Update dependency gemmi to >=0.5.5, <=0.6.4

[renovate]

This PR contains the following updates:

Package	Change	Age	Adoption	Passing	Confidence
gemmi	>=0.5.5, <=0.6.3 -> >=0.5.5, <=0.6.4

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Release Notes

project-gemmi/gemmi (gemmi)

v0.6.4: 0.6.4

Compare Source

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

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[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (0e2f5e2) 92.39% compared to head (e6d9fa9) 92.39%.
Report is 3 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #236   +/-   ##
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  Coverage   92.39%   92.39%           
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  Files          37       37           
  Lines        2434     2434           
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  Hits         2249     2249           
  Misses        185      185           

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