Function index_search

pub fn index_search(
    mol: &Molecule,
    enumerate_mode: EnumerateMode,
    canonize_mode: CanonizeMode,
    parallel_mode: ParallelMode,
    memoize_mode: MemoizeMode,
    kernel_mode: KernelMode,
    bounds: &[Bound],
) -> (u32, u32, usize)

Compute a molecule’s assembly index and related information using a top-down recursive algorithm, parameterized by the specified options.

See EnumerateMode, CanonizeMode, ParallelMode, KernelMode, and Bound for details on how to customize the algorithm. Notably, bounds are applied in the order they appear in the bounds slice. It is generally better to provide bounds that are quick to compute first.

The results returned are:

• The molecule’s u32 assembly index.
• The molecule’s u32 number of non-overlapping isomorphic subgraph pairs.
• The usize total number of assembly states searched, where an assembly state is a collection of fragments. Note that, depending on the algorithm parameters used, some states may be searched/counted multiple times.

Example

use assembly_theory::{
    assembly::{index_search, ParallelMode},
    bounds::Bound,
    canonize::CanonizeMode,
    enumerate::EnumerateMode,
    kernels::KernelMode,
    loader::parse_molfile_str,
    memoize::MemoizeMode,
};

// Load a molecule from a .mol file.
let path = PathBuf::from(format!("./data/checks/anthracene.mol"));
let molfile = fs::read_to_string(path)?;
let anthracene = parse_molfile_str(&molfile).expect("Parsing failure.");

// Compute the molecule's assembly index without parallelism, memoization,
// kernelization, or bounds.
let (slow_index, _, _) = index_search(
    &anthracene,
    EnumerateMode::GrowErode,
    CanonizeMode::TreeNauty,
    ParallelMode::None,
    MemoizeMode::None,
    KernelMode::None,
    &[],
);

// Compute the molecule's assembly index with parallelism, memoization, and
// some bounds.
let (fast_index, _, _) = index_search(
    &anthracene,
    EnumerateMode::GrowErode,
    CanonizeMode::TreeNauty,
    ParallelMode::DepthOne,
    MemoizeMode::CanonIndex,
    KernelMode::None,
    &[Bound::Log, Bound::Int],
);

assert_eq!(slow_index, 6);
assert_eq!(fast_index, 6);