changelog.md

Changelog

All versions are properly annotated on github so there the source code for each version can be retrieved.

v0.12.0

• 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

• Added support for zipped (.gz) files (Thanks to OWisset)
• Does not automatically convert chain names to uppercase anymore (Thanks to OWisset)

v0.10.2

• 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

• Added more amino acids for is_amino_acid
• Implemented Display for StrictnessLevel

v0.10.0 'Enumerated Elements'

• 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

• 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

• 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'

• 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'

• 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'

• 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

v0.6.3

• Added Anisotropic temperature factor support for mmCIF files
• Fixed an issue in the aniso matrix
• Added a full_sort function on PDB
• Fixed small bugs in the PDB saving logic

v0.6.2

• Fixed a bug in PDB b factor and occupancy validation which showed an error when the value was 0.00
• Fixed a bug in atom.atomic_radius(), it used to give the radius of the previous atom in the periodic table
• Added more atomic radii (vanderwaals and covalent bonds)

v0.6.1

• Fixed a bug arbitrarily constraining the maximum value of atom serial numbers in PDB files

v0.6.0 'Hetero atoms remastered'

• Reworked the library to handle Hetero atoms as normal atoms (with the atom.hetero() function returning true) instead of saving them in model.hetero_chains()
• Implemented the standard traits (Clone/PartialEq/Eq/PartialOrd/Ord) for most structures
• Fixed conformers in pdb.renumber() they were disregarded before
• The symmetry structure now also accepts and provides Hall symbols
• Fixed multiple bugs
• Added many more unit tests and started tracking test coverage

v0.5.1

• Fixed bugs in .remove_empty to work better with hetero chains
• Added support for negative residue sequence numbers
• Standardised the precision of floating points in the mmCIF output, at least 1 and at most 5 decimals will be shown
• Fixed an issue with the occupancy of atoms shared between multiple conformers, it will now add up to the original value

v0.5.0 'Alternative location support'

• Added Conformer which sits between Residue and Atom and is analogous to atom_group in cctbx
• Added editing functions for Conformers
• Added HEADER identifier support for parsing PDB and saving PDB and mmCIF
• Reverted mmCIF output atom_site column ordering to v0.3.3, the newly introduced ordering gave issues with Phenix
• Added remove_empty functions on all structs, to remove all empty layers after large scale deletions

v0.4.1

• All string based properties for atom/residue/chain are trimmed and converted to uppercase before being set
• A .extend function is provided for residue/chain/model/pdb to easily add an iterator to the list of children

v0.4.0 'basic mmCIF support'

• Added mmCIF/PDBx open support
• Changed open and save to determine the filetype based on the extension
• Added validate_pdb to validate a PDB model before saving it in a PDB file
• Added support for bigger serial numbers and names to allow for bigger models to be saved in mmCIF files
• Fixed some issues with mmCIF output

v0.3.3

• Added very basic exporting to mmCIF, it will only export the unit cell, symmetry and atomic data.

v0.3.2

• Added saving of DBREF/SEQADV/SEQRES
• Generates default matrices for SCALE and ORIGX if not available and the strictness level on save is Strict
• Added constructor scale to TransformationMatrix to have a magnifying matrix with 3 different factors

v0.3.1

• Added distance_wrapping and overlaps_wrapping functions to Atom which wrap around the unit cell to find the shortest distance

v0.3.0 'Primary Sequence Support'

• Added support for parsing and validating DBREF/SEQADV/SEQRES/MODRES
• Added saving of MODRES records, the other primary structure sections will follow soon
• Added differential saving, which changes the output based on the StrictnessLevel provided
• Redefined overlaps function on Atoms, the calculation was faulty before
• Added distance function between two Atoms
• Removed renumber on save

v0.2.1

• Exported save_raw was created in v0.2.0 but not accessible
• Added ENDMDL records after model definitions while saving making saved ensemble files valid in other software
• Extended warnings for validation of ensemble files, it will now generate a LooseWarning if HETATMs do not correspond
• Changed the implementation of the .remove_*_by functions to be 75% faster

v0.2.0

• Made add_child methods for model/chain/residue public.
• Extended saving it now validates and renumbers the given PDB. It fails upon generation of validation errors, while the user can specify the error levels to allow
• Added save_raw to save to a BufWriter. This function is called save_raw.
• Extended parser error generation and handling. It now fails upon generation of errors, while the user can specify the error levels to allow
• Added parser from BufReader. This function is called parse and the function previously called parse is renamed to open.
• Rewrote pdb.total_*_count() as the previous version was inaccurate
• Saved 21.4 MB in the published crate by ignoring certain files (thanks Byron!)

v0.1.5

• Finally fixed the full bug encountered in v0.1.3

v0.1.4 (yanked)

• Fixed a bug in which strings that are too short cause setter functions of various character based properties of atoms/residues/chains to panic

v0.1.3 (yanked)

• Fixed a mistake witch prevented valid characters from being used to set various character based properties of atoms/residues/chains

v0.1.2

• Added .join() on PDB.
• Added atomic data lookup (number & radius) on Atoms
• Added .overlaps() function to Atom, which uses the atomic radius to determine if two atoms overlap
• Added support for the MASTER PDB Record both while reading and saving
• Fixed the behaviour of .join() on Model/Chain/Residue

v0.1.1

Textual changes to documentation

v0.1.0

Initial release

• Basic PDB parsing, editing and saving functionality