Refactor query_pdb and make_query_map functions

src/cli/workflows/query_pdb.rs

@@ -250,8 +250,8 @@ mod tests {
         let index_path = Some(String::from("data/serine_peptidases_pdb"));
         let exact_match = false;
         let retrieve = false;
-        let dist_threshold = Some(String::from("0.5,1.0"));
-        let angle_threshold = Some(String::from("5.0,10.0,15.0"));
+        let dist_threshold = Some(String::from("0.5"));
+        let angle_threshold = Some(String::from("5.0,10.0"));
         let help = false;
         let match_cutoff = 0.0;
         let score_cutoff = 0.0;

src/controller/query.rs

@@ -144,6 +144,7 @@ pub fn make_query_map(
     path: &String, query_residues: &Vec<(u8, u64)>, hash_type: HashType, 
     nbin_dist: usize, nbin_angle: usize, dist_thresholds: Vec<f32>, angle_thresholds: Vec<f32>
 ) -> HashMap<GeometricHash, ((usize, usize), bool)> {
+    let check_neighboring_index: bool = true;
     let pdb_reader = PDBReader::from_file(path).expect("PDB file not found");
     let compact = pdb_reader.read_structure().expect("Failed to read PDB file");
     let compact = compact.to_compact();
@@ -170,6 +171,16 @@ pub fn make_query_map(
             print_log_msg(INFO, &format!("Found residue: {}:{:?}({})", chain as char, ri, residue));
             indices.push(index);
         }
+        if check_neighboring_index {
+            let index = compact.get_index(&chain, &(ri + 1));
+            if let Some(index) = index {
+                indices.push(index);
+            }
+            let index = compact.get_index(&chain, &(ri - 1));
+            if let Some(index) = index {
+                indices.push(index);
+            }
+        }
     }
     let dist_indices = hash_type.dist_index();
     let angle_indices = hash_type.angle_index();