Fixed test typo; Updated README with explanation on sampling parameter

README.md

@@ -81,13 +81,16 @@ folddisco query -p query/1LAP.pdb -q 250,255,273,332,334 -i index/h_sapiens_fold
 folddisco query -q query/zinc_finger.txt -i index/h_sapiens_folddisco -t 6 -d 0.5 -a 5
 
 # Querying a whole structure
-folddisco query -i index/e_coli_folddisco -p query/2N6N.pdb --skip-match -t 6
+folddisco query -i index/h_sapiens_folddisco -p query/1G2F.pdb -t 6 --skip-match
+# For a long query, low `--sampling-ratio` can be used to speed up the search
+folddisco query -i index/h_sapiens_folddisco -p query/1G2F.pdb -t 6  --skip-match --sampling-ratio 0.3
 
 # Using a query file with distance and angle thresholds
 folddisco query -i index/h_sapiens_folddisco -q query/knottin.txt -d 0.5 -a 5 --skip-match -t 6
 
 # Query with amino-acid substitutions and range. 
 # Alternative amino acids can be given after colon. 
+# X: substitute to any amino acid, p: positive-charged, n: negative-charged, h: hydrophilic, b: hydrophobic, a: aromatic
 # Here's enolase query with 3 substitutions; Allow His at 164, Asp & Asn at 247, and His at 297.
 folddisco query -p query/2MNR.pdb -q 164:H,195,221,247:ND,297:H -i index/e_coli_folddisco -d 0.5 -a 5 --top 10 --header --per-structure
 # Range can be given with dash. This will query first 10 residues and 11th residue with subsitution to any amino acid.

src/cli/workflows/query_pdb.rs

@@ -50,8 +50,8 @@ search parameters:
  -d, --distance <FLOAT>           Distance threshold in Angstroms. Multiple values can be separated by comma [0.0]
  -a, --angle <FLOAT>              Angle threshold. Multiple values can be separated by comma [0.0]
  --ca-distance <FLOAT>            C-alpha distance threshold in matching residues [1.5]
- --sampling-count <INT>           Number of samples to use for sampling [all]
- --sampling-ratio <FLOAT>         Sampling ratio to use for sampling [1.0]
+ --sampling-count <INT>           Number of sampled hashes to search [all]
+ --sampling-ratio <FLOAT>         Sampling ratio for hashes used in searching. For long queries, smaller ratio is recommended [1.0]
  --skip-match                     Skip matching residues
  --serial-index                   Handle residue indices serially
 

src/controller/query.rs

@@ -563,7 +563,7 @@ mod tests {
     }
     #[test]
     fn test_parse_query_string_with_range() {
-        let query_string = "A250-252,B232-234,C269:";
+        let query_string = "A250-252,B232-234,C269:Q";
         let query_residues = parse_query_string(query_string, b'A');
         assert_eq!(query_residues, (vec![
             (b'A', 250), (b'A', 251), (b'A', 252),