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Merge pull request #72 from rdkit-rs/convert-mol-blocks-to-smiles
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Convert mol blocks to smiles with optional sanitization
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@xrl
xrl authored Feb 28, 2024
2 parents d20d82a + 38a6c53 commit 4108ebb
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300 changes: 300 additions & 0 deletions src/rest_api/api/compound_processing/convert_mol_block_to_smiles.rs
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use crate::rest_api::models::MolBlock;
use poem_openapi::payload::Json;
use poem_openapi_derive::{ApiResponse, Object};
use rdkit::RWMol;

#[derive(ApiResponse)]
pub enum ConvertedSmilesResponse {
#[oai(status = "200")]
Ok(Json<Vec<ConvertedSmiles>>),
}

#[derive(Object, Debug)]
pub struct ConvertedSmiles {
#[oai(skip_serializing_if_is_none)]
pub smiles: Option<String>,
#[oai(skip_serializing_if_is_none)]
pub error: Option<String>,
}

pub async fn v1_convert_mol_block_to_smiles(
sanitize: String,
mol: Json<Vec<MolBlock>>,
) -> ConvertedSmilesResponse {
let sanitize = match sanitize.as_str() {
"" | "false" | "no" => (false, false, false),
_ => (true, true, false),
};

let smiles = mol
.0
.into_iter()
.map(|mb| {
let rw_mol = RWMol::from_mol_block(&mb.mol_block, sanitize.0, sanitize.1, sanitize.2);

let error = if rw_mol.is_none() {
Some(format!("could not convert molblock\n{}\n", mb.mol_block))
} else {
None
};

ConvertedSmiles {
smiles: rw_mol.map(|rw_mol| rw_mol.as_smiles()),
error,
}
})
.collect::<Vec<_>>();

ConvertedSmilesResponse::Ok(Json(smiles))
}

#[cfg(test)]
mod tests {
use super::ConvertedSmilesResponse;
use super::*;
use crate::indexing::index_manager::IndexManager;
use crate::rest_api::openapi_server::Api;
use poem::{handler, Route};
use poem_openapi::param::Query;
use poem_openapi::payload::Json;

const MOL_BLOCK: &'static str = r#"
-OEChem-05172223082D
31 30 0 1 0 0 0 0 0999 V2000
2.8660 0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.8660 -2.2500 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
2.0000 -0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.7320 2.2500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.4641 0.2500 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
4.5981 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7320 0.2500 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0
6.3301 -0.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9641 1.1160 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9641 -0.6160 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7320 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8660 -1.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8660 1.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0000 2.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9966 1.2250 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
4.1996 1.2250 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
3.7320 0.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
6.0201 -0.7869 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
6.8671 -0.5600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
6.6401 0.2869 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
6.5010 0.8060 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
6.2741 1.6530 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
5.4272 1.4260 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
4.4272 -0.3060 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
4.6541 -1.1530 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
5.5010 -0.9260 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
3.9441 -1.3326 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
4.3426 -0.6423 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.3100 2.7869 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4631 2.5600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6900 1.7131 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 7 1 0 0 0 0
1 13 1 0 0 0 0
2 12 1 0 0 0 0
3 12 2 0 0 0 0
4 13 2 0 0 0 0
5 6 1 0 0 0 0
5 8 1 0 0 0 0
5 9 1 0 0 0 0
5 10 1 0 0 0 0
6 7 1 0 0 0 0
6 15 1 0 0 0 0
6 16 1 0 0 0 0
7 11 1 0 0 0 0
7 17 1 0 0 0 0
8 18 1 0 0 0 0
8 19 1 0 0 0 0
8 20 1 0 0 0 0
9 21 1 0 0 0 0
9 22 1 0 0 0 0
9 23 1 0 0 0 0
10 24 1 0 0 0 0
10 25 1 0 0 0 0
10 26 1 0 0 0 0
11 12 1 0 0 0 0
11 27 1 0 0 0 0
11 28 1 0 0 0 0
13 14 1 0 0 0 0
14 29 1 0 0 0 0
14 30 1 0 0 0 0
14 31 1 0 0 0 0
M CHG 2 2 -1 5 1
M END
> <PUBCHEM_COMPOUND_CID>
1
> <PUBCHEM_COMPOUND_CANONICALIZED>
1
> <PUBCHEM_CACTVS_COMPLEXITY>
214
> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
4
> <PUBCHEM_CACTVS_HBOND_DONOR>
0
> <PUBCHEM_CACTVS_ROTATABLE_BOND>
5
> <PUBCHEM_CACTVS_SUBSKEYS>
AAADceByOAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAHgAAAAAACBThgAYCCAMABAAIAACQCAAAAAAAAAAAAAEIAAACABQAgAAHAAAFIAAQAAAkAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA==
> <PUBCHEM_IUPAC_OPENEYE_NAME>
3-acetoxy-4-(trimethylammonio)butanoate
> <PUBCHEM_IUPAC_CAS_NAME>
3-acetyloxy-4-(trimethylammonio)butanoate
> <PUBCHEM_IUPAC_NAME_MARKUP>
3-acetyloxy-4-(trimethylazaniumyl)butanoate
> <PUBCHEM_IUPAC_NAME>
3-acetyloxy-4-(trimethylazaniumyl)butanoate
> <PUBCHEM_IUPAC_SYSTEMATIC_NAME>
3-acetyloxy-4-(trimethylazaniumyl)butanoate
> <PUBCHEM_IUPAC_TRADITIONAL_NAME>
3-acetoxy-4-(trimethylammonio)butyrate
> <PUBCHEM_IUPAC_INCHI>
InChI=1S/C9H17NO4/c1-7(11)14-8(5-9(12)13)6-10(2,3)4/h8H,5-6H2,1-4H3
> <PUBCHEM_IUPAC_INCHIKEY>
RDHQFKQIGNGIED-UHFFFAOYSA-N
> <PUBCHEM_XLOGP3_AA>
0.4
> <PUBCHEM_EXACT_MASS>
203.11575802
> <PUBCHEM_MOLECULAR_FORMULA>
C9H17NO4
> <PUBCHEM_MOLECULAR_WEIGHT>
203.24
> <PUBCHEM_OPENEYE_CAN_SMILES>
CC(=O)OC(CC(=O)[O-])C[N+](C)(C)C
> <PUBCHEM_OPENEYE_ISO_SMILES>
CC(=O)OC(CC(=O)[O-])C[N+](C)(C)C
> <PUBCHEM_CACTVS_TPSA>
66.4
> <PUBCHEM_MONOISOTOPIC_WEIGHT>
203.11575802
> <PUBCHEM_TOTAL_CHARGE>
0
> <PUBCHEM_HEAVY_ATOM_COUNT>
14
> <PUBCHEM_ATOM_DEF_STEREO_COUNT>
0
> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
1
> <PUBCHEM_BOND_DEF_STEREO_COUNT>
0
> <PUBCHEM_BOND_UDEF_STEREO_COUNT>
0
> <PUBCHEM_ISOTOPIC_ATOM_COUNT>
0
> <PUBCHEM_COMPONENT_COUNT>
1
> <PUBCHEM_CACTVS_TAUTO_COUNT>
1
> <PUBCHEM_COORDINATE_TYPE>
1
5
255
> <PUBCHEM_BONDANNOTATIONS>
7 11 3
"#;

#[handler]
async fn no_sanitize_index() -> ConvertedSmilesResponse {
let sanitize = Query("".to_string());
let smiles = Json(vec![MolBlock {
mol_block: MOL_BLOCK.to_string(),
}]);
Api {
index_manager: IndexManager::new("/tmp/blah", false).unwrap(),
}
.v1_convert_mol_block_to_smiles(sanitize, smiles)
.await
}

#[handler]
async fn sanitize_index() -> ConvertedSmilesResponse {
let sanitize = Query("true".to_string());
let smiles = Json(vec![MolBlock {
mol_block: MOL_BLOCK.to_string(),
}]);
Api {
index_manager: IndexManager::new("/tmp/blah", false).unwrap(),
}
.v1_convert_mol_block_to_smiles(sanitize, smiles)
.await
}

#[tokio::test]
async fn test_poem() {
let app = Route::new()
.at("/no_sanitize", poem::post(no_sanitize_index))
.at("/sanitize", poem::post(sanitize_index));
let client = poem::test::TestClient::new(app);

// First test
let resp = client.post("/no_sanitize").send().await;

resp.assert_status_is_ok();

let json = resp.json().await;
let json_value = json.value();

json_value
.array()
.iter()
.map(|value| value.object().get("smiles"))
.collect::<Vec<_>>()
.first()
.expect("first_value")
.assert_string("[H]C([H])([H])C(=O)OC([H])(C([H])([H])C(=O)[O-])C([H])([H])[N+](C([H])([H])[H])(C([H])([H])[H])C([H])([H])[H]");

// Second test
let resp = client.post("/sanitize").send().await;

resp.assert_status_is_ok();

let json = resp.json().await;
let json_value = json.value();

json_value
.array()
.iter()
.map(|value| value.object().get("smiles"))
.collect::<Vec<_>>()
.first()
.expect("first_value")
.assert_string("CC(=O)OC(CC(=O)[O-])C[N+](C)(C)C");
}
}
3 changes: 3 additions & 0 deletions src/rest_api/api/compound_processing/mod.rs
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mod compound_processing_management;
pub use compound_processing_management::*;

mod convert_mol_block_to_smiles;
pub use convert_mol_block_to_smiles::*;

mod standardize;
pub use standardize::*;
3 changes: 3 additions & 0 deletions src/rest_api/models/mod.rs
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mod mol_block;
pub use mol_block::*;

mod smiles;
pub use smiles::*;
6 changes: 6 additions & 0 deletions src/rest_api/models/mol_block.rs
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use poem_openapi_derive::Object;

#[derive(Object, Debug)]
pub struct MolBlock {
pub mol_block: String,
}
21 changes: 16 additions & 5 deletions src/rest_api/openapi_server.rs
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@@ -1,11 +1,12 @@
use crate::indexing::index_manager::IndexManager;
use crate::rest_api::api::{
v1_get_index, v1_index_search_basic, v1_index_search_substructure, v1_list_indexes,
v1_list_schemas, v1_post_index, v1_post_index_bulk, v1_standardize, BulkRequest,
GetIndexResponse, GetQuerySearchResponse, GetStructureSearchResponse, ListIndexesResponse,
ListSchemasResponse, PostIndexResponse, PostIndexesBulkIndexResponse, StandardizeResponse,
v1_convert_mol_block_to_smiles, v1_get_index, v1_index_search_basic,
v1_index_search_substructure, v1_list_indexes, v1_list_schemas, v1_post_index,
v1_post_index_bulk, v1_standardize, BulkRequest, ConvertedSmilesResponse, GetIndexResponse,
GetQuerySearchResponse, GetStructureSearchResponse, ListIndexesResponse, ListSchemasResponse,
PostIndexResponse, PostIndexesBulkIndexResponse, StandardizeResponse,
};
use crate::rest_api::models::Smiles;
use crate::rest_api::models::{MolBlock, Smiles};

use poem::{listener::TcpListener, EndpointExt, Route, Server};
use poem_openapi::{
Expand Down Expand Up @@ -84,6 +85,16 @@ impl Api {
v1_standardize(mol).await
}

#[oai(path = "/v1/convert/mol_block_to_smiles", method = "post")]
/// Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
pub async fn v1_convert_mol_block_to_smiles(
&self,
sanitize: Query<String>,
mol: Json<Vec<MolBlock>>,
) -> ConvertedSmilesResponse {
v1_convert_mol_block_to_smiles(sanitize.0, mol).await
}

#[oai(path = "/v1/schemas", method = "get")]
/// List schemas available for creating indexes
pub async fn v1_list_schemas(&self) -> ListSchemasResponse {
Expand Down

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