implementented generating backbone for first residue and the ghost residue

src/test.py

@@ -1,17 +1,67 @@
 from backbone.ramachandran import RamachandranSampler
 from rotamers.dunbrack import DunbrackRotamerLibrary
+from geometry.backbone import GEO, ORI
+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"],
+        GEO["C_N_length"],
+        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"],
+        GEO["N_CA_length"],
+        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"],
+        GEO["CA_C_length"],
+        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"],
+        GEO["C_O_length"],
+        GEO["CA_C_O_angle"],
+        residue.backbone["psi"] + 180,
+        )
+
+    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