Started GEO dictionary

src/geometry/backbone.py

@@ -1,23 +1,25 @@
-
-# Ideal geometry. Angstroms for lengths, degrees for angles.
+import numpy as np
+# Ideal geometry. Angstroms for lengths, degrees for angles. Engh & Huber parameters
 GEO = {
-    'N_CA_len': 1.46,
-    'CA_C_len': 1.51,
-    'C_N_len':  1.33, 
-    'N_H_len':  1.01,  
+    'N_CA_length': 1.46,
+    'CA_C_length': 1.51,
+    'C_N_length':  1.33, 
+    'N_H_length':  1.01,  
+    'C_O_length': 1.23,
 
     'N_CA_C_angle': 111.0,
     'CA_C_N_angle': 116.0, 
     'C_N_CA_angle': 122.0,
     'C_N_H_angle': 119.0, 
+    'CA_C_O_angle': 121.0,
 }
 
 # First residue backbone hardcoded. From 6G4A MET1
 ORI = {
-     'N': [ -17.396, -12.153, -13.987 ],
-    'CA': [ -16.295, -12.486, -13.259 ],
-     'C': [ -16.534, -10.993, -13.428 ],
-     'O': [ -16.891, -10.572, -14.520 ],
+     'N': np.array([ -17.396, -12.153, -13.987 ]),
+    'CA': np.array([ -16.295, -12.486, -13.259 ]),
+     'C': np.array([ -16.534, -10.993, -13.428 ]),
+     'O': np.array([ -16.891, -10.572, -14.520 ]),
 }
 
 if __name__ == "__main__":

src/geometry/sidechain.py

@@ -0,0 +1,8 @@
+GEO = {
+    'CA_CB_length': 1.53,
+
+    'N_CA_CB_angle': 109.5,
+    'C_CA_CB_angle': 109.5,
+
+    'L_torsion': 122.55
+}

src/main.py

@@ -2,15 +2,3 @@
 # Build first residue including sidechain
 # Add ghost C' for first NeRF iteration
 # Using C 
-
-from protein.residue import Residue, ResidueName
-from geometry.backbone import GEO, ORI
-
-met1 = Residue(ResidueName.MET)
-
-print(met1.name.value)
-
-for atom in ORI:
-    met1.backbone["atoms"][atom] = ORI[atom]
-
-print(met1.backbone["atoms"])

src/protein/residue.py

@@ -29,12 +29,15 @@ class Residue():
         self.name = name
 
         self.backbone = {
-            'atoms': { "N": None, "CA": None, "C": None, "O": None },
-            'phi': None,
-            'psi': None
+            "atoms": { "N": None, "CA": None, "C": None, "O": None },
+            "phi": None,
+            "psi": None
         }
         
         self.sidechain = {
-            'atoms': {},
-            'chis': []
+            "atoms": {},
+            "chis": []
         }
+
+    def summary(self):
+        return f"ResidueName: {self.name.value}"

src/test.py

@@ -1,17 +1,69 @@
 from backbone.ramachandran import RamachandranSampler
 from rotamers.dunbrack import DunbrackRotamerLibrary
+from geometry.backbone import GEO as BACKBONE_GEO, ORI
+from geometry.sidechain import GEO as SIDECHAIN_GEO
+from geometry.nerf import nerf
+from protein.residue import ResidueName, Residue
 
 rs = RamachandranSampler()
 rl = DunbrackRotamerLibrary()
 
-res_name = "PHE"
+ghost_residue = Residue(ResidueName.GLY)
+backbone_atoms = ["N", "CA", "C", "O"]
+for atom in backbone_atoms:
+    ghost_residue.backbone["atoms"][atom] = ORI[atom]
 
-print(f"Backbone torsion angles for {res_name}:")
-phi, psi = rs.sample(res_name)
-print(f"phi: {phi}, psi: {psi}")
-print(" ")
+primary_sequence = ["PHE", "SER", "THR"]
 
-print(f"Sidechain rotamers for {res_name} (top 5):")
-for rotamer in rl.rotamer_params(res_name, 100, 100)[:5]:
-    print(rotamer.p, rotamer.chis)
-print(" ")
+residues = [ ghost_residue ]
+
+# First 2 residues of the sequence
+for residue_index, residue_name in enumerate(primary_sequence[:2]):
+    residue = Residue(ResidueName(residue_name))
+    residue.backbone["phi"], residue.backbone["psi"] = rs.sample(residue.name.value)
+    
+    residue.backbone["atoms"]["N"] = nerf(
+        residues[residue_index].backbone["atoms"]["N"],
+        residues[residue_index].backbone["atoms"]["CA"],
+        residues[residue_index].backbone["atoms"]["C"],
+        BACKBONE_GEO["C_N_length"],
+        BACKBONE_GEO["CA_C_N_angle"],
+        residues[residue_index].backbone["psi"],
+        )
+    
+    residue.backbone["atoms"]["CA"] = nerf(
+        residues[residue_index].backbone["atoms"]["CA"],
+        residues[residue_index].backbone["atoms"]["C"],
+        residue.backbone["atoms"]["N"],
+        BACKBONE_GEO["N_CA_length"],
+        BACKBONE_GEO["C_N_CA_angle"],
+        180,
+        )
+    
+    residue.backbone["atoms"]["C"] = nerf(
+        residues[residue_index].backbone["atoms"]["C"],
+        residue.backbone["atoms"]["N"],
+        residue.backbone["atoms"]["CA"],
+        BACKBONE_GEO["CA_C_length"],
+        BACKBONE_GEO["N_CA_C_angle"],
+        residue.backbone["phi"],
+        )
+    
+    residue.backbone["atoms"]["O"] = nerf(
+        residue.backbone["atoms"]["N"],
+        residue.backbone["atoms"]["CA"],
+        residue.backbone["atoms"]["C"],
+        BACKBONE_GEO["C_O_length"],
+        BACKBONE_GEO["CA_C_O_angle"],
+        residue.backbone["psi"] + 180,
+        )
+
+    residue.sidechain
+    residues.append(residue)
+
+    residue.sidechain["chis"] =  rl.rotamer_params(residue.name.value, residue.backbone["phi"], residue.backbone["psi"])
+
+    print(residue.summary())
+
+# Generate a tripeptide backbone
+# Populate the sidechain of the middle residue