Implemented obtaining phi, psi, chi angles in main

src/backbone/ramachandran.py

@@ -0,0 +1,75 @@
+import numpy as np
+
+class RamachandranSampler:
+    def __init__(self):
+        # the weights tend towards the beta strand region to avoid collapse
+
+        # generalised for 18 amino acids
+        self.general_dist = [
+            # beta strand (top left)
+            {'phi_m': -120, 'phi_s': 20, 'psi_m': 140, 'psi_s': 20, 'w': 0.70},
+            # right handed helix (bottom left)
+            {'phi_m': -65,  'phi_s': 15, 'psi_m': -40, 'psi_s': 15, 'w': 0.25},
+            # left handed helix (top right)
+            {'phi_m': 60,   'phi_s': 15, 'psi_m': 40,  'psi_s': 15, 'w': 0.05}
+        ]
+
+        # glycine more flexible
+        self.glycine_dist = [
+            # beta strand (top left)
+            {'phi_m': -100, 'phi_s': 30, 'psi_m': 140, 'psi_s': 30, 'w': 0.3},
+            # right handed helix (bottom left)
+            {'phi_m': -60,  'phi_s': 30, 'psi_m': -30, 'psi_s': 30, 'w': 0.2},
+            # left handed helix (top right)
+            {'phi_m': 60,   'phi_s': 30, 'psi_m': 30,  'psi_s': 30, 'w': 0.2},
+            # bottom right for glycine
+            {'phi_m': 100,  'phi_s': 30, 'psi_m': -140,'psi_s': 30, 'w': 0.3}
+        ]
+
+        # proline no left handed helix
+        self.proline_dist = [
+            # beta strand (top left)
+            {'phi_m': -63,  'phi_s': 5,  'psi_m': 150, 'psi_s': 20, 'w': 0.8},
+            # right handed helix (bottom left)
+            {'phi_m': -63,  'phi_s': 5,  'psi_m': -35, 'psi_s': 20, 'w': 0.2}
+        ]
+
+    # returns the correct distribution
+    def _get_distribution(self, res_name):
+        if res_name == 'GLY':
+            return self.glycine_dist
+        elif res_name == 'PRO':
+            return self.proline_dist
+        else:
+            return self.general_dist
+
+    # returns (phi, psi) for the residue (units degrees)
+    def sample(self, res_name): 
+        # the possible regions to sample 
+        dist_options = self._get_distribution(res_name)
+        
+        weights = [d['w'] for d in dist_options]
+        # normalise the weights to ensure sum is exactly 1.0 (no float errors)
+        weights = np.array(weights) / np.sum(weights)
+        # choose a region based on the weights 
+        choice_idx = np.random.choice(len(dist_options), p=weights)
+        selected = dist_options[choice_idx]
+        
+        # do a gaussian sample to get some variation
+        phi = np.random.normal(selected['phi_m'], selected['phi_s'])
+        psi = np.random.normal(selected['psi_m'], selected['psi_s'])
+        
+        # wrap angles to +-180 degrees
+        phi = (phi + 180) % 360 - 180
+        psi = (psi + 180) % 360 - 180
+        
+        return phi, psi
+
+# example
+if __name__ == "__main__":
+    sampler = RamachandranSampler()
+    
+    print("Sampling 5 residues...")
+    for res in ['ALA', 'GLY', 'PRO', 'TRP', 'VAL']:
+        phi, psi = sampler.sample(res)
+        print(f"{res}: Phi={phi:.1f}, Psi={psi:.1f}")

src/legacy/backbone.py

@@ -4,23 +4,20 @@ from mpl_toolkits.mplot3d import Axes3D
 from nerf import place_atom_nerf
 from ramachandran import RamachandranSampler
 
-# --- Constants (Idealized Geometry in Angstroms & Degrees) ---
+# Ideal geometry. Angstroms for lengths, degrees for angles.
 GEO = {
     'N_CA_len': 1.46,
     'CA_C_len': 1.51,
-    'C_N_len':  1.33,  # Peptide bond length
-    
-    # --- MISSING KEYS ADDED HERE ---
-    'N_H_len':  1.01,  # Backbone Amide H bond length
-    'C_N_H_angle': 119.0, # Angle for placing the H
-    # -------------------------------
+    'C_N_len':  1.33, 
+    'N_H_len':  1.01,  
 
-    # Bond Angles (Standard idealized values)
     'N_CA_C_angle': 111.0,
     'CA_C_N_angle': 116.0, 
     'C_N_CA_angle': 122.0,
+    'C_N_H_angle': 119.0, 
 }
 
+# Legacy function checking if two atoms (implementation as CAs) are within threshold.
 def check_clashes(new_coord, existing_coords, threshold=3.0):
     if len(existing_coords) == 0: return False
     diff = existing_coords - new_coord
@@ -165,4 +162,4 @@ if __name__ == "__main__":
     backbone = generate_backbone_chain(test_seq, place_atom_nerf, sampler)
     
     # 4. Visualize
-    plot_backbone(backbone)
+    plot_backbone(backbone)

src/legacy/ramachandran.py

@@ -2,45 +2,38 @@ import numpy as np
 
 class RamachandranSampler:
     def __init__(self):
-        # Format: 'Region_Name': { 
-        #     'phi_mean': x, 'phi_sigma': x, 
-        #     'psi_mean': x, 'psi_sigma': x, 
-        #     'weight': probability 
-        # }
         
-        # 1. GENERAL (18 Amino Acids)
-        # Tuned for "Random Coil" (High Beta/PPII, Low Alpha)
+        # Generalised for 18 amino acids. Weighted for beta strand region
         self.general_dist = [
-            # Beta / PPII Region (Favored in unfolded states)
-            {'phi_m': -120, 'phi_s': 20, 'psi_m': 140, 'psi_s': 20, 'w': 0.60},
-            # Alpha-Right Region (Less common in unfolded, but present)
-            {'phi_m': -60,  'phi_s': 15, 'psi_m': -40, 'psi_s': 15, 'w': 0.30},
-            # Alpha-Left / Bridge (Rare)
-            {'phi_m': 60,   'phi_s': 15, 'psi_m': 40,  'psi_s': 15, 'w': 0.10}
+            # beta strand (top left)
+            {'phi_m': -120, 'phi_s': 20, 'psi_m': 140, 'psi_s': 20, 'w': 0.70},
+            # right handed helix (bottom left)
+            {'phi_m': -65,  'phi_s': 15, 'psi_m': -40, 'psi_s': 15, 'w': 0.25},
+            # left handed helix (top right)
+            {'phi_m': 60,   'phi_s': 15, 'psi_m': 40,  'psi_s': 15, 'w': 0.05}
         ]
 
-        # 2. GLYCINE (Flexible)
-        # Glycine can visit valid regions in all 4 quadrants
+        # Glycine more flexible
         self.glycine_dist = [
-            # Top Left (Beta/PPII)
+            # beta strand (top left)
             {'phi_m': -100, 'phi_s': 30, 'psi_m': 140, 'psi_s': 30, 'w': 0.3},
-            # Bottom Left (Alpha-R)
+            # right handed helix (bottom left)
             {'phi_m': -60,  'phi_s': 30, 'psi_m': -30, 'psi_s': 30, 'w': 0.2},
-            # Top Right (Left-handed Helix - Unique to Gly)
+            # left handed helix (top right)
             {'phi_m': 60,   'phi_s': 30, 'psi_m': 30,  'psi_s': 30, 'w': 0.2},
-            # Bottom Right (Inverted Beta)
+            # bottom right for glycine
             {'phi_m': 100,  'phi_s': 30, 'psi_m': -140,'psi_s': 30, 'w': 0.3}
         ]
 
-        # 3. PROLINE (Rigid)
-        # Phi is strictly locked around -63 degrees
+        # Proline no left handed helix
         self.proline_dist = [
-            # Beta/PPII (Dominant)
+            # beta strand (top left)
             {'phi_m': -63,  'phi_s': 5,  'psi_m': 150, 'psi_s': 20, 'w': 0.8},
-            # Alpha (Minor)
+            # right handed helix (bottom left)
             {'phi_m': -63,  'phi_s': 5,  'psi_m': -35, 'psi_s': 20, 'w': 0.2}
         ]
 
+    # returns the correct distribution
     def _get_distribution(self, res_name):
         if res_name == 'GLY':
             return self.glycine_dist
@@ -49,31 +42,29 @@ class RamachandranSampler:
         else:
             return self.general_dist
 
-    def sample(self, res_name):
-        """
-        Returns a tuple (phi, psi) in degrees for the given residue.
-        """
+    # returns (phi, psi) for the residue (units degrees)
+    def sample(self, res_name): 
+        # the possible regions to sample 
         dist_options = self._get_distribution(res_name)
         
-        # 1. Pick a region based on weights
         weights = [d['w'] for d in dist_options]
-        # Normalize weights to ensure sum is 1.0 (to avoid float errors)
+        # normalise the weights to ensure sum is exactly 1.0 (no float errors)
         weights = np.array(weights) / np.sum(weights)
-        
+        # choose a region based on the weights 
         choice_idx = np.random.choice(len(dist_options), p=weights)
         selected = dist_options[choice_idx]
         
-        # 2. Sample Gaussian for that region
+        # do a gaussian sample to get some variation
         phi = np.random.normal(selected['phi_m'], selected['phi_s'])
         psi = np.random.normal(selected['psi_m'], selected['psi_s'])
         
-        # 3. Wrap angles to [-180, 180] range (optional but good practice)
+        # wrap angles to +-180 degrees
         phi = (phi + 180) % 360 - 180
         psi = (psi + 180) % 360 - 180
         
         return phi, psi
 
-# --- Usage Example ---
+# example
 if __name__ == "__main__":
     sampler = RamachandranSampler()
     

src/main.py

@@ -0,0 +1,15 @@
+from backbone.ramachandran import RamachandranSampler
+from rotamers.dunbrack import DunbrackRotamerLibrary
+
+rs = RamachandranSampler()
+rl = DunbrackRotamerLibrary()
+
+res_name = "PHE"
+
+print(f"Backbone torsion angles for {res_name}")
+phi, psi = rs.sample(res_name)
+print(f"phi: {phi}, psi: {psi}")
+
+print(f"Sidechain rotamers for {res_name}")
+for rotamer in rl.rotamer_params(res_name, 100, 100):
+    print(rotamer.p, rotamer.chis)

src/rotamers/dunbrack.py

@@ -25,7 +25,7 @@
 _dependent_cache = {}
 _independent_cache = {}
 
-from rotamers import RotamerLibrary, RotamerParams, UnsupportedResTypeError, NoResidueRotamersError
+from rotamers.rotamers_lib import RotamerLibrary, RotamerParams, UnsupportedResTypeError, NoResidueRotamersError
 
 class DunbrackRotamerLibrary(RotamerLibrary):