assembly-theory 0.6.1

Open, reproducible calculation of assembly indices
Documentation 
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//! Kernelize match-compatibility graphs to improve top-down search efficiency.
//!
//! The problem of computing the minimum assembly index of a molecule can be
//! reduced to finding the maximum weight clique in a compatibility graph over
//! matches (i.e., pairs of edge-disjoint isomorphic subgraphs). Strucutral
//! properties of this graph can be used to determine match pairs (i.e., nodes)
//! that *definitely will* or *definitely won't* be used in an optimal
//! solution. We call the process of identifying these nodes *kernelization*.
//! Uses the strategies of neighborhood removal, isolated vertex removal, and
//! domination as described in Section 5.2 of [Lamm et al.
//! (2019)](https://doi.org/10.1137/1.9781611975499.12). (Note that they solve
//! the equivalent problem of weighted independent set.)

use clap::ValueEnum;

/// Graph kernelization strategy when searching using the clique reduction.
#[derive(Debug, Copy, Clone, PartialEq, Eq, PartialOrd, Ord, ValueEnum)]
pub enum KernelMode {
    /// Do not apply any kernelizations.
    None,
    /// Apply kernels only after the initial construction of the compatibility
    /// graph.
    Once,
    /// Apply kernels after the initial construction of the compability graph
    /// and again after any fragmentations of the full molecule.
    DepthOne,
    /// Apply kernels after every fragmentation step.
    Always,
}