libcifpp/changelog

Version 10.0.4
- Fixed find_by_value in the index of a category,
  avoid swapping columns in the search keys

Version 10.0.3
- Clear pdbx_nonpoly_scheme before filling it in reconstruction
- Changed handling of numbers with a preceding plus character,
  these are now stored as strings to avoid inadvertently
  mutilating phone numbers.

Version 10.0.2
- Fixed regression in reconstruction introduced in 10.0.1
- Fixed symmetry operations
- Added validation for pdbx_item_enumeration as well as
  case-sensitive checks for enumerations when needed.

Version 10.0.1
- Fixed some regressions, like assigning to items.
- At emplace time (in category) values that are
  in the wrong type according to a dictionary
  will be converted/casted. May fail of course.

Version 10.0.0
- Major rewrite of the internal storage of values.
  Used to be strings only, now there are several
  basic types.
- Modernised code and cleaned up warnings using lint
  tools

Version 9.0.6
- Various small fixes
Version 10.0.0
- Added a SQLite interface.

Version 9.0.5
- Added exists to compound_factory
- Added sub_matrix, fix and extend determinant calculation
- Added yet another structure::create_non_poly
- Remove revision.hpp file in make clean (new VersionString.cmake)

Version 9.0.4
- Fix various stopping and reconstruction errors

Version 9.0.3
- Reconstruction fixed when some entity ids are missing

Version 9.0.2
- Fix code that reconstructs sequences, could throw a map::at
- Many optimisations in validation and reconstruction code.

Version 9.0.1
- Use pcre2 from pkg-config if available, if not
  build a version from the original code.

Version 9.0.0
- Rename fields of cif::mm::polymer to match the naming
  in mmcif_pdbx.dic. Also, related, fix building mm::structure
  using the correct mapping between atom_site and residues.
- _atom_site.auth_alt_id does not exist, it should be
  _atom_site.pdbx_auth_alt_id of course.
- Added a more lightweight fixup for mmcif_pdbx files
  that lack certain categories.

Version 8.0.1
- Fix cif::mm::structure::cleanup_empty_categories, removed too much
- Add default value for B_iso_or_equiv in residue::create_new_atom
- Reconstruct some branch records in bare pdbx files
- Fix parsing PDB files (bug due to missing validator in dest. cat.)
- Do not fail conversion of PDB files when compound info is missing

Version 8.0.0
- A dictionary is for a datablock and a file can have
  datablocks with differing dictionaries.

Version 7.0.10
- Deal with missing _entity.type in reconstructing mmCIF files
- Replace code creating quaternions from rotation matrices
  that might sometimes give incorrect results. Or at least,
  the test code failed on this particular kind of code. Sometimes.
- Fix reconstruction to build pdbx_nonpoly_scheme

Version 7.0.9
- Using cif::file::load_dictionary it is now possible to
  load a dictionary along with its extensions in one go.
  E.g. file.load_dictionary("mmcif_pdbx;dssp-extension")
- Fix in compound factory to avoid errors with lower case
  compound id's
- Fix sac_parser's index to be case insensitive

Version 7.0.8
- Fix PDB Remark 3 parser
- Added three way comparison for point

Version 7.0.7
- Set CIFPP_DATA_DIR on target cifpp for use in projects that include
  libcifpp directly

Version 7.0.6
- Fix linking to std::atomic

Version 7.0.5
- Fix case where category index was not updated for updated value

Version 7.0.4
- Do not install headers and library in case we're not the top project

Version 7.0.3
- Fix installation, write exports.hpp again

Version 7.0.2
- Fix in testing error_code results.

Version 7.0.1
- Various reconstruction fixes
- category order in output fixed
- better implementation of constructors for file, datablock and category
- small optimisation in iterator

Version 7.0.0
- Renaming many methods and parameters to be more
  consistent with the mmCIF dictionaries.
  (Most notably, item used to be called column or
  tag sometimes).
- validation_error is now a std::system_error error
  value. The exception is gone.
- Added repairSequenceInfo to repair invalid files

Version 6.1.0
- Add formula weight to entity in pdb2cif
- Change order of categories inside a datablock to match order in file
- Change default order to write out categories in a file based on
  parent/child relationship
- Added validate_pdbx and recover_pdbx
- Fixed a serious bug in category_index when moving categories

Version 6.0.0
- Drop the use of CCP4's monomer library for compound information

Version 5.2.5
- Correctly import the Eigen3 library

Version 5.2.4
- Changes required to build on Windows

Version 5.2.3
- New constructors for cif::item, one taking std::optional values
  and another taking only a name resulting in a value '.' (i.e. inapplicable).
- added cif::cell::get_volume

Version 5.2.2
- Remove dependency on Eigen3 for users of libcifpp
- Fix typos in documentation
- Do not build latex files in documentation
- Fixed conversion from string to integer, would fail on +2 e.g.
- sqrt is not constexpr, thus kGoldenRatio should be const, not constexpr

Version 5.2.1
- New versionstring module
- small fixes for generating documentation
- correctly setting SONAME

Version 5.2.0
- With lots of documentation
- Refactored coloured text output
- Removed the subdirectory cif++/pdb, there now is a single
  header file pdb.hpp for I/O of legacy PDB files.

Version 5.1.3
- Dropped pkgconfig support

Version 5.1.2
- New version string code
- Added check for Eigen3 in cifppConfig.cmake

Version 5.1.1
- Added missing include <compare> in symmetry.hpp
- Added empty() to matrix
- Fix for parsing legacy PDB files with a last line that does
  not end with a new line character.

Version 5.1
- New parser, optimised for speed
- Fix in unique ID generator

Version 5.0.10
- Fix in progress_bar, was using too much CPU
- Optimised mmCIF parser

Version 5.0.9
- Fix in dihedral angle calculations
- Added create_water to model
- Writing twin domain info in PDB files and more PDB fixes
- remove_atom improved (remove struct_conn records)
- Added a specialisation for category::find1<std::optional>
- fix memory leak in category

Version 5.0.8
- implemented find_first, find_min, find_max and count in category
- find1 now throws an exception if condition does not not exactly match one row
- Change in writing out PDB files, now looking up the original auth_seq_num
  via the pdbx_xxx_scheme categories based on the atom_site.auth_seq_num ->
  pdbx_xxx_scheme.pdb_seq_num relationship.
- fix memory leak in category

Version 5.0.7.1
- Use the implementation from zeep for std::experimental::is_detected

Version 5.0.7
- Reintroduce exports file. For DLL's

Version 5.0.6
- Fix file::contains, using iequals
- Fix is_cis

Version 5.0.5
- Fix code to work on 32 bit machines

Version 5.0.4
- Revert removal of CIFPP_SHARE_DIR export

Version 5.0.3
- Fix installation of libcifpp into the correct locations

Version 5.0.2
- Fix export of CISPEP records in PDB format
- Better support for exporting package_source

Version 5.0.1
- Fix loading dictionaries
- Support for cifv1.0 files

Version 5.0.0
- Total rewrite of cif part
- Removed DSSP code, moved into dssp project itself

Version 4.2.1
- Improved REMARK 3 parser (for TLS in large molecules)

Version 4.2.0
- Yet another rewrite of resource loading

Version 4.1.1
- Fall back to zero charge for scattering factors if the atom
  was not found in the table.
- Improve code to locate resources, failing less.

Version 4.1.0
- Some interface changes for mmcif::Atom

Version 4.0.1
- Added a bunch of const methods to Datablock and Category.
- Changed PDB writing interface to accept Datablock instead of File.

Version 4.0.0
- getResidue in mmcif::Structure now requires both a
  sequence ID and an auth sequence ID. As a result the code was cleaned
  up considerably.

Version 3.0.5
- mmcif::Structure redesign. It is now a wrapper around a cif::Datablock.

Version 3.0.4
- Fix in mmCIF parser, now correctly handles the unquoted
  string ??

Version 3.0.3
- Better configuration checks, for atomic e.g.
- Fixed a problem introduced in refactoring mmcif::Atom
- Version string creation

Version 3.0.2
- refactored mmcif::Atom for performance reasons

Version 3.0.1
- Fixed processing of proline restraints file from CCP4, proline
  is a peptide, really.
- Added code to facilitate DSSP

Version 3.0.0
- Replaced many strings in the API with string_view for
  performance reasons.
- Upgraded mmcif::Structure
- various other small fixes

Version 2.0.5
- Backporting updated CMakeLists.txt file

Version 2.0.4
- Reverted a too strict test when reading cif files.

Version 2.0.3
- Fixed reading mmCIF files where model numbers are used and
  model number 1 is missing.

Version 2.0.2
- Added configuration flag to disable downloading CCD data during build
  Note that there are now two flags for CCD data:
  DOWNLOAD_CCD to enable downloading during build
  INSTALL_UPDATE_SCRIPT to install an update mechanism for this file
- Updated unit tests to work even if no CCD data is available

Version 2.0.1
- Fixed the generator for the symmetry operator table

Version 2.0.0
- New API interface for accessing query results
- Removed bzip2 support
- improved makefiles

Version 1.1.1
- Now with full support for MS Windows

Version 1.1.0
- Changed from GNU configure to CMake.
- Loading compound information from CCD file

Version 1.0.1
- Changed the way resources are looked up, local dir first,
  then /var/cache and finally compiled in resources (with mrc).

Version 1.0.0
- First public release