[IN PROGRESS] optimizing feature extraction

Cargo.toml

@@ -24,14 +24,15 @@ pico-args = { version = "0.5.0", features = ["combined-flags"], path = "lib/pico
 rayon = "1.8.0"
 byteorder = "1.5.0"
 memmap2 = "0.9.0"
-dashmap = { version = "5.5.3", features = ["rayon"] }
 rustc-hash = "1.1.0"
 peak_alloc = "0.2.1"
 flate2 = { version = "1.0.28" }
 toml = "0.8.12"
 regex = "1.10.4"
 petgraph = "0.6.4"
 libc = "0.2.155"
+lazy_static = "1.5.0"
+dashmap = { version = "6.1.0", features = ["rayon"] }
 
 
 [build-dependencies]
@@ -40,4 +41,4 @@ cmake = { version = "0.1.50", optional = true }
 
 
 [features]
-foldcomp = ["bindgen", "cmake"]
+foldcomp = ["bindgen", "cmake"]

src/structure/core.rs

@@ -383,12 +383,13 @@ impl CompactStructure {
             (ca1, ca2, cb1, cb2, n1, n2)
         {
 
-            let ca_dist = self.get_ca_distance(idx1, idx2).unwrap();
+            let ca_dist = ca1.calc_distance(&ca2);
             if ca_dist > dist_cutoff {
                 return None;
             }
-            let cb_dist = self.get_cb_distance(idx1, idx2).unwrap();
-            let ca_cb_angle = self.get_ca_cb_angle(idx1, idx2, true).unwrap();
+            let cb_dist = cb1.calc_distance(&cb2);
+            // let ca_cb_angle = self.get_ca_cb_angle(idx1, idx2, true).unwrap();
+            let ca_cb_angle = ca1.calc_angle(&cb1, &ca2, &cb2, true);
             let theta1 = calc_torsion_radian(&n1, &ca1, &cb1, &cb2);
             let theta2 = calc_torsion_radian(&cb1, &cb2, &ca2, &n2);
             Some((ca_dist, cb_dist, ca_cb_angle, theta1, theta2))