Prototype origin residue

src/geometry/backbone.py

@@ -1,25 +1,23 @@
-import numpy as np
+
-# Ideal geometry. Angstroms for lengths, degrees for angles. Engh & Huber parameters
+# Ideal geometry. Angstroms for lengths, degrees for angles.
 GEO = {
-    'N_CA_length': 1.46,
+    'N_CA_len': 1.46,
-    'CA_C_length': 1.51,
+    'CA_C_len': 1.51,
-    'C_N_length':  1.33, 
+    'C_N_len':  1.33, 
-    'N_H_length':  1.01,  
+    'N_H_len':  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': np.array([ -17.396, -12.153, -13.987 ]),
+     'N': [ -17.396, -12.153, -13.987 ],
-    'CA': np.array([ -16.295, -12.486, -13.259 ]),
+    'CA': [ -16.295, -12.486, -13.259 ],
-     'C': np.array([ -16.534, -10.993, -13.428 ]),
+     'C': [ -16.534, -10.993, -13.428 ],
-     'O': np.array([ -16.891, -10.572, -14.520 ]),
+     'O': [ -16.891, -10.572, -14.520 ],
 }
 
 if __name__ == "__main__":

src/geometry/sidechain.py

@@ -1,8 +0,0 @@
-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

@@ -2,3 +2,15 @@
 # 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

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

src/test.py

@@ -1,69 +1,17 @@
 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()
 
-ghost_residue = Residue(ResidueName.GLY)
+res_name = "PHE"
-backbone_atoms = ["N", "CA", "C", "O"]
-for atom in backbone_atoms:
-    ghost_residue.backbone["atoms"][atom] = ORI[atom]
 
-primary_sequence = ["PHE", "SER", "THR"]
+print(f"Backbone torsion angles for {res_name}:")
+phi, psi = rs.sample(res_name)
+print(f"phi: {phi}, psi: {psi}")
+print(" ")
 
-residues = [ ghost_residue ]
+print(f"Sidechain rotamers for {res_name} (top 5):")
-
+for rotamer in rl.rotamer_params(res_name, 100, 100)[:5]:
-# First 2 residues of the sequence
+    print(rotamer.p, rotamer.chis)
-for residue_index, residue_name in enumerate(primary_sequence[:2]):
+print(" ")
-    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