#3: switched to FixedBitSet, using bincode to performa binary encoding and decoding

Author: mkviatkovskii

Cargo.toml

@@ -11,8 +11,7 @@ repository = "https://github.com/mkviatkovskii/ringo.git"
 version = "0.0.1"
 
 [dependencies]
-bitcode = "0.6.0"
-bit-set = "0.6.0"
-bit-vec = "0.7.0"
+bincode = "2.0.0-rc.3"
+fixedbitset = "0.5.7"
 nom = "7.1.3"
 petgraph = "0.6.5"

src/ringo/math/similarity/tanimoto.rs

@@ -1,72 +1,34 @@
-use bit_vec::BitVec;
+use fixedbitset::FixedBitSet;
 
-pub fn tanimoto_vec(a: &BitVec, b: &BitVec) -> f32 {
+pub fn tanimoto_bitset(a: &FixedBitSet, b: &FixedBitSet) -> f32 {
     let mut and_ = a.clone();
-    let mut or_ = a.clone();
-    and_.and(b);
-    or_.or(b);
-
-    let mut dividend: u32 = 0;
-    for b in and_.blocks() {
-        dividend += b.count_ones();
-    }
-    let mut divisor: u32 = 0;
-    for b in or_.blocks() {
-        divisor += b.count_ones();
-    }
-
-    return dividend as f32 / divisor as f32;
-}
-
-pub unsafe fn tanimoto_array(a: &[u64; 4], b: &[u64; 4]) -> f32 {
-    let mut dividend: u32 = 0;
-    let mut divisor: u32 = 0;
-
-    for i in 0..4 {
-        dividend += ((a[i] & b[i]) as i64).count_ones();
-        divisor += ((a[i] | b[i]) as i64).count_ones();
-    }
-    return dividend as f32 / divisor as f32;
+    and_.intersect_with(b);
+    return and_.count_ones(..) as f32 / (a.count_ones(..) + b.count_ones(..) - and_.count_ones(..)) as f32;
 }
 
 #[cfg(test)]
 mod tests {
-    use bit_vec::BitVec;
-    use crate::ringo::math::similarity::tanimoto::{tanimoto_array, tanimoto_vec};
+    use fixedbitset::FixedBitSet;
+    use crate::ringo::math::similarity::tanimoto::{tanimoto_bitset};
 
     #[test]
-    fn test_tanimoto_vec_033() {
-        let a: BitVec = BitVec::from_bytes(&[0b00000101]);
-        let b = BitVec::from_bytes(&[0b00000011]);
-
-        assert_eq!(tanimoto_vec(&a, &b), 0.33333334);
+    fn test_tanimoto_bitset_033() {
+        let mut a = FixedBitSet::with_capacity(8);
+        a.insert(0);
+        a.insert(2);
+        let mut b = FixedBitSet::with_capacity(8);
+        b.insert(0);
+        b.insert(1);
+        assert_eq!(tanimoto_bitset(&a, &b), 0.33333334);
     }
 
     #[test]
-    fn test_tanimoto_vec_05() {
-        let a: BitVec = BitVec::from_bytes(&[0b0000001]);
-        let b = BitVec::from_bytes(&[0b00000011]);
-
-        assert_eq!(tanimoto_vec(&a, &b), 0.5);
+    fn test_tanimoto_bitset_05() {
+        let mut a = FixedBitSet::with_capacity(8);
+        a.insert(0);
+        let mut b = FixedBitSet::with_capacity(8);
+        b.insert(0);
+        b.insert(1);
+        assert_eq!(tanimoto_bitset(&a, &b), 0.5);
     }
-
-    #[test]
-    fn test_tanimoto_array_033() {
-        let a: [u64; 4] = [0b00000101, 0, 0, 0];
-        let b = [0b00000011, 0, 0, 0];
-
-        unsafe {
-            assert_eq!(tanimoto_array(&a, &b), 0.33333334);
-        }
-    }
-
-    #[test]
-    fn test_tanimoto_array_05() {
-        let a: [u64; 4] = [0b00000001, 0, 0, 0];
-        let b = [0b00000011, 0, 0, 0];
-
-        unsafe {
-            assert_eq!(tanimoto_array(&a, &b), 0.5);
-        }
-    }
-}
+}

src/ringo/molecule/model/molecule.rs

@@ -1,17 +1,16 @@
 use crate::ringo::molecule::model::atom::Atom;
 use crate::ringo::molecule::model::bond::Bond;
 use crate::ringo::molecule::model::element::atomic_weight;
-use bit_set::BitSet;
-use bit_vec::BitVec;
+use crate::ringo::ringo::fingerprint::Fingerprint;
 use petgraph::stable_graph::{EdgeIndex, NodeIndex, StableGraph};
 use petgraph::visit::EdgeRef;
 use petgraph::Undirected;
 use std::borrow::Borrow;
 use std::collections::{BTreeSet};
 use std::collections::hash_map::DefaultHasher;
-use std::fmt::Debug;
 use std::hash::Hasher;
-use crate::ringo::math::similarity::tanimoto::tanimoto_vec;
+use fixedbitset::FixedBitSet;
+use crate::ringo::math::similarity::tanimoto::tanimoto_bitset;
 use crate::ringo::molecule::smiles::reader::molecule::parse_molecule;
 
 pub struct Molecule {
@@ -89,14 +88,14 @@ impl Molecule {
     }
 
     // TODO: move to Descriptors crate
-    pub fn ecfp(&self, radius: usize, fp_length: usize) -> BitVec {
-        let mut fp = BitSet::new();
+    pub fn ecfp(&self, radius: usize, fp_length: usize) -> Fingerprint {
+        let mut fp = FixedBitSet::new();
 
         for node in self.graph.node_indices() {
             ecfp_recursive(&self.graph, radius, 1, node, &mut fp, fp_length, &mut DefaultHasher::new());
         }
 
-        BitVec::from_fn(fp_length, |idx| fp.contains(idx))
+        Fingerprint(fp)
     }
 }
 
@@ -105,7 +104,7 @@ fn ecfp_recursive(
     radius: usize,
     depth: usize,
     node: NodeIndex,
-    fp: &mut BitSet,
+    fp: &mut FixedBitSet,
     fp_length: usize,
     hasher: &mut DefaultHasher,
 ) {
@@ -142,6 +141,6 @@ fn ecfp_recursive(
 fn test_ecfp() {
     let ecfp_ibuprofen = parse_molecule("CC(C)CC1=CC=C(C=C1)C(C)C(=O)O").unwrap().1.ecfp(2, 128);
     let ecfp_naproxen = parse_molecule("CC(C1=CC2=C(C=C1)C=C(C=C2)OC)C(=O)O").unwrap().1.ecfp(2, 128);
-    let sim = tanimoto_vec(&ecfp_ibuprofen, &ecfp_naproxen);
+    let sim = tanimoto_bitset(&ecfp_ibuprofen.0, &ecfp_naproxen.0);
     assert!(0.53 < sim && sim < 0.54);
 }

src/ringo/molecule/smiles/reader/molecule.rs

@@ -388,10 +388,7 @@ mod tests {
             println!("{}: ", smiles);
             let m = parse_molecule(smiles).unwrap().1;
             let result = m.ecfp(2, 512);
-            for bit in result {
-                print!("{}", if bit { 1 } else { 0 });
-            }
-            println!("");
+            println!("{:?}", result);
         }
     }
 }

src/ringo/ringo.rs

@@ -1,3 +1,4 @@
 mod index;
 mod search;
 mod index_item;
+pub(crate) mod fingerprint;

src/ringo/ringo/fingerprint.rs

@@ -0,0 +1,48 @@
+use bincode::de::BorrowDecoder;
+use bincode::error::{DecodeError, EncodeError};
+use fixedbitset::{Block, FixedBitSet};
+
+pub const FINGERPRINT_SIZE: usize = 512;
+
+#[derive(Debug)]
+pub struct Fingerprint(pub FixedBitSet);
+
+impl bincode::Encode for Fingerprint {
+    fn encode<E: bincode::enc::Encoder>(&self, encoder: &mut E) -> Result<(), EncodeError> {
+        self.0.as_slice().encode(encoder)?;
+        Ok(())
+    }
+}
+
+impl bincode::Decode for Fingerprint {
+    fn decode<D: bincode::de::Decoder>(decoder: &mut D) -> Result<Self, DecodeError> {
+        let slice = Vec::<Block>::decode(decoder)?;
+        let fp = FixedBitSet::with_capacity_and_blocks(FINGERPRINT_SIZE, slice);
+        Ok(Fingerprint(fp))
+    }
+}
+
+impl<'de> bincode::BorrowDecode<'de> for Fingerprint {
+    fn borrow_decode<D: BorrowDecoder<'de>>(decoder: &mut D) -> Result<Self, DecodeError> {
+        let slice = Vec::<Block>::borrow_decode(decoder)?;
+        let fp = FixedBitSet::with_capacity_and_blocks(FINGERPRINT_SIZE, slice);
+        Ok(Fingerprint(fp))
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use fixedbitset::{FixedBitSet};
+    use crate::ringo::ringo::fingerprint::{Fingerprint, FINGERPRINT_SIZE};
+
+    #[test]
+    fn test_fingerprint_encode_decode() {
+        let mut fp = Fingerprint(FixedBitSet::with_capacity(FINGERPRINT_SIZE));
+        fp.0.set(1, true);
+        fp.0.set(17, true);
+
+        let encoded = bincode::encode_to_vec(&fp, bincode::config::standard()).unwrap();
+        let decoded: Fingerprint = bincode::decode_from_slice(&encoded, bincode::config::standard()).unwrap().0;
+        assert_eq!(decoded.0.ones().collect::<Vec<usize>>(), vec![1, 17]);
+    }
+}

src/ringo/ringo/index.rs

@@ -13,11 +13,12 @@ fn index(smiles_file: &str) {
     for line in std::io::BufReader::new(fi).lines() {
         let line = line.unwrap();
         let molecule = parse_molecule(&line).unwrap().1;
-        IndexItem::new(offset, molecule.ecfp(2, 512));
+        IndexItem{position: offset, fingerprint: molecule.ecfp(2, 512)};
         offset += line.len() + 1;
     }
 }
 
+
 #[test]
 fn test_index() {
     index("molecules.smi");

src/ringo/ringo/index_item.rs

@@ -1,15 +1,30 @@
-use bit_vec::BitVec;
+use bincode::{Decode, Encode};
+use crate::ringo::ringo::fingerprint::Fingerprint;
 
+#[derive(Debug, Encode, Decode)]
 pub struct IndexItem {
     pub position: usize,
-    pub fingerprint: Vec<u8>
+    pub fingerprint: Fingerprint
 }
 
-impl IndexItem {
-    pub fn new(position: usize, fingerprint: BitVec) -> IndexItem {
-        IndexItem {
-            position,
-            fingerprint: fingerprint.to_bytes()
-        }
+#[cfg(test)]
+mod tests {
+    use bincode::config::standard;
+    use bincode::{decode_from_slice, encode_to_vec};
+    use fixedbitset::FixedBitSet;
+    use crate::ringo::ringo::index_item::IndexItem;
+    use crate::ringo::ringo::fingerprint::Fingerprint;
+
+    #[test]
+    fn test_index_item_encode_decode() {
+        let fp = Fingerprint(FixedBitSet::with_capacity(512));
+        let mut ii = IndexItem {position: 0, fingerprint: fp};
+        ii.position = 0;
+        ii.fingerprint.0.set(1, true);
+        ii.fingerprint.0.set(17, true);
+
+        let encoded = encode_to_vec(&ii, standard()).unwrap();
+        let decoded: IndexItem = decode_from_slice(&encoded, standard()).unwrap().0;
+        assert_eq!(decoded.fingerprint.0.ones().collect::<Vec<usize>>(), vec![1, 17]);
     }
-}
+}