Releases | Open Source Science

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)

- Rust
Published by douweschulte over 1 year ago

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

- Rust
Published by douweschulte over 2 years ago

Added remove_models_except and remove_models_except_first (Thanks to OWisset) (#103)
Improved some errors generated by pdbtbx
Fixed panic (#102)

- Rust
Published by douweschulte about 3 years ago

- Rust
Published by douweschulte over 3 years ago

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)

- Rust
Published by douweschulte almost 4 years ago

- Rust
Published by douweschulte almost 4 years ago

- Rust
Published by douweschulte about 4 years ago

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.

- Rust
Published by douweschulte over 4 years ago

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.

- Rust
Published by douweschulte over 4 years ago

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

- Rust
Published by douweschulte about 5 years ago

- Rust
Published by douweschulte about 5 years ago

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)

- Rust
Published by douweschulte about 5 years ago

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

- Rust
Published by douweschulte about 5 years ago

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

- Rust
Published by douweschulte about 5 years ago

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

- Rust
Published by douweschulte about 5 years ago