.10.
• Minor documentation improvements.

1.3 - 2021-04-21

• All RMF binaries now support the –version flag, and the RMF library itself is versioned.

1.2 - 2021-04-19

• A new category of decorators 'provenance' allows information about how the structure was generated to be added to the file.
• The new RMF::decorator::Reference decorator allows for a node to mark another node as its reference.
• The new RMF::decorator::ExplicitResolution decorator allows attaching an explicitly-set resolution to a node. (This allows such values from IMP to be accurately stored in the file.)

1.1 - 2014-03-07

• To be more consistent, RMF::decorator::Domain and RMF::decorator::Fragment had their access methods modified to include residue in the name.
• A Pymol plugin was added
• RMF now uses the new avro-based format with the .rmf suffix, you should use this and .rmfz as your suffixes.
• RMF::decorator::Bond and RMF::decorator::BondConst now return RMF::NodeHandle and RMF::NodeConstHandle instead of ints.
• RMF::decorator::Representation and RMF::decorator::RepresentationConst now return RMF::NodeHandles and RMF::NodeConstHandles instead of ints.
• RMF::decorator::Domain takes two ints in its set method rather than a list
• RMF::NodeConstHandle::get_index() went away as it was a duplicate of RMF::NodeConstHandle::get_id()
• RMF::NodeType and RMF::FrameType were replaced with RMF::Enum instances. This increases type safety in python and makes converting to and from strings easier (you can now use str() in python).
• RMF::decorator::Residue::get_residue_index() and RMF::decorator::Residue::get_residue_type() replace the versions without residue in the name
• Decorators and factories have been moved into the RMF::decorator namespace in C++.
• You can now only either create a new RMF or open an existing one read only. Most backends only supported those two anyway.
• Managing of data buffers has been revamped and wrapped in the RMF::BufferHandle class which tracks a shared buffer.
• You now get keys by passing the appropriate traits object instead of having the type in the function name: eg f.get_key(cat, "name", RMF.IntTraits())
• Appropriate decorators now return RMF::Vector3, RMF::Vector4 or RMF::Vector3s instead of RMF::Floats or RMF::FloatsList.
• There are now static and non-static versions of the decorators.
• You now have to explicitly add a frame or set the current frame before manipulating frame data.
• RMF::NodeConstHandle::get_value() subsumes get_value_always() which was removed. If there is no value, then either a RMF::Nullable for which RMF::Nullable::get_is_null() is true is returned (C++) or None is returned (python).
• RMF::FileHandle::get_node_from_id() was renamed to RMF::FileHandle::get_node()
• Various methods that took ints to identify frames now expect RMF::FrameID.
• A VMD plugin was added