Bump gemmi from 0.6.3 to 0.6.6 in the pip-version group

[dependabot]

Bumps the pip-version group with 1 update: gemmi.

Updates gemmi from 0.6.3 to 0.6.6

Release notes

Sourced from gemmi's releases.

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 ChemComp to RDKit Mol

and a number of less important changes

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

... (truncated)

Commits

• 0b23c06 change version to 0.6.6
• d224ddf update serialize.hpp
• c14f3f1 add missing #include
• 77150a9 rename function from the previous commit
• e69466d fileutil.hpp: change deleter of fileptr_t
• 61fc1c8 avoid floating point == comparisons in static_assert
• 0186acb add cif::Table::ensure_loop()
• 64b6554 fix the previous commit
• afd2f48 DensityCalculator::set_refmac_compatible_blur(): add option allow_negative
• f3c57ea scaling: trying to estimate b_star before actual optimization
• Additional commits viewable in compare view

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[janbridley]

Dependabot is once again unable to resolve the correct versions for Python 3.6. I will revisit at a later date

[dependabot]

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