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use chiral_common::{Operator, OperatorOutput, OperatorReport};
use chiral_operator::substructure::ob_ss_match::{Input, Output, MatchResult, Report};
pub struct Data {
dsk: chiral_common::kinds::Dataset,
ids: Vec<chiral_common::DatasetID>,
mols: Vec<openbabel::molecule::Molecule>
}
impl From<(&chiral_common::kinds::Dataset, &chiral_data::DocSMILES)> for Data {
fn from((dsk_in, doc): (&chiral_common::kinds::Dataset, &chiral_data::DocSMILES)) -> Self {
let mols = doc.get_smiles_vec().iter()
.map(|smiles| openbabel::molecule::Molecule::new_from_smiles(smiles))
.collect();
let ids = doc.get_ids().to_vec();
Self { dsk: dsk_in.to_owned(), ids, mols }
}
}
impl chiral_common::OperatorData for Data {
fn len(&self) -> usize {
self.ids.len()
}
}
struct OpenBabelSSMatcher {
sp: openbabel::smartspattern::SmartsPattern
}
impl OpenBabelSSMatcher {
pub fn new(smarts: &chiral_common::SMARTS) -> Self {
let sp = openbabel::smartspattern::SmartsPattern::new_from_smarts(smarts);
Self { sp }
}
pub fn find_match(&self, mol: &openbabel::molecule::Molecule) -> MatchResult {
self.sp.find_match(mol)
}
}
pub struct OpenBabelSSMatching {
}
impl OpenBabelSSMatching {
pub fn new() -> Self {
Self {}
}
}
impl chiral_common::Operator for OpenBabelSSMatching {
type InputType = Input;
type DataType = Data;
type OutputType = Output;
type ReportType = Report;
fn compute(&self, input: &Self::InputType, data: &Self::DataType) -> Self::OutputType {
let matcher = OpenBabelSSMatcher::new(input);
let results = data.mols.iter()
.map(|mol| matcher.find_match(mol))
.zip(data.ids.iter())
.filter(|(mr, _)| mr.len() > 0)
.map(|(mr, id)| (mr, id.to_string()))
.collect();
Output { results }
}
fn report(&self, input: Self::InputType, data: &Self::DataType, output: Self::OutputType) -> Self::ReportType {
Report {
input,
dsk: data.dsk.to_owned(),
output
}
}
}
pub struct OpenBabelSSMatchingUnit {
op: OpenBabelSSMatching,
data: Data,
output: Output
}
impl From<(&chiral_common::kinds::Dataset, &chiral_data::DocSMILES)> for OpenBabelSSMatchingUnit {
fn from((dsk, doc): (&chiral_common::kinds::Dataset, &chiral_data::DocSMILES)) -> Self {
let op = OpenBabelSSMatching::new();
let data = Data::from((dsk, doc));
Self { op, data, output: Output::blank() }
}
}
impl chiral_common::ComputingUnit for OpenBabelSSMatchingUnit {
fn compute(&mut self, serialized_input: &chiral_common::SerializedFormat) {
self.output.clear();
self.output = self.op.compute(serialized_input, &self.data);
}
fn report(&self, serialized_input: &chiral_common::SerializedFormat) -> chiral_common::SerializedFormat {
self.op.report(serialized_input.to_owned(), &self.data, self.output.to_owned()).serialize()
}
fn output_len(&self) -> usize {
self.output.len()
}
}
#[cfg(test)]
mod tests {
use super::*;
use chiral_common::{Operator, OperatorData, OperatorOutput, OperatorReport, ComputingUnit};
use chiral_data::Dummy;
#[test]
fn test_cu() {
let dsk = chiral_common::kinds::Dataset::Dummy;
let doc_smiles = chiral_data::DocSMILES::dummy();
let mut cu = OpenBabelSSMatchingUnit::from((&dsk, &doc_smiles));
cu.compute(&String::from("C(=O)O"));
assert_eq!(cu.output_len(), 2);
}
#[test]
fn test_matcher() {
let matcher = OpenBabelSSMatcher::new(&String::from("O=CN*"));
let mol_1 = openbabel::molecule::Molecule::new_from_smiles("NCC(=O)NCC");
let match_result_1 = matcher.find_match(&mol_1);
assert_eq!(match_result_1.len(), 1);
assert_eq!(vec![vec![4, 3, 5, 6]], match_result_1);
let matcher_2 = OpenBabelSSMatcher::new(&String::from("c1ccccc1N=O"));
let mol_2 = openbabel::molecule::Molecule::new_from_smiles("COc1cc([N+](=O)[O-])c(OC)cc1CC(C)N");
let match_result_2 = matcher_2.find_match(&mol_2);
assert_eq!(match_result_2.len(), 2);
assert_eq!(vec![vec![4, 3, 13, 12, 9, 5, 6, 7], vec![9, 12, 13, 3, 4, 5, 6, 7]], match_result_2);
}
#[test]
fn test_op() {
let dsk = chiral_common::kinds::Dataset::Dummy;
let doc_smiles = chiral_data::DocSMILES::dummy();
let data = Data::from((&dsk, &doc_smiles));
assert_eq!(data.len(), 4);
let op = OpenBabelSSMatching::new();
let input = String::from("C(=O)O");
let output = op.compute(&input, &data);
assert_eq!(output.len(), 2);
let report = op.report(input, &data, output);
let serialized_report = OperatorReport::serialize(&report);
let report_deserialized: Report = OperatorReport::deserialize(&serialized_report);
assert_eq!(report_deserialized.dsk, dsk);
assert_eq!(report_deserialized.output.len(), 2);
let input_1 = String::from("C(=O)O");
let output_1 = op.compute(&input_1, &data);
let mut report_1 = op.report(input_1, &data, output_1);
let input_2 = String::from("C(=O)O");
let output_2 = op.compute(&input_2, &data);
let report_2 = op.report(input_2, &data, output_2);
report_1.extend(report_2);
assert_eq!(report_1.output.len(), 4);
}
}