Crate lib3dmol

Lib3Dmol

Lib3Dmol is a library to parser, filter, create, edit and convert molecules in PDB format. It provide functions to filter atoms according to text pattern matching, compute distances between structures and sub-structures. A file is represented as a [Structure] You can create a [Structure] by parsing with [read_pdb] function. Then you can add filters on your Structure. And save it with write_pdb function.

Examples

use lib3dmol::parser;

fn main() {
    let my_structure = parser::read_pdb("tests/tests_file/f2.pdb", "Protein f2");

    println!(
        "Structure name: {}
Number of chain: {}
Number of residue: {}
Number of atom: {}",
        my_structure.name,
        my_structure.get_chain_number(),
        my_structure.get_residue_number(),
        my_structure.get_atom_number()
    );

    // Now we will extract the backbone

    let backbone = my_structure.select_atoms("backbone").unwrap();

    println!(
        "Number of chain: {}
Number of residue: {}
Number of atom: {}",
        backbone.get_chain_number(),
        backbone.get_residue_number(),
        backbone.get_atom_number()
    );
}

Modules

build

Build molecules according to a set of existing molecules. This can be Amino Acid, Nucleid Acid or Lipid. Used to test functions or to build examples. It return a [Structure] containing the molecule. This cannot be used to create entire protein or entire structure. Just for small molecules.

parser

Functions to parse files or text and create [Structure]

structures

tools

Various functions to compute distances, apply modifications on structures, extract sequences, …

writer