cargo fix

src/controller/mod.rs

@@ -16,25 +16,24 @@ pub mod mode;
 
 use std::cell::UnsafeCell;
 use std::io::Write;
-use std::sync::{Arc, Mutex};
+use std::sync::Arc;
 use feature::get_geometric_hash_as_u32_from_structure;
 use mode::IndexMode;
 // External imports
 use rayon::prelude::*;
 
 use crate::index::indextable::FolddiscoIndex;
 // Internal imports
-use crate::{measure_time, PDBReader};
-use crate::geometry::core::{GeometricHash, HashType};
-use crate::index::alloc::IndexBuilder;
+use crate::PDBReader;
+use crate::geometry::core::HashType;
 use crate::utils::log::{ print_log_msg, log_msg, FAIL, WARN, INFO };
 
 #[cfg(feature = "foldcomp")]
 use crate::structure::io::fcz::FoldcompDbReader;
 
 const DEFAULT_NUM_THREADS: usize = 4;
-const DEFAULT_HASH_TYPE: HashType = HashType::PDBTrRosetta;
-const DEFAULT_MAX_RESIDUE: usize = 50000;
+// const DEFAULT_HASH_TYPE: HashType = HashType::PDBTrRosetta;
+const DEFAULT_MAX_RESIDUE: usize = 65535;
 const DEFAULT_DIST_CUTOFF: f32 = 20.0;
 
 unsafe impl Send for FoldDisco {}

src/controller/retrieve.rs

@@ -1,7 +1,7 @@
 // 
 use std::{collections::{BTreeSet, HashMap, HashSet}, fs::File};
 use petgraph::Graph;
-use rayon::iter::{IntoParallelRefIterator, ParallelDrainFull, ParallelIterator};
+use rayon::iter::{IntoParallelRefIterator, ParallelIterator};
 
 use crate::utils::convert::{map_aa_to_u8, map_u8_to_aa}; 
 use crate::prelude::*; 
@@ -13,7 +13,6 @@ use crate::controller::feature::get_single_feature;
 #[cfg(feature = "foldcomp")]
 use crate::structure::io::fcz::FoldcompDbReader;
 
-use super::feature;
 
 pub fn hash_vec_to_aa_pairs(hash_vec: &Vec<GeometricHash>) -> HashSet<(u32, u32)> {
     let mut output: HashSet<(u32, u32)> = HashSet::new();
@@ -348,7 +347,7 @@ pub fn retrieval_wrapper_for_foldcompdb(
             } else {
                 res_vec_from_hash.push("_".to_string());
                 if candidate_pair_map.contains_key(&i) {
-                    let mut pairs = candidate_pair_map.get(&i).unwrap().clone();
+                    let pairs = candidate_pair_map.get(&i).unwrap().clone();
                     for (j, k) in pairs {
                         // If retrieved_indices contains k, add j to mapping
                         if retrieved_indices.contains(&k) {
@@ -501,7 +500,7 @@ pub fn retrieval_wrapper(
             } else {
                 res_vec_from_hash.push("_".to_string());
                 if candidate_pair_map.contains_key(&i) {
-                    let mut pairs = candidate_pair_map.get(&i).unwrap().clone();
+                    let pairs = candidate_pair_map.get(&i).unwrap().clone();
                     // pairs.sort_by(|a, b| a.0.cmp(&b.0));
                     // pairs.dedup();
                     for (j, k) in pairs {

src/geometry/pdb_tr.rs

@@ -186,8 +186,8 @@ mod tests {
         ];
         let start = std::time::Instant::now();
         for _ in 0..10000 {
-            let hash = HashValue::perfect_hash_default(&raw_feature);
-            let hash2 = HashValue::perfect_hash_default(&raw_feature2);
+            let _ = HashValue::perfect_hash_default(&raw_feature);
+            let _ = HashValue::perfect_hash_default(&raw_feature2);
         }
         let duration = start.elapsed();
         println!("Time elapsed in perfect_hash_default() is: {:?}", duration);

src/geometry/trrosetta.rs

@@ -64,7 +64,7 @@ impl HashValue {
         let h_cb_dist = discretize_value(cb_dist, MIN_DIST, MAX_DIST, nbin_dist);
 
         // Convert angles to sin and cos
-        let angles = [omega, theta1, theta2, phi1, phi2];
+        // let angles = [omega, theta1, theta2, phi1, phi2];
         let sin_cos_angles = [
             (omega.sin(), omega.cos()), (theta1.sin(), theta1.cos()),
             (theta2.sin(), theta2.cos()), (phi1.sin(), phi1.cos()),

src/index/lookup.rs

@@ -4,7 +4,7 @@
 // id\tpath\tinteger\tfloat
 // id\tpath\tn_res\tplddt
 
-use std::io::{Write, BufRead};
+use std::io::Write;
 use std::fs::File;
 use std::io::BufWriter;
 

src/structure/io/fcz.rs

@@ -11,7 +11,6 @@ use rayon::prelude::ParallelSliceMut;
 use rayon::prelude::ParallelString;
 use rayon::prelude::*;
 use std::fs::File;
-use std::io::BufRead;
 use std::mem::ManuallyDrop;
 
 use crate::structure::atom::Atom;

src/utils/convert.rs

@@ -80,11 +80,12 @@ pub fn map_aa_to_u8(aa: &[u8; 3]) -> u8 {
 }
 
 mod tests {
-    use super::*;
+
     #[test]
     fn test_map_aa_to_u8() {
+        use super::map_aa_to_u8;
         let start = std::time::Instant::now();
-        for i in 0..1000 {
+        for _ in 0..1000 {
             assert_eq!(map_aa_to_u8(b"ALA"), 0);
             assert_eq!(map_aa_to_u8(b"ARG"), 1);
             assert_eq!(map_aa_to_u8(b"ASN"), 2);