0.6.7

This is primarily a bug-fix release. New Python bindings are not included yet.

Enhancements:

• New subcommand gemmi set for changing coordinates, B-factors and occupancies in coordinate files (mmCIF and PDB). Unlike other tools, it replaces numbers while leaving the rest of the file intact. An alternative to CCP4 PDBSET keywords: BFACTOR, OCCUPANCY, SHIFT, NOISE. Note that gemmi convert offers overlapping capabilities. For instance, gemmi convert --apply-symop=x+0.123,y,z shifts the coordinates similarly to gemmi set --shift='9.3 0 0' (the latter takes the shift in Angstroms).

• Improved anisotropic scaling of structure factors. More work is planned in this area.

Fixes:

• fixed reading of mmCIF files without _atom_site.auth_seq_id
• in Topology preparation: fixed a couple of bugs, peptide links are now assumed to be CIS for ω=0±60° (previously, ω=0±30°)
• fixed re-assignment of ATOM/HETATM record types (gemmi convert --assign-records)
• fixed gemmi convert --sifts-num for UniProt sequence numbers >5000

And various minor changes that are hard to describe concisely.

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 ChemComp to RDKit Mol

and a number of less important changes

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

Note: this list is meant to show important changes only.

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

0.6.3

• new: normalization of amplitudes using so-called "Karle" approach, similar as in the CCP4 program ECALC
• added X-ray scattering coefficients for ions (previously, the charge of atom was ignored)
• pdb: reading CONECT records, and an option to also write them
• when reading pdb, if any chain has 2+ TER records, all TER records are ignored
• more configuration options for writing pdb files
• added functions Mtz::expand_to_p1() and Mtz::read_file_gz()
• cif::Block::find_value(tag) now returns also value from the corresponding loop if that loop has only one row
• changes in gemmi-validate related to validation with DDL2
• gemmi-sfcalc: added option --sigma-cutoff
• gemmi sf2map --mapmask: if the unit cells in coordinate file is different than in SF file, use only the latter
• improved transform_to_assembly(), expand_ncs() and rename_chain()
• cif2mtz: Mtz column for pdbx_DELPHWT has now label PHDELWT (#272)
• fixed ensure_asu(): phase-shift (for phases and H-L coefficients) was wrong
• fixed UnitCell::find_nearest_image() for non-crystals with NCS
• fixed DensityCalculator::requested_grid_spacing()
• changes and enhancements in add_chemcomp_to_block(), in solvent masking, in mtz2cif,
  and in several other places
• added python bindings to MtzToCif, cif::Ddl, PdbWriteOptions, changed how options for PDB writing are passed, more bindings for Mtz::Batch

0.6.2

• a number of fixes, mostly in topology preparation
• support for extended (longer) CCD and PDB codes that are about to be introduced by the PDB
• gemmi-convert: added option to rename a monomer
• a few changes and additions in cif2mtz, including:
  • anomalous data written as separate rows for F+ and F- is now converted as expected
  • _refln.F_squared_meas is now a synonym for F_squared_meas
• gemmi-grep: new option --only-tags
• gemmi-validate: a couple of new checks and options
• pdb and mmCIF: convert MODRES <-> _pdbx_struct_mod_residue
• cif.Block: blocks with no name (just data_) used to have the name set to "#", now it's " "

0.6.1

• changed how CISPEP is stored: previously, it was assumed that a link between two residues is either TRANS or CIS; if the residues have atoms with alternative conformations, both link types can be present at the same time
• riding hydrogens: previously, hydrogens had the same altlocs as the parent atom; now if the parent atom has a single conformation, but it has neighbors in multiple conformations, the hydrogens will be also added in multiple conformations
• major changes in NearestNeighbor: now it's possible to search atoms not only in the first nearest cells, but in any number of nearest cells; find_nearest_atom() was changed to find, by default, a nearest atom within any distance
• changes in Mtz.reindex(), primarily to fix determination of the new space group
• gemmi-convert: added option --all-auth to write _atom_site.auth_atom_id and auth_comp_id, which are skipped by default (because they are always the same as label_…_id)
• added more options to gemmi-rmsz, gemmi-xds2mtz, gemmi-cif2mtz
• fix a recent regression in check_polymer_type(): RNA was returned instead of DNA
• improved heuristic of detecting where the polymer ends (if TER record is missing)
• selection syntax: fix parsing a single sequence id such as "A/208" (it was parsed as A/208-/)
• removed SMat33::calculate_eigenvector() – use eigen_decomposition() instead; SoftwareItem::pdbx_ordinal; NeighborSearch::Mark::x,y,z (use ::pos)
• more code was moved from headers to src/*.cpp

0.6.0

• C++ library is no longer header-only, several function were moved from headers to src/ to make compilation faster
• major changes in cmake build, requiring now cmake 3.15+
• improvements in calculating riding hydrogen positions
• changed again the scheme of automatically assigned subchain names (A-p -> Axp, because PDB software can't handle non-alphanumeric characters there)
• a function for calculating polarization correction for XDS INTEGRATE.HKL
• improvements in xds2mtz, converting more data and filling more records in MTZ batch headers
• added SpaceGroup::change_of_hand_op()
• various bug fixes and small improvements

0.5.8

• gemmi program has new subcommand xds2mtz that converts from XDS_ASCII to multirecord MTZ
• subcommand gemmi-residues has new option -s (--short) for shorter overview of model chains (can be used twice)
• cif2mtz: more flexible spec for converting symbols to numbers
• preparation of Refmac intermediate files – it can be used to substitute a part of Refmac
• MonLib and Topo: a number of changes related to reading a monomer library and in prepare_topology()
• changed the scheme of automatically assigned subchain names (Apoly -> A-p)
• read_structure(): added optional arg save_doc that stores cif.Document if the read file is mmCIF or mmJSON
• reading PDB files: more metadata is read by default
• writing mmCIF files: _atom_site.group_PDB is written by default
• support for mmCIF extension _atom_site.ccp4_deuterium_fraction
• added function copy_from_mmdb(mmdb::Manager* manager) -> Structure
• improved check_polymer_type()
• Grid::set_size_from_spacing() with different rounding modes
• rename src/ to prog/; in the next version the library won't be fully header-only, cpp files will go into src/

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)