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0.6.4
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@wojdyr wojdyr released this 13 Dec 16:20
· 417 commits to master since this release
v0.6.4
84b5803

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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