Changelog for libgemmi_cpp0-0.6.7-2.2.x86_64.rpm :

* Tue Sep 10 2024 Friedrich Haubensak - update to version 0.6.7, primarily a bug-fix release:
* enhancements: - new subcommand \"gemmi set\" for changing coordinates, B-factors and occupancies in coordinate files - improved anisotropic scaling of structure factors
* fixes: - fixed reading of mmCIF files without _atom_site.auth_seq_id - fixed a couple of bugs in Topology preparation - fixed re-assignment of ATOM/HETATM record types - fixed gemmi convert --sifts-num for UniProt seq numbers >5000
* various minor changes - patches dropped as fixed upstream: gemmi-0.6.6-numpy2.patch, gemmi-soversion.patch
* Fri Jun 28 2024 Friedrich Haubensak - add gemmi-0.6.6-numpy2.patch from upstream to fix tests w/ numpy2
* Tue Jun 11 2024 Atri Bhattacharya - Add gemmi-soversion.patch: Add shared object versioning [gh#project-gemmi/gemmi#320].- Split out shared library in keeping with shlib packaging policy.- Build and run tests.- Build python modules for multiple python flavours in separate directories.- Drop unnecessary hashbangs from example scripts not installed to executable path.
* Mon Jun 10 2024 Friedrich Haubensak - package static library only, as upstream does not (yet ?) use .so-versioning for shared library
* Mon Jun 10 2024 Friedrich Haubensak - to silence rpmlint wrt the examples, insert and fix python shebangs and fix permissions
* Sun Jun 02 2024 Friedrich Haubensak - update to version 0.6.6
* Library: - SmallStructure: changed how the space group is read and accessed. - Relying on H-M space group names alone was not always sufficient. The new mechanism uses the list of operations and Hall symbol in preference to the H-M symbol – the order is configurable. - symmetry triplets: parse decimal fractions (small molecule files may use notation such as x+0.25 instead of x+1/4) - tabulated space groups: a few more settings: B 1 2 1, B 1 21 1, F 1 m 1, F 1 d 1, F 1 2 1 - X-ray scattering coefficients: changed the default value of IT92::ignore_charge to true (i.e. charges are now ignored by default; before version 0.6.3 they were always ignored) - cif::Table: added method ensure_loop() that converts tag-value pairs into a loop; might be needed before calling append_row() - place_hydrogens(): fix for NH3-like configurations - improved gemmi->mmdb conversion - Grid: tweaked good_grid_size() to ensure that when creating a grid up to a certain d_min, all reflections up to d_min are in the grid (it matters when no oversampling is applied) - DensityCalculator: deprecated function set_grid_cell_and_spacegroup(), use grid.setup_from() - fixed TNT-compatible reciprocal space ASU calculation for non-standard settings - infer_polymer_end(): complicate the heuristic even more, to detect files that have HETATM incorrectly used for standard residues in a polymer (such files were reported, they are either a result of mutating from non-standard residues, or a buggy program) - added function assign_het_flags() to re-set ATOM/HETATM flags - Model: added funtions calculate_b_iso_range() and calculate_b_aniso_range(); the first one can be used to detect if pLDDT is in the range 0-100 (like from AlphaFold) or 0-1 (like from ESMFold) - writing mmCIF: write _entity_poly_seq.hetero - added flag Entity::reflects_microhetero that shows if sequences were read from SEQRES (and don\'t account for point mutations) or from _entity_poly_seq; new function add_microhetero_to_sequences() changes the former to the latter
* Program: - gemmi sfcalc: added a few more options - gemmi convert: added options --assign-records[=A|H], improved --sifts-num, adding microheterogeneities to _entity_poly_seq when converting from PDB - gemmi cifdiff: added option -t for basic comparison of values for a single tag
* Other: - minimal WebAssembly port (C++ code compiled with emscripten) of Structure, as a proof-of-concept and for reading mmCIF files in UglyMol - examples/to_rdkit.py: example of conversion of gemmi ChemCom to RDKit Mol
* Wed Feb 21 2024 Friedrich Haubensak - update to version 0.6.5
* Library - gemmi can now be built with zlib-ng, a faster fork of zlib (good for working with large, compressed files) - experimental: binary serialization of Structure (contained objects, such as Model, Chain or UnitCell, can also be serialized separately) - finalized handling of 5-character monomer names; uses the tilde-hetnam extension (ABCDE ↔ ~DE) for PDB files - when atom names in the coordinate file match previous names (_chem_comp_atom.alt_atom_id) from the monomer library (the names in the CCD and therefore also in the ML change occasionally), print better diagnostic; added function MonLib::update_old_atom_names() to update the names in a Structure - topology: fixed handling of two bonds between the same two residues - options for handling mmCIF files with incorrect entities (modified add_entity_ids() when called with overwrite=true) - added function Intensities::prepare_merged_mtz() - a few bug fixes (for instance, in handling of negative residue numbers in the selection syntax)
* Python bindings - generating type stubs - see #293 - python: cif.Loop.val() has been replaced with __getitem__/__setitem__ - fixed Mtz.Batch.ints and Mtz.Batch.floats
* Program - subcommand diff has been renamed to cifdiff - subcommand prep has been renamed to crd - validate: more options for checking monomer files - gemmi-grep: added option --extended-regexp - mtz2cif: added column names Iplus/Iminus (used by ccp4i2) to the default conversion spec
* Fri Dec 29 2023 Friedrich Haubensak - update to version 0.6.4
* Library - completely changed build system for Python module, from setuptools to scikit-build-core - optimized electron density calculation: single-precision version is now about 2x faster and slightly less exact; some other grid-based calculations also got optimized in the process - as part of the above optimizations, some of the grid computations require that the model is in the standard orientation (conventional axis directions); in other cases (which are very rare after the remediation of non-standard coordinate frames in the PDB) call standardize_crystal_frame() - CIF output: more flexible formatting - mmCIF writing: category _entity_poly is included by default, with pdbx_strand_id and pdbx_seq_one_letter_code - minor changes in reading mmCIF coordinate files - cif: added functions Loop::add_columns(), Loop::remove_column(), Column::erase() - MRC map format: ORIGIN record is ignored (previously, if ORIGIN was non-zero, Ccp4::full_cell() returned false and some map properties were not set) - new function Grid::symmetrize_avg() - fixed bug in ReciprocalGrid::prepare_asu_data() - added function read_pir_or_fasta() for reading sequences (previously it was undocumented and more limited) - added function pdbx_one_letter_code() which returns a string like AA(MSE)H…, for _entity_poly.pdbx_seq_one_letter_code - new functions expand_one_letter() and expand_one_letter_sequence() that take ResidueKind.AA/RNA/DNA as argument replaced expand_protein_one_letter
*() - adjusted weights in align_sequence_to_polymer() - added function assign_best_sequences() - PDB reading: added Structure::ter_status flag to indicate if TER records were: absent, present, clearly in wrong places - experimental (not documented yet) new functions: Model::get_cra(), Model::get_parent_of() - Topo::Bond stores a flag for bonds between different symmetry images - ChemComp::Atom: store _chem_comp_atom.alt_atom_id as old_id, use it in new function update_old_atom_names() - riding hydrogens: added H had wrong occupancy in special, rare cases - added Vec3f – Vec3 with single-precision numbers - minor API changes: Binner::setup() doesn\'t return anything, changed argument types of Scaling::scale_data(), align_sequences()
* Program - new tool gemmi-diff that compares categories and tags in two (mm)CIF files - gemmi-align prints vertical list with option --verbose - gemmi-residues has new options: -e, -sss, --chains - gemmi-rmsz: added option --missing to print missing atoms - gemmi-validate: more options for validating monomer files - gemmi-h: more options - gemmi-mtz: prints info about SYMM records
* Sun Nov 26 2023 Friedrich Haubensak - Initial package release at version 0.6.3