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use std::io::prelude::*;
use rand::prelude::*;
type ChemblID = String;
type CanonicalSMILES = String;
type StandardInchi = String;
type StandardInchiKey = String;
#[derive(PartialEq, Debug)]
pub struct EntryChembl {
pub chembl_id: ChemblID,
pub smiles: CanonicalSMILES,
pub inchi: StandardInchi,
pub inchi_key: StandardInchiKey
}
impl EntryChembl {
pub fn new(v: Vec<&str>) -> Self {
let (chembl_id, smiles, inchi, inchi_key) = (String::from(v[0]), String::from(v[1]), String::from(v[2]), String::from(v[3]));
Self { chembl_id, smiles, inchi, inchi_key }
}
}
type DataChembl = std::collections::HashMap<String, EntryChembl>;
pub struct SourceChembl {
path: std::path::PathBuf,
data: DataChembl
}
impl std::default::Default for SourceChembl {
fn default() -> Self {
let mut sc = Self::new();
let kind = chiral_common::kinds::Dataset::Chembl30;
let chembl_txt = std::env::var_os(kind.env_key()).expect("ChEMBL path not set");
sc.set_path(&chembl_txt);
sc.load_all();
sc
}
}
impl SourceChembl {
pub fn new() -> Self {
Self {
path: std::path::PathBuf::new(),
data: DataChembl::new(),
}
}
pub fn set_path(&mut self, path_str: &std::ffi::OsStr) {
self.path = std::path::PathBuf::from(path_str)
}
fn sanitize(&mut self) {
self.data.remove("chembl_id");
}
fn convert_lines(&mut self, lines: impl std::iter::Iterator<Item = std::io::Result<String>>) {
self.data.clear();
self.data = lines.map(|l| {
let line = l.unwrap();
let v = line.as_str().split("\t").collect::<Vec<&str>>(); (String::from(v[0]), EntryChembl::new(v))
}
)
.collect::<Vec<(ChemblID, EntryChembl)>>()
.into_iter()
.collect();
self.sanitize();
}
pub fn load_all(&mut self) {
let file = std::fs::File::open(&self.path).unwrap();
let lines = std::io::BufReader::new(file).lines();
self.convert_lines(lines);
}
pub fn load_partial(&mut self, range: &std::ops::Range<usize>) {
let file = std::fs::File::open(&self.path).unwrap();
let reader = std::io::BufReader::new(file);
self.convert_lines(reader.lines().skip(range.start).take(range.len()));
}
pub fn get(&self, id: &ChemblID) -> Option<&EntryChembl> { self.data.get(id) }
pub fn get_all(&self) -> &DataChembl { &self.data }
pub fn len(&self) -> usize { self.data.len() }
pub fn get_smiles_id_pairs(&self) -> (Vec<String>, Vec<String>) {
(
self.data.values()
.map(|ec| ec.smiles.clone())
.collect(),
self.data.keys()
.map(|id| id.clone())
.collect()
)
}
pub fn choices(&self, size: usize) -> Vec<&EntryChembl> {
let mut rng = thread_rng();
let marks: Vec<bool> = (0..self.len())
.map(|_| rng.gen_range(0..self.len()) <= size * 2 )
.collect();
self.data.values().enumerate()
.filter(|(idx, _)| marks[*idx])
.map(|(_, v)| v)
.take(size)
.collect()
}
}
#[cfg(test)]
mod test_chembl {
use super::*;
#[test]
fn test_source_chembl() {
let mut sc = SourceChembl::new();
sc.set_path(&std::ffi::OsString::from("../../../chiral-db-example-data/ChEMBL/chembl_30_chemreps_100.txt"));
sc.load_all();
assert_eq!(sc.len(), 100);
let ec = sc.get(&String::from("CHEMBL503634")).unwrap();
assert_eq!(ec.smiles, "COc1c(O)cc(O)c(C(=N)Cc2ccc(O)cc2)c1O");
assert_eq!(ec.inchi, "InChI=1S/C15H15NO5/c1-21-15-12(19)7-11(18)13(14(15)20)10(16)6-8-2-4-9(17)5-3-8/h2-5,7,16-20H,6H2,1H3");
assert_eq!(ec.inchi_key, "OPELSESCRGGKAM-UHFFFAOYSA-N");
let data_all = sc.get_all();
assert_eq!(data_all.keys().count(), 100);
let selected = sc.choices(10);
assert_eq!(selected.len(), 10);
sc.load_partial(&(30..40));
assert_eq!(sc.len(), 10);
assert_eq!(sc.get(&String::from("CHEMBL503634")), None);
let ec = sc.get(&String::from("CHEMBL501923")).unwrap();
assert_eq!(ec.smiles, "CC(C)=CCC/C(C)=C/Cc1c2c(c3oc4c(c(=O)c3c1O)CC1c3c(c(O)cc(O)c3-4)OC1(C)C)C=CC(C)(C)O2");
assert_eq!(ec.inchi, "InChI=1S/C35H38O7/c1-17(2)9-8-10-18(3)11-12-19-28(38)27-29(39)21-15-22-25-26(23(36)16-24(37)33(25)42-35(22,6)7)32(21)40-31(27)20-13-14-34(4,5)41-30(19)20/h9,11,13-14,16,22,36-38H,8,10,12,15H2,1-7H3/b18-11+");
assert_eq!(ec.inchi_key, "UJHMTIUPFDVYQA-WOJGMQOQSA-N");
}
}