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0.6.5
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@wojdyr wojdyr released this 17 Feb 13:40
· 227 commits to master since this release
v0.6.5
e471b13

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.

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