File gemmi.changes of Package gemmi
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Tue Sep 10 15:16:27 UTC 2024 - Friedrich Haubensak <hsk17@mail.de>
- update to version 0.6.7, primarily a bug-fix release:
* enhancements:
- new subcommand "gemmi set" for changing coordinates,
B-factors and occupancies in coordinate files
- improved anisotropic scaling of structure factors
* fixes:
- fixed reading of mmCIF files without _atom_site.auth_seq_id
- fixed a couple of bugs in Topology preparation
- fixed re-assignment of ATOM/HETATM record types
- fixed gemmi convert --sifts-num for UniProt seq numbers >5000
* various minor changes
- patches dropped as fixed upstream: gemmi-0.6.6-numpy2.patch,
gemmi-soversion.patch
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Fri Jun 28 13:52:51 UTC 2024 - Friedrich Haubensak <hsk17@mail.de>
- add gemmi-0.6.6-numpy2.patch from upstream to fix tests w/ numpy2
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Tue Jun 11 14:52:21 UTC 2024 - Atri Bhattacharya <badshah400@gmail.com>
- Add gemmi-soversion.patch: Add shared object versioning
[gh#project-gemmi/gemmi#320].
- Split out shared library in keeping with shlib packaging policy.
- Build and run tests.
- Build python modules for multiple python flavours in separate
directories.
- Drop unnecessary hashbangs from example scripts not installed to
executable path.
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Mon Jun 10 19:41:47 UTC 2024 - Friedrich Haubensak <hsk17@mail.de>
- package static library only, as upstream does not (yet ?) use
.so-versioning for shared library
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Mon Jun 10 19:16:38 UTC 2024 - Friedrich Haubensak <hsk17@mail.de>
- to silence rpmlint wrt the examples, insert and fix python shebangs
and fix permissions
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Sun Jun 2 19:52:51 UTC 2024 - Friedrich Haubensak <hsk17@mail.de>
- update to version 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 ChemCom
to RDKit Mol
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Wed Feb 21 18:34:37 UTC 2024 - Friedrich Haubensak <hsk17@mail.de>
- update to version 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
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Fri Dec 29 16:37:21 UTC 2023 - Friedrich Haubensak <hsk17@mail.de>
- update to version 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
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Sun Nov 26 19:39:56 UTC 2023 - Friedrich Haubensak <hsk17@mail.de>
- Initial package release at version 0.6.3
