Dmitry Roshchin
9115e963dc
add a package for the GEMMI library to the openSUSE:Science project OBS-URL: https://build.opensuse.org/request/show/1199917 OBS-URL: https://build.opensuse.org/package/show/science/gemmi?expand=0&rev=1
197 lines
9.6 KiB
Plaintext
197 lines
9.6 KiB
Plaintext
-------------------------------------------------------------------
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Tue Sep 10 15:16:27 UTC 2024 - Friedrich Haubensak <hsk17@mail.de>
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- update to version 0.6.7, primarily a bug-fix release:
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* enhancements:
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- new subcommand "gemmi set" for changing coordinates,
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B-factors and occupancies in coordinate files
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- improved anisotropic scaling of structure factors
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* fixes:
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- fixed reading of mmCIF files without _atom_site.auth_seq_id
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- fixed a couple of bugs in Topology preparation
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- fixed re-assignment of ATOM/HETATM record types
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- fixed gemmi convert --sifts-num for UniProt seq numbers >5000
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* various minor changes
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- patches dropped as fixed upstream: gemmi-0.6.6-numpy2.patch,
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gemmi-soversion.patch
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-------------------------------------------------------------------
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Fri Jun 28 13:52:51 UTC 2024 - Friedrich Haubensak <hsk17@mail.de>
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- add gemmi-0.6.6-numpy2.patch from upstream to fix tests w/ numpy2
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-------------------------------------------------------------------
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Tue Jun 11 14:52:21 UTC 2024 - Atri Bhattacharya <badshah400@gmail.com>
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- Add gemmi-soversion.patch: Add shared object versioning
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[gh#project-gemmi/gemmi#320].
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- Split out shared library in keeping with shlib packaging policy.
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- Build and run tests.
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- Build python modules for multiple python flavours in separate
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directories.
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- Drop unnecessary hashbangs from example scripts not installed to
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executable path.
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-------------------------------------------------------------------
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Mon Jun 10 19:41:47 UTC 2024 - Friedrich Haubensak <hsk17@mail.de>
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- package static library only, as upstream does not (yet ?) use
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.so-versioning for shared library
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-------------------------------------------------------------------
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Mon Jun 10 19:16:38 UTC 2024 - Friedrich Haubensak <hsk17@mail.de>
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- to silence rpmlint wrt the examples, insert and fix python shebangs
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and fix permissions
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-------------------------------------------------------------------
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Sun Jun 2 19:52:51 UTC 2024 - Friedrich Haubensak <hsk17@mail.de>
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- update to version 0.6.6
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* Library:
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- SmallStructure: changed how the space group is read and accessed.
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- Relying on H-M space group names alone was not always sufficient.
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The new mechanism uses the list of operations and Hall symbol in
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preference to the H-M symbol – the order is configurable.
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- symmetry triplets: parse decimal fractions (small molecule files
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may use notation such as x+0.25 instead of x+1/4)
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- tabulated space groups: a few more settings: B 1 2 1, B 1 21 1,
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F 1 m 1, F 1 d 1, F 1 2 1
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- X-ray scattering coefficients: changed the default value of
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IT92::ignore_charge to true (i.e. charges are now ignored by
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default; before version 0.6.3 they were always ignored)
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- cif::Table: added method ensure_loop() that converts tag-value
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pairs into a loop; might be needed before calling append_row()
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- place_hydrogens(): fix for NH3-like configurations
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- improved gemmi->mmdb conversion
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- Grid: tweaked good_grid_size() to ensure that when creating a grid
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up to a certain d_min, all reflections up to d_min are in the grid
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(it matters when no oversampling is applied)
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- DensityCalculator: deprecated function set_grid_cell_and_spacegroup(),
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use grid.setup_from()
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- fixed TNT-compatible reciprocal space ASU calculation for
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non-standard settings
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- infer_polymer_end(): complicate the heuristic even more, to detect
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files that have HETATM incorrectly used for standard residues in a
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polymer (such files were reported, they are either a result of
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mutating from non-standard residues, or a buggy program)
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- added function assign_het_flags() to re-set ATOM/HETATM flags
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- Model: added funtions calculate_b_iso_range() and
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calculate_b_aniso_range(); the first one can be used to detect if
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pLDDT is in the range 0-100 (like from AlphaFold) or 0-1 (like
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from ESMFold)
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- writing mmCIF: write _entity_poly_seq.hetero
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- added flag Entity::reflects_microhetero that shows if sequences
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were read from SEQRES (and don't account for point mutations) or
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from _entity_poly_seq; new function add_microhetero_to_sequences()
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changes the former to the latter
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* Program:
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- gemmi sfcalc: added a few more options
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- gemmi convert: added options --assign-records[=A|H],
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improved --sifts-num, adding microheterogeneities to _entity_poly_seq
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when converting from PDB
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- gemmi cifdiff: added option -t for basic comparison of values for
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a single tag
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* Other:
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- minimal WebAssembly port (C++ code compiled with emscripten) of
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Structure, as a proof-of-concept and for reading mmCIF files in
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UglyMol
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- examples/to_rdkit.py: example of conversion of gemmi ChemCom
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to RDKit Mol
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-------------------------------------------------------------------
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Wed Feb 21 18:34:37 UTC 2024 - Friedrich Haubensak <hsk17@mail.de>
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- update to version 0.6.5
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* Library
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- gemmi can now be built with zlib-ng, a faster fork of zlib (good
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for working with large, compressed files)
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- experimental: binary serialization of Structure (contained objects,
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such as Model, Chain or UnitCell, can also be serialized separately)
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- finalized handling of 5-character monomer names; uses the
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tilde-hetnam extension (ABCDE ↔ ~DE) for PDB files
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- when atom names in the coordinate file match previous names
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(_chem_comp_atom.alt_atom_id) from the monomer library (the names
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in the CCD and therefore also in the ML change occasionally), print
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better diagnostic; added function MonLib::update_old_atom_names()
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to update the names in a Structure
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- topology: fixed handling of two bonds between the same two residues
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- options for handling mmCIF files with incorrect entities (modified
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add_entity_ids() when called with overwrite=true)
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- added function Intensities::prepare_merged_mtz()
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- a few bug fixes (for instance, in handling of negative residue
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numbers in the selection syntax)
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* Python bindings
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- generating type stubs - see #293
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- python: cif.Loop.val() has been replaced with __getitem__/__setitem__
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- fixed Mtz.Batch.ints and Mtz.Batch.floats
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* Program
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- subcommand diff has been renamed to cifdiff
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- subcommand prep has been renamed to crd
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- validate: more options for checking monomer files
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- gemmi-grep: added option --extended-regexp
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- mtz2cif: added column names Iplus/Iminus (used by ccp4i2) to the
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default conversion spec
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-------------------------------------------------------------------
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Fri Dec 29 16:37:21 UTC 2023 - Friedrich Haubensak <hsk17@mail.de>
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- update to version 0.6.4
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* Library
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- completely changed build system for Python module, from setuptools
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to scikit-build-core
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- optimized electron density calculation: single-precision version
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is now about 2x faster and slightly less exact; some other
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grid-based calculations also got optimized in the process
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- as part of the above optimizations, some of the grid computations
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require that the model is in the standard orientation (conventional
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axis directions); in other cases (which are very rare after the
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remediation of non-standard coordinate frames in the PDB) call
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standardize_crystal_frame()
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- CIF output: more flexible formatting
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- mmCIF writing: category _entity_poly is included by default,
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with pdbx_strand_id and pdbx_seq_one_letter_code
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- minor changes in reading mmCIF coordinate files
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- cif: added functions Loop::add_columns(), Loop::remove_column(),
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Column::erase()
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- MRC map format: ORIGIN record is ignored (previously, if ORIGIN was
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non-zero, Ccp4::full_cell() returned false and some map properties
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were not set)
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- new function Grid::symmetrize_avg()
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- fixed bug in ReciprocalGrid::prepare_asu_data()
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- added function read_pir_or_fasta() for reading sequences (previously
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it was undocumented and more limited)
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- added function pdbx_one_letter_code() which returns a string like
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AA(MSE)H…, for _entity_poly.pdbx_seq_one_letter_code
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- new functions expand_one_letter() and expand_one_letter_sequence()
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that take ResidueKind.AA/RNA/DNA as argument replaced
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expand_protein_one_letter*()
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- adjusted weights in align_sequence_to_polymer()
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- added function assign_best_sequences()
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- PDB reading: added Structure::ter_status flag to indicate if TER
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records were: absent, present, clearly in wrong places
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- experimental (not documented yet) new functions: Model::get_cra(),
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Model::get_parent_of()
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- Topo::Bond stores a flag for bonds between different symmetry images
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- ChemComp::Atom: store _chem_comp_atom.alt_atom_id as old_id,
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use it in new function update_old_atom_names()
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- riding hydrogens: added H had wrong occupancy in special, rare cases
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- added Vec3f – Vec3 with single-precision numbers
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- minor API changes: Binner::setup() doesn't return anything,
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changed argument types of Scaling::scale_data(), align_sequences()
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* Program
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- new tool gemmi-diff that compares categories and tags in two
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(mm)CIF files
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- gemmi-align prints vertical list with option --verbose
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- gemmi-residues has new options: -e, -sss, --chains
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- gemmi-rmsz: added option --missing to print missing atoms
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- gemmi-validate: more options for validating monomer files
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- gemmi-h: more options
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- gemmi-mtz: prints info about SYMM records
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-------------------------------------------------------------------
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Sun Nov 26 19:39:56 UTC 2023 - Friedrich Haubensak <hsk17@mail.de>
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- Initial package release at version 0.6.3
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