project-gemmi/gemmi (gemmi)
### [`v0.6.5`](https://togithub.com/project-gemmi/gemmi/releases/tag/v0.6.5): 0.6.5
[Compare Source](https://togithub.com/project-gemmi/gemmi/compare/v0.6.4...v0.6.5)
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](https://togithub.com/project-gemmi/gemmi/issues/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.
Configuration
📅 Schedule: Branch creation - At any time (no schedule defined), Automerge - At any time (no schedule defined).
🚦 Automerge: Disabled by config. Please merge this manually once you are satisfied.
â™» Rebasing: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox.
🔕 Ignore: Close this PR and you won't be reminded about this update again.
[ ] If you want to rebase/retry this PR, check this box
This PR has been generated by Mend Renovate. View repository job log here.
This PR contains the following updates:
>=0.5.5, <=0.6.4->>=0.5.5, <=0.6.5Release Notes
project-gemmi/gemmi (gemmi)
### [`v0.6.5`](https://togithub.com/project-gemmi/gemmi/releases/tag/v0.6.5): 0.6.5 [Compare Source](https://togithub.com/project-gemmi/gemmi/compare/v0.6.4...v0.6.5) 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](https://togithub.com/project-gemmi/gemmi/issues/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.Configuration
📅 Schedule: Branch creation - At any time (no schedule defined), Automerge - At any time (no schedule defined).
🚦 Automerge: Disabled by config. Please merge this manually once you are satisfied.
â™» Rebasing: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox.
🔕 Ignore: Close this PR and you won't be reminded about this update again.
This PR has been generated by Mend Renovate. View repository job log here.