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bench: sdf reading bench (#598)
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@tshauck
tshauck authored Aug 6, 2024
1 parent 803d0f8 commit 3a3e4e8
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1 change: 1 addition & 0 deletions Cargo.lock
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9 changes: 9 additions & 0 deletions exon/exon-sdf/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -16,3 +16,12 @@ regex = "1"
tracing = { workspace = true }
futures = { workspace = true }
tokio = { workspace = true }


[dev-dependencies]
criterion = { version = "0.5", features = ["async_tokio"] }

[[bench]]
harness = false
name = "sdf"
path = "benches/sdf.rs"
190 changes: 190 additions & 0 deletions exon/exon-sdf/benches/sdf.rs
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@@ -0,0 +1,190 @@
// Copyright 2024 WHERE TRUE Technologies.
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.

use criterion::{criterion_group, criterion_main, BenchmarkId, Criterion};
use exon_sdf::parse_to_record;

fn bench_parse_to_record(c: &mut Criterion) {
let mut group = c.benchmark_group("sdf_parse");

let content = "
SciTegic02060916132D
50 60 0 0 0 0 999 V2000
-5.2740 4.8598 0.0000 O 0 0
-5.4300 3.6700 0.0000 C 0 0
-6.8500 3.0700 0.0000 C 0 0
-8.0800 4.0100 0.0000 C 0 0
-9.5100 3.4300 0.0000 C 0 0
-9.6700 1.7700 0.0000 C 0 0
-8.3900 0.8900 0.0000 C 0 0
-6.9800 1.4800 0.0000 C 0 0
-5.7800 0.6200 0.0000 C 0 0
-5.9171 -0.5721 0.0000 O 0 0
-4.3800 1.2000 0.0000 C 0 0
-4.2200 2.7300 0.0000 C 0 0
-2.8300 3.3500 0.0000 C 0 0
-1.5900 2.4100 0.0000 C 0 0
-1.7800 0.8500 0.0000 C 0 0
-3.1400 0.2700 0.0000 C 0 0
-2.9600 -1.2600 0.0000 N 0 0
-1.5000 -1.5300 0.0000 C 0 0
-0.7400 -2.8600 0.0000 C 0 0
-1.4800 -4.1900 0.0000 C 0 0
-2.6797 -4.2171 0.0000 O 0 0
-0.6900 -5.4700 0.0000 C 0 0
-1.4800 -6.8500 0.0000 C 0 0
-0.7400 -8.1800 0.0000 C 0 0
0.7900 -8.1800 0.0000 C 0 0
1.5300 -6.8500 0.0000 C 0 0
0.7900 -5.4700 0.0000 C 0 0
1.5300 -4.1500 0.0000 C 0 0
2.7300 -4.1519 0.0000 O 0 0
0.7900 -2.8200 0.0000 C 0 0
1.5300 -1.4800 0.0000 C 0 0
3.0000 -1.1900 0.0000 N 0 0
3.1500 0.3200 0.0000 C 0 0
4.3800 1.2600 0.0000 C 0 0
5.7900 0.6800 0.0000 C 0 0
5.9393 -0.5107 0.0000 O 0 0
7.0400 1.6100 0.0000 C 0 0
8.4400 1.0700 0.0000 C 0 0
9.6800 2.0400 0.0000 C 0 0
9.4000 3.5400 0.0000 C 0 0
8.0000 4.0900 0.0000 C 0 0
6.7800 3.1400 0.0000 C 0 0
5.3800 3.7200 0.0000 C 0 0
5.2120 4.9082 0.0000 O 0 0
4.1900 2.7700 0.0000 C 0 0
2.7300 3.3900 0.0000 C 0 0
1.5100 2.4400 0.0000 C 0 0
1.7700 0.8500 0.0000 C 0 0
0.7400 -0.2700 0.0000 C 0 0
-0.7700 -0.2700 0.0000 C 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 7 1 0
7 8 2 0
8 3 1 0
8 9 1 0
9 10 2 0
9 11 1 0
11 12 2 0
12 2 1 0
12 13 1 0
13 14 2 0
14 15 1 0
15 16 2 0
16 11 1 0
16 17 1 0
17 18 1 0
18 19 2 0
19 20 1 0
20 21 2 0
20 22 1 0
22 23 2 0
23 24 1 0
24 25 2 0
25 26 1 0
26 27 2 0
27 22 1 0
27 28 1 0
28 29 2 0
28 30 1 0
30 19 1 0
30 31 2 0
31 32 1 0
32 33 1 0
33 34 2 0
34 35 1 0
35 36 2 0
35 37 1 0
37 38 2 0
38 39 1 0
39 40 2 0
40 41 1 0
41 42 2 0
42 37 1 0
42 43 1 0
43 44 2 0
43 45 1 0
45 34 1 0
45 46 2 0
46 47 1 0
47 48 2 0
48 33 1 0
48 49 1 0
49 31 1 0
49 50 2 0
50 15 1 0
50 18 1 0
M END
> <canonical_smiles>
O=C1c2ccccc2C(=O)c3c1ccc4c3[nH]c5c6C(=O)c7ccccc7C(=O)c6c8[nH]c9c%10C(=O)c%11ccccc%11C(=O)c%10ccc9c8c45
> <CAS_NO>
2475-33-4
> <Source>
VITIC
> <Activity>
0
> <WDI_Name>
.
> <REFERENCE>
JUDSON, PN, COOKE, PA, DOERRER, NG, GREENE, N, HANZLIK, RP, HARDY, C, HARTMANN, A, HINCHLIFFE, D, HOLDER, J, MUELLER, L, STEGER-HARTMANN, T, ROTHFUSS, A, SMITH, M, THOMAS, K, VESSEY, JD AND ZEIGER E.
TOWARDS THE CREATION OF AN INTERNATIONAL TOXICOLOGY INFORMATION CENTRE. TOXICOLOGY 213(1-2):117-28, 2005
> <MC_Example>
0
> <MC_Pred>
0
> <DEREK_Example>
0
> <DEREK_Pred>
1
> <Molecular_Weight>
646.60212
> <Set>
CV3
$$$$
";

group.bench_with_input(
BenchmarkId::new("sdf_parse", "content"),
&content,
|b, content| {
b.iter(|| {
parse_to_record(content).expect("Failed to parse record");
});
},
);

group.finish();
}

criterion_group!(benches, bench_parse_to_record);
criterion_main!(benches);
1 change: 1 addition & 0 deletions exon/exon-sdf/src/lib.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -29,4 +29,5 @@ mod schema_builder;

pub use batch_reader::BatchReader;
pub use config::SDFConfig;
pub use record::parse_to_record;
pub use schema_builder::SDFSchemaBuilder;
15 changes: 10 additions & 5 deletions exon/exon-sdf/src/record.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -79,23 +79,28 @@ impl Record {
let line = line.trim_end();

// Parse the atom and bond counts from their fixed positions
let atom_count_str = &line[0..3].trim();
let bond_count_str = &line[3..6].trim();
// let atom_count_str = &line[0..3].trim();
let atom_count_str = line.get(0..3).ok_or(ExonSDFError::ParseError(
"Failed to parse atom count".to_string(),
))?;
let bond_count_str = line.get(3..6).ok_or(ExonSDFError::ParseError(
"Failed to parse bond count".to_string(),
))?;

// Convert the parsed strings to usize
let atom_count = atom_count_str.parse().map_err(|_| {
let atom_count = atom_count_str.trim().parse().map_err(|_| {
ExonSDFError::ParseError(format!("Failed to parse atom count: {}", atom_count_str))
})?;

let bond_count = bond_count_str.parse().map_err(|_| {
let bond_count = bond_count_str.trim().parse().map_err(|_| {
ExonSDFError::ParseError(format!("Failed to parse bond count: {}", bond_count_str))
})?;

Ok((atom_count, bond_count))
}
}

pub(crate) fn parse_to_record(content: &str) -> crate::Result<Record> {
pub fn parse_to_record(content: &str) -> crate::Result<Record> {
tracing::trace!("Parsing SDF content: {:?}", content);
let mut lines = content.lines();

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