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Releases: douweschulte/pdbtbx

v0.12.0

14 Oct 15:24
9691575
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  • Added unified file read logic, see ReadOptions (Thanks to y1zhou and OWisset)
    • This deprecates the original read functions open_gz (still around for ease of updating) and open_raw (fully removed in this update)
  • Added unique_conformer_names for a PDB (Thanks to rvhonorato)
  • Added chains_in_contact for a PDB (Thanks to rvhonorato)

v0.11.0

01 Sep 19:28
6c9a1af
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  • Added support for zipped (.gz) files (Thanks to OWisset)
  • Does not automatically convert chain names to uppercase anymore (Thanks to OWisset)

v0.10.2

23 May 21:25
9c42f4b
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  • Added remove_models_except and remove_models_except_first (Thanks to OWisset) (#103)
  • Improved some errors generated by pdbtbx
  • Fixed panic (#102)

v0.10.1

04 Dec 21:22
780cc59
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  • Added more amino acids for is_amino_acid
  • Implemented Display for StrictnessLevel

v0.10.0 Enumerated Elements

13 Aug 09:47
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  • Moved from string based elements to enums see Element, this means that the Atom::set_element, Atom::element, and Term::element have changed
  • Deprecated the following functions Atom::atom_number, Atom::atomic_radius, Atom::covalent_bond_radii,
    and Atom::vanderwaals_radius the radius functions are replaced with Element::atomic_radius which contains
    all these measures in the struct AtomicRadius
  • Added Element::weight and Element::electro_negativity data
  • Implemented Extend for all levels in the PDB hierarchy
  • Implemented FromIterator for the PDB struct
  • Removed requirement for atom_site.pdbx_formal_charge, atom_site.group_PDB, atom_site.occupancy, and atom_site.B_iso_or_equiv for mmCIF files (thanks to #93)
  • Added support for SCALE, ORIGX, and MTRIX in mmCIF files (open and save)
  • Fixed ignoring some of the auth_* series of mmCIF columns, by giving them precedence over the label_* columns in seq_id and asym_id (thanks to #95)
  • Fixed remark-type-number 400 missing from the valid number list (thanks to #96)
  • Fixed a small bug in saving MtriX records (thanks to #96)

v0.9.2

20 Jun 15:54
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  • Added open_mmcif_raw
  • Fixed a bug in atom parsing (#92)
  • Removed below precision errors in validation
  • Changed many functions to accept AsRef<str> instead of &str
  • Marked all applicable functions as const

v0.9.1

29 Mar 13:32
eb86778
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  • Added more search terms
  • Added angle and dihedral angle calculations on atoms (Thanks to DocKDE)
  • Added extra examples (Thanks to DocKDE)
  • Added support for DBREF1/2
  • Improved PDB parsing performance (Thanks to DocKDE)
  • Improved error message styling and merged common errors
  • Additional code and documentation improvements

v0.9.0 Structured search

25 Jan 13:27
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  • Added find method on all levels in the PDB, this should allow for human friendly atom(s) searching.
    pdb.find(Term::ConformerName("ALA".to_string()) + Term::AtomName("CA".to_string()))
  • Added bounding_box to the PDB struct.
  • Added atom.overlaps_bound() which uses covalent bond radii instead of unbound radii. (Thanks to raised issue)
  • Extended atomic_number to take the first character of the name if this is one of "CHONS" and the element is unset and the name is not an element name.
  • Updated covalent bond radii to work in Å as well (was picometers).
  • Respecified the dependencies versions to allow cargo to more often reuse dependencies in complex projects.

v0.8.0 All the hierarchy

18 Nov 17:30
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  • Added support for residue serial numbers over 9999 and atom serial numbers over 99999 for PDB files. (Thanks to DocKDE)
  • Changed argument type of save_pdb from PDB to &PDB. (Thanks to DocKDE)
  • Allow lack of chain name in PDB files. (Thanks to DocKDE)
  • Added mutable structs to extend the use of AtomWithHierarchy alongside a refactor which created a struct for every hierarchy level. See the docs for more information.
  • Removed Atom.pos_array() and moved the rstar::rtree to use (f64, f64, f64) instead of [f64; 3]. This was made possible by the adoption of tuples as points in rstar.

v0.7.0 Ecosystem integration

14 May 09:39
0a6c3a5
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  • Added parallel iterators based on Rayon (Thanks to DocKDE)
  • Added support for generating r*trees from Rstar, this has to be opted in by using the feature rstar
  • Added support for serialization using Serde, this has to be opted in using the feature serde
  • Added a new struct AtomWithHierarchy to have access to the containing layers of an atom in an easy way and added functions to generate and work with this struct
  • Added binary_find_atom to all hierarchies to find atoms in less time
  • Added more names for amino acids and backbone atoms (Thanks to DocKDE)
  • Added support for bonds (can only read Disulfide bonds from PDBs for now)
  • And many more small fixes and docs updates