Crate coordgen

source ·
Expand description

coordgen-rs

A thin wrapper around coordgen.

This exposes a pair of functions that interface with libcoordgen to generate 2D coordinates for a molecule given its connectivity. The purpose of this crate is to simply generate the coordinates, it does not perform any drawing functionality on its own.

Requires CMake version 3.2 or later, a Boost installation, a c++ compiler supporting c++11. These requirements are inherited from the original project. This will not compile on windows.

This crate is not endorsed or supported by the original authors of coordgen.

Molecular Graphs

Molecular graphs can be represented a few different ways. This crate adopts an opinionated definition where molecular graphs are undirected simple graphs with atomic numbers as node labels and bond multiplicities as edge labels.

Implementation

This implementation defines a simple wrapper function with a C-like interface that is essentially a modified version of the example in the coordgen repository. This wrapper does not allow for any configuration.

Versioning

crate versioncoordgen version
^0.1.02.0.3

Example

// this corresponds to an equivalent to the example in
// https://github.com/schrodinger/coordgenlibs/blob/master/example_dir/example.cpp

// the molecule has a carbon (idx 0) and a nitrogen (idx 1)
let atoms = vec![6u8, 7];
// it has one single bond connecting the two atoms with 
let bonds = vec![[0u16, 1, 1]];

let coords = coordgen::gen_coords(&atoms, &bonds).unwrap();
assert_eq!(coords, vec![(-50.0, 0.0), (0.0, 0.0)])

Enums

  • Error
    A pre-condition violation that may cause undefined behavior when generating coordinates.

Functions