Add benchmarks for indexing and searching

benches/compound_processing_benches.rs

@@ -0,0 +1,49 @@
+#![feature(test)]
+
+use cheminee::search::compound_processing::*;
+
+extern crate test;
+use rdkit::ROMol;
+use test::Bencher;
+
+#[bench]
+fn bench_process_cpd(b: &mut Bencher) {
+    let smiles1 =
+        "C[S+](CC[C@@H](C(=O)[O-])[NH3+])C[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=NC3=C(N=CN=C32)N)O)O";
+
+    b.iter(|| {
+        let _ = process_cpd(smiles1, false);
+    });
+}
+
+// running 1 test
+// test bench_process_cpd ... bench:   5,527,616.65 ns/iter (+/- 337,547.33)
+
+#[bench]
+fn bench_standardize_mol(b: &mut Bencher) {
+    let mol = ROMol::from_smiles(
+        "C[S+](CC[C@@H](C(=O)[O-])[NH3+])C[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=NC3=C(N=CN=C32)N)O)O",
+    )
+    .unwrap();
+
+    b.iter(|| {
+        let _ = standardize_mol(&mol);
+    });
+}
+
+// running 1 test
+// test bench_standardize_mol ... bench:   3,906,768.75 ns/iter (+/- 230,949.77)
+
+#[bench]
+fn bench_get_cpd_properties(b: &mut Bencher) {
+    let smiles1 =
+        "C[S+](CC[C@@H](C(=O)[O-])[NH3+])C[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=NC3=C(N=CN=C32)N)O)O";
+    let canon_taut = standardize_smiles(smiles1, false).unwrap();
+
+    b.iter(|| {
+        let _ = get_cpd_properties(&canon_taut);
+    });
+}
+
+// running 1 test
+// test bench_get_cpd_properties ... bench:   1,329,194.77 ns/iter (+/- 183,436.78)

benches/fingerprint_benches.rs

@@ -18,16 +18,31 @@ fn bench_tanimoto_distance(b: &mut Bencher) {
 }
 
 // running 1 test
-// Before: test bench_tanimoto_similarity ... bench:     132,690 ns/iter (+/- 2,681)
-// Now: test bench_tanimoto_distance ... bench:       2,653 ns/iter (+/- 790)
+// test bench_tanimoto_distance ... bench:       2,520.20 ns/iter (+/- 151.54)
 
 #[bench]
 fn bench_fingerprint_generation(b: &mut Bencher) {
-    let smiles = "[N]Cc1cncc2c(=O)c3cccc(CCC(=O)O)c3[nH]c12";
+    let smiles =
+        "C[S+](CC[C@@H](C(=O)[O-])[NH3+])C[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=NC3=C(N=CN=C32)N)O)O";
     let romol = ROMol::from_smiles(smiles).unwrap();
 
     b.iter(|| romol.fingerprint());
 }
 
 // running 1 test
-// test bench_fingerprint_generation ... bench:   1,161,160 ns/iter (+/- 274,184)
+// test bench_fingerprint_generation ... bench:     784,123.44 ns/iter (+/- 137,752.50)
+
+#[bench]
+fn bench_fingerprint_exact_match(b: &mut Bencher) {
+    let mol1 = ROMol::from_smiles(
+        "C[S+](CC[C@@H](C(=O)[O-])[NH3+])C[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=NC3=C(N=CN=C32)N)O)O",
+    )
+    .unwrap();
+    let fp1 = mol1.fingerprint();
+    let fp2 = fp1.clone();
+
+    b.iter(|| fp1.0 == fp2.0);
+}
+
+// running 1 test
+// test bench_fingerprint_exact_match ... bench:         372.45 ns/iter (+/- 30.19)

benches/indexing_benches.rs

@@ -0,0 +1,43 @@
+#![feature(test)]
+
+extern crate test;
+
+use cheminee::command_line::indexing::bulk_index::create_tantivy_doc;
+use cheminee::indexing::KNOWN_DESCRIPTORS;
+use cheminee::schema::LIBRARY;
+use serde_json::Value;
+use std::collections::HashMap;
+use tantivy::schema::Field;
+use test::Bencher;
+
+#[bench]
+fn bench_create_tantivy_doc(b: &mut Bencher) {
+    let schema = LIBRARY.get("descriptor_v1").unwrap().clone();
+    let smiles_field = schema.get_field("smiles").unwrap();
+    let fingerprint_field = schema.get_field("fingerprint").unwrap();
+    let extra_data_field = schema.get_field("extra_data").unwrap();
+    let descriptor_fields = KNOWN_DESCRIPTORS
+        .iter()
+        .map(|kd| (*kd, schema.get_field(kd).unwrap()))
+        .collect::<HashMap<&str, Field>>();
+
+    let smi =
+        "C[S+](CC[C@@H](C(=O)[O-])[NH3+])C[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=NC3=C(N=CN=C32)N)O)O";
+    let mut map = serde_json::Map::new();
+    map.insert("smiles".to_string(), Value::String(smi.to_string()));
+
+    let record: Value = Value::Object(map);
+
+    b.iter(|| {
+        let _ = create_tantivy_doc(
+            record.clone(),
+            smiles_field,
+            fingerprint_field,
+            &descriptor_fields,
+            extra_data_field,
+        );
+    });
+}
+
+// running 1 test
+// test bench_create_tantivy_doc ... bench:   6,527,306.20 ns/iter (+/- 562,411.21)

benches/scaffold_benches.rs

@@ -13,3 +13,6 @@ fn bench_scaffold_search(b: &mut Bencher) {
 
     b.iter(|| scaffold_search(&fp.0, &mol, &PARSED_SCAFFOLDS));
 }
+
+// running 1 test
+// test bench_scaffold_search ... bench:     756,170.85 ns/iter (+/- 27,301.91)

benches/structure_matching_benches.rs

@@ -0,0 +1,80 @@
+#![feature(test)]
+
+extern crate test;
+use cheminee::search::structure_matching::exact_match;
+use rdkit::{substruct_match, ROMol, SubstructMatchParameters};
+use test::Bencher;
+
+#[bench]
+fn bench_exact_match_no_chirality(b: &mut Bencher) {
+    let romol1 = ROMol::from_smiles(
+        "C[S+](CC[C@@H](C(=O)[O-])[NH3+])C[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=NC3=C(N=CN=C32)N)O)O",
+    )
+    .unwrap();
+
+    let romol2 = romol1.clone();
+
+    b.iter(|| {
+        let _ = exact_match(&romol1, &romol2, false);
+    });
+}
+
+// running 1 test
+// test bench_exact_match_no_chirality ... bench:      10,117.06 ns/iter (+/- 423.84)
+
+#[bench]
+fn bench_exact_match_yes_chirality(b: &mut Bencher) {
+    let romol1 = ROMol::from_smiles(
+        "C[S+](CC[C@@H](C(=O)[O-])[NH3+])C[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=NC3=C(N=CN=C32)N)O)O",
+    )
+    .unwrap();
+
+    let romol2 = romol1.clone();
+
+    b.iter(|| {
+        let _ = exact_match(&romol1, &romol2, true);
+    });
+}
+
+// running 1 test
+// test bench_exact_match_yes_chirality ... bench:      18,131.02 ns/iter (+/- 790.45)
+
+#[bench]
+fn bench_substructure_match_no_chirality(b: &mut Bencher) {
+    let super_mol = ROMol::from_smiles(
+        "C[S+](CC[C@@H](C(=O)[O-])[NH3+])C[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=NC3=C(N=CN=C32)N)O)O",
+    )
+    .unwrap();
+    let sub_mol =
+        ROMol::from_smiles("C[C@@H]1[C@H]([C@H]([C@@H](O1)[N]2C=NC3=C(N=CN=C23)N)O)O").unwrap();
+
+    let mut params = SubstructMatchParameters::default();
+    params.set_use_chirality(false);
+
+    b.iter(|| {
+        let _ = substruct_match(&super_mol, &sub_mol, &params);
+    });
+}
+
+// running 1 test
+// test bench_substructure_match_no_chirality ... bench:       4,209.80 ns/iter (+/- 318.14)
+
+#[bench]
+fn bench_substructure_match_yes_chirality(b: &mut Bencher) {
+    let super_mol = ROMol::from_smiles(
+        "C[S+](CC[C@@H](C(=O)[O-])[NH3+])C[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=NC3=C(N=CN=C32)N)O)O",
+    )
+    .unwrap();
+    let sub_mol =
+        ROMol::from_smiles("C[C@@H]1[C@H]([C@H]([C@@H](O1)[N]2C=NC3=C(N=CN=C23)N)O)O").unwrap();
+
+    let mut params = SubstructMatchParameters::default();
+    params.set_use_chirality(true);
+
+    b.iter(|| {
+        let _ = substruct_match(&super_mol, &sub_mol, &params);
+    });
+}
+
+// running 1 test
+// test bench_substructure_match_yes_chirality ... bench:       7,313.00 ns/iter (+/- 532.24)

src/command_line/indexing/bulk_index.rs

@@ -100,7 +100,7 @@ pub fn action(matches: &ArgMatches) -> eyre::Result<()> {
     Ok(())
 }
 
-fn create_tantivy_doc(
+pub fn create_tantivy_doc(
     record: serde_json::Value,
     smiles_field: Field,
     fingerprint_field: Field,

src/search/identity_search.rs

@@ -39,7 +39,7 @@ pub fn identity_search(
                 smiles_field,
                 fingerprint_field,
                 extra_data_field,
-                &searcher,
+                searcher,
                 &query_mol_mutex.lock().unwrap(),
                 query_fingerprint,
                 use_chirality,

src/search/structure_search.rs

@@ -68,7 +68,7 @@ pub fn structure_search(
                     smiles_field,
                     fingerprint_field,
                     extra_data_field,
-                    &searcher,
+                    searcher,
                     &query_mol_mutex.lock().unwrap(),
                     query_fingerprint,
                     method,