0.5.7

• new functions for working with Structure: assign_serial_numbers(), assign_cis_flags(), has_hydrogen()
• enhanced transform_to_assembly()
• functions count_atom_sites() and count_occupancies() now take Selection as an optional arg
• deprecated count_hydrogen_sites(): can be replaced with has_hydrogen() or count_atom_sites(Selection("[H,D]"))
• selection syntax extended with ";polymer" and ";solvent" (it can also be "!polymer,solvent")
• improved preparation of the intermediate file (crd) for Refmac
• gemmi program: several options were added to subprograms
• Ccp4.setup() now returns void (previously – number)
• python: cif.Block.find_pair() and Item.pair were changed to return tuple (previously – list)

0.5.6

• calculating ASU brick for given space group settings
• add reciprocal ASU definitions used by TNT
• add option style to Op.triplet()
• add cif.Block.set_pairs() – it adds name-value pairs to a given category
• various bug fixes, as usual
• Python 2.7 is no longer listed as supported

0.5.5

• determining lattice symmetry and (psuedo-)merohedral twinning laws
• added GroupOps::derive_symmorphic() and GroupOps::add_inversion()
• getting change-of-basis in the Niggli reduction
• added transform_to_assembly() – it does a bit more than make_assembly()
• removed Op::negated()
• python: add bindings to UnitCell.orth and UnitCell.frac
• additional options in gemmi-mtz2cif and gemmi-cif2mtz
• bug fixes (in Ccp4::set_extent(), merge_atoms_in_expanded_model(), status column in mtz2cif)

0.5.4

• new sub-program under development: gemmi-prep
• parse pdb AUTHOR record and corresponding mmCIF category
• new function flood_fill_above()
• mtz2cif: rhombohedral groups in hexagonal settings start with H now
• renamed MonLib::find_link() to get_link(), modified MonLib::match_link()
• CIF files can be written with left-aligned columns
• bug fixes and minor changes (in particular in class Topo)

0.5.3

• API change: changed arguments for Ccp4.setup()
• added Binner class for analyzing reflections in resolution bins
• added support for neutron scattering in gemmi-sfcalc and the library
• new functions: seitz_to_op, normalize_grid, Grid.get_subarray, Grid.set_subarray
• minor improvements in programs mtz2cif, cif2mtz, map
• fix: CIF tags are now case insensitive
• changes in preparing topology accounting for changes in Refmac and CCP4 monomer library

0.5.2

• various bug fixes and small improvements, many of them for the MTZ -> mmCIF conversion
• new and documented functions: cif.Table.move_row(), ResidueInfo.fasta_code(), GroupOps.add_missing_elements(), NeighborSearch.add_chain()
• added customizable form factors for unknown element (X) #167
• improved reading of unusual PDB files #169
• calculate_superposition(): added option to use backbone only
• calculating RMSD without superposition is a separate function now: calculate_current_rmsd()
• simplified MaskedGrid, Grid.asu() renamed to masked_asu()
• renamed Intensities.Type to DataType
• a few experimental functions (not documented and not sufficiently tested yet):
  • read_first_block_gz() – read only first block of CIF without reading the whole file
  • Mtz.ensure_asu() – changes Miller indices together with phase shifts and anomalous data swapping
  • interpolate_grid_of_aligned_model() – for grid interpolation based on model alignment (currently global alignment only, local alignment such as in PanDDA is not implemented yet)
  • check_data_type_under_symmetry() – for checking if mmCIF refln category contains mean, anomalous or unmerged data

0.5.1

• various bug fixes
• support for huge MTZ files (>2GB) using the format extension added in CCP4 8.0 – implemented by Claus
• better handling of NaNs in maps
• option to detect the format of a coordinate file (format=CoorFormat.Detect)
• major changes in class Topo (which is undocumented yet)
• store _atom_site.label_entity_id from mmCIF as Residue::entity_id
• two more tabulated space group settings: C 4 2 2 and C 4 2 21
• new functions Mtz.copy_column() and Mtz.replace_column(), SmallStructure.make_cif_block()
• and a number of minor additions including: Grid.clone(), Grid.change_values(), Model.remove_*(), transform_pos_and_adp(), MonLib.mon_lib_list, SmallStructure.wavelength, UnitCell.approx(), SMat33.multiply(), Structure.input_format
• new options in the command-line program: gemmi mtz --histogram, gemmi cif2mtz --add

0.5.0

• bug fixes
• Selling-Delaunay reduction
• gemmi program: enhancements in mtz2cif, cif2mtz and merge
• SymImage renamed to NearestImage, its properties has also changed
• calculate_superposition(): optional outlier rejection (inspired by PyMOL)

0.4.9

• centred to primitive lattce transformation
• Niggli reduction and Buerger reduction for lattice basis
• added UnitCell::is_compatible_with_spacegroup()
• Topology-related improvements (Keitaro)
• functions SMat33::elements() and change_basis() were replaced – each was replaced with two new functions
• more options in gemmi-merge
• more Python bindings
• various fixes, in particular in validation in gemmi mtz2cif --depo.

0.4.8

• reindexing MTZ files,
• tricubic map interpolation,
• extended selection syntax,
• merge_atoms_in_expanded_model() – sort out atoms on special positions after expanding NCS or making bioassembly,
• IT92::normalize() – makes exactly the same scattering coefficients that Refmac uses,
• Mtz::remove_column(),
• understanding triplets with x/N ("h/2+k/2, -h/2+k/2, l"),
• better inference of elements in a PDB file with missing element field,
• Topo::Force was renamed to Topo::Rule,
• various other additions and, most importantly, bug fixes.