Add assembly index calculations using reduction to clique

Cargo.toml

@@ -31,3 +31,7 @@ crate-type = ["rlib","cdylib"]
 name = "benchmark"
 harness = false
 
+[[bench]]
+name = "search_benchmark"
+harness = false
+

benches/search_benchmark.rs

@@ -0,0 +1,70 @@
+use bit_set::BitSet;
+use criterion::{criterion_group, criterion_main, Criterion};
+use std::time::Duration;
+use std::{ffi::OsStr, time::Instant};
+use std::fs;
+use std::path::Path;
+
+use assembly_theory::{
+    assembly::{clique_index_search_bench, Kernel, Bound},
+    loader,
+    molecule::Molecule,
+};
+
+pub fn reference_datasets(c: &mut Criterion) {
+    // Define a new criterion benchmark group of dataset benchmarks.
+    let mut group = c.benchmark_group("reference_datasets");
+
+    // Define datasets, bounds, and labels.
+    let datasets = ["gdb13_1201", "gdb17_200", "coconut_55"];
+    let bounds = [
+        Bound::IntChain,
+    ];
+    let kernel = Kernel::Never;
+
+    // Loop over all datasets of interest.
+    for dataset in datasets.iter() {
+        // Load all molecules from the given dataset.
+        let paths = fs::read_dir(Path::new("data").join(dataset)).unwrap();
+        let mut mol_list: Vec<Molecule> = Vec::new();
+        for path in paths {
+            let name = path.unwrap().path();
+            if name.extension().and_then(OsStr::to_str) != Some("mol") {
+                continue;
+            }
+            mol_list.push(
+                loader::parse_molfile_str(
+                    &fs::read_to_string(name.clone())
+                        .expect(&format!("Could not read file {name:?}")),
+                )
+                .expect(&format!("Failed to parse {name:?}")),
+            );
+        }
+
+        group.bench_function(*dataset, move |b| {
+            b.iter_custom(|iters| {
+                    let mut total = Duration::new(0, 0);
+                    for _ in 0..iters {
+                        for mol in mol_list.iter() {
+                            let matches: Vec<(BitSet, BitSet)> = mol.matches().collect();
+                            let start = Instant::now();
+                            clique_index_search_bench(mol, matches, &bounds, kernel);
+                            total += start.elapsed()
+                        }
+                    }
+
+                    total
+                },
+            );
+        });
+    }
+
+    group.finish();
+}
+
+criterion_group! {
+    name = benchmark;
+    config = Criterion::default().sample_size(10);
+    targets = reference_datasets
+}
+criterion_main!(benchmark);