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douweschulte
A library to open/edit/save (crystallographic) Protein Data Bank (PDB) and mmCIF files in Rust.
In mmCIF, every atom is addressable in two ways: - As a tuple (`label_asym_id`, `label_seq_id`) e.g. ('A', 1) - As a tuple (`auth_asym_id`, `auth_seq_id`, `pdbx_PDB_ins_code`) e.g. ('A', -1, 'X') mmCIF...
Fixes #80. The bonds are now implemented using `Arc`, meaning they behave in the way I envisioned them to be. The major problem before merging this into the main branch...
If you create a hierarchy you could potentially delete the selected lower levels from a higher level. For example you select (Model(0), Chain("A"), Residue(123), Conformer("ALA"), Atom("CA", 450, "C")) and then...
When creating a `Vec` from a string, `s.chars().collect()` is the standard practice. The `.chars()` method works on any UTF-8 encoded string and it takes time to find the boundary for...
Update the image and the planning based on the following link. https://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html
Bonds are currently partly supported, only disulfide bonds are read from PDBs. The main issue is in the implementation design. Currently the bonds are saved as a list of bond...
MMTF is a more compact and easier to parse (apperently) file format for molecular structures. See https://mmtf.rcsb.org/ for more details. Also there already is a (WIP) crate to parse these...
I have developed a Rust port of the C library, freesasa, which performs protein surface area calculations. I want to know if you think that this can be incorporated into...
I've been working with some AFDB structures, and most of them have very long REMARK lines. I had a look in the PDB spec, and couldn't see if there was...
PDB files are relatively poor in quality, generally speaking, and it isn't uncommon for PDB files to raise errors during parsing. Notably, I have seen that quite a few PDB...
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A library to open/edit/save (crystallographic) Protein Data Bank (PDB) and mmCIF files in Rust.