full output except STRUCTURE column

src/atom.py

@@ -28,10 +28,21 @@ class Residue:
             self.atoms[atom.atom_name] = atom
             self.resid = atom.res_seq_nb
             self.res_name = atom.res_name
+            self.res_letter = self.get_amino_letter(atom.res_name)
             self.chain_id = atom.chain_id
             self.insertion_code = atom.insertion_code
             self.indice = indice
             
+    def get_amino_letter(self, res_name):
+        code3 = ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLU', 'GLN', 'GLY',
+                 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER',
+                 'THR', 'TRP', 'TYR', 'VAL']
+
+
+        code1 = ['A','R','N','D','C','E','Q','G','H','I','L','K','M','F','P',
+                 'S','T','W','Y','V']
+
+        return code1[code3.index(res_name)]
 
     def h_bond(self, res2):
         if("H" not in res2.atoms.keys()):
@@ -70,6 +81,18 @@ class Residue:
 
         return False
 
+    def get_bends(self, residues):
+        i = residues.index(self)
+        if i >=2 and i <len(residues)-2:
+            angle = math.degrees(vector_angles(vectors_substr(position_vector(residues[i].atoms["CA"].coords),
+                                                              position_vector(residues[i-2].atoms["CA"].coords)),
+                                               vectors_substr(position_vector(residues[i+2].atoms["CA"].coords),
+                                                              position_vector(residues[i].atoms["CA"].coords))))
+           
+            return angle
+        else:
+            return 360.0
+
     def get_bridges(self, residues):
         bridges = {}
         bridge = {}
@@ -163,6 +186,58 @@ class Residue:
                         return ladder
         return False   
 
+    def get_tco(self, residues):
+        i = residues.index(self)
+        if(i!=0):
+            res2 = residues[i-1]
+            CO_res1 = vector_from_pos(self.atoms["C"].coords,
+                                      self.atoms["O"].coords)
+            CO_res2 = vector_from_pos(res2.atoms["C"].coords,
+                                      res2.atoms["O"].coords)
+            angle = vector_angles(CO_res1, CO_res2)
+        else:
+            angle = math.pi/2
+        return(math.cos(angle))
+
+    def get_chirality(self, residues):
+        i = residues.index(self)
+        if (i >=1 and i < len(residues)-2):
+            chirality = {}
+            angle = calc_dihedral(residues[i-1].atoms["CA"].coords,
+                                  residues[i].atoms["CA"].coords,
+                                  residues[i+1].atoms["CA"].coords,
+                                  residues[i+2].atoms["CA"].coords)
+
+            if(angle>0 and angle<=180):
+                sign="+"
+
+            if(angle<=0 and angle > -180):
+                sign="-"
+
+        else:
+            angle = 360.0
+            sign = ''
+
+        return [angle, sign]
+    
+    def get_phi_psi(self, residues):
+        i = residues.index(self)  
+        if(i==0):
+            phi = 360.0
+        else:
+            phi = calc_dihedral(residues[i-1].atoms["C"].coords,
+                                residues[i].atoms["N"].coords,
+                                residues[i].atoms["CA"].coords,
+                                residues[i].atoms["C"].coords)
+        if(i==len(residues)-1):
+            psi = 360.0
+        else:
+            psi = calc_dihedral(residues[i].atoms["N"].coords,
+                                residues[i].atoms["CA"].coords,
+                                residues[i].atoms["C"].coords,
+                                residues[i+1].atoms["N"].coords)
+
+        return((phi, psi))
 def get_bridges(residues):
     bridges = {}
     bridge = {}

src/dssp.py

@@ -13,22 +13,12 @@ if(len(sys.argv)<2):
           "call structure and parameters.")
 else:
     pdb_file = pdb.PDBFile(sys.argv[1])
-   # print(pdb_file.residues[15].atoms["C"].coord_x)
-    #print(pdb_file.residues[2].atoms["N"].res_seq_nb, pdb_file.residues[2].atoms["N"].coord_x, pdb_file.residues[2].atoms["N"].coord_y, pdb_file.residues[2].atoms["N"].coord_z)
-    #print(pdb_file.residues[2].atoms["H"].coord_x)
-    #print(pdb_file.residues[2].h_bond(pdb_file.residues[40]))
-    #print(get_turns(pdb_file.residues))
-    #print(pdb_file.residues[27].h_bond(pdb_file.residues[28]))
-    #print(get_bridges(pdb_file.residues))
-
   
     #turns = get_turns(pdb_file.residues)
     #get_helix(pdb_file.residues, turns)
     #get_bends(pdb_file.residues)
     # get_chirality(pdb_file.residues)
-    bridges = get_bridges(pdb_file.residues)
+
-    ladders = get_ladders(bridges, pdb_file.residues)
-    sheets = get_sheets(ladders)  
 
     # print("NBRIDGES",len(bridges))
 
@@ -36,32 +26,51 @@ else:
 
     # get_bonds(pdb_file.residues)
 
-    residues = pdb_file.residues
+
-    e_min = 0
+    # e_min = 0
-    for res in residues:
+    # for res in residues:
-        ene = residues[1].h_bond(res)
+    #     ene = residues[1].h_bond(res)
-        if ene <= e_min:
+    #     if ene <= e_min:
-            e_min = ene
+    #         e_min = ene
-            best_res = res
+    #         best_res = res
     #print(residues[1].resid, best_res.resid,e_min)
 
     #get_phi_psi(residues)
     #print(residues[2].atoms, residues[0].resid, residues[1].resid)
     #print(get_TCO(residues[2],residues[3]))
 
+
+# for i,ladder in enumerate(ladders.values()):
+#     print(chr(65+i))
+    
+# for ind, sheet in sheets.items():
+#     print(ind, sheet)
+#     for ladder in sheet:
+#         print(ladder['start'], ladder['end'])
+
+
+################### OUTPUT ####################
+# print DSSP-style formatted header of PDB file
+for elem in pdb_file.get_header() : 
+    print(pdb_file.get_header()[elem], end="")
+
+# Get preliminary data for print loop
+residues = pdb_file.residues
+bridges = get_bridges(residues)
+ladders = get_ladders(bridges, residues)
+sheets = get_sheets(ladders)  
+
+# iterating over residues
 for i,res in enumerate(residues):
     #res.get_turns(residues, turns)
-        res.get_helix(residues)
+    #res.get_helix(residues)
-        #res.get_bridges(residues)
+    kappa = res.get_bends(residues)
-        #res.get_ladders(residues, ladders)
+    t_co = res.get_tco(residues)
-        #res.get_sheets(residues)
+    alpha = res.get_chirality(residues)[0]
-
+    phi = res.get_phi_psi(residues)[0]
-for i,ladder in enumerate(ladders.values()):
+    psi = res.get_phi_psi(residues)[1]
-    print(chr(65+i))
+    x_ca = res.atoms["CA"].coord_x
-    
+    y_ca = res.atoms["CA"].coord_y
-for ind, sheet in sheets.items():
+    z_ca = res.atoms["CA"].coord_z
-    print(ind, sheet)
+    print(i+1, res.resid, res.chain_id, res.res_letter, round(t_co, 3), round(kappa,1),
-    for ladder in sheet:
+          round(alpha, 1), round(phi, 1), round(psi,1), round(x_ca,1), round(y_ca,1), round(z_ca,1))
-        print(ladder['start'], ladder['end'])
-
-

src/geom.py

@@ -1,4 +1,5 @@
 import math
+import numpy as np
 def vector_from_pos(a, b):
     xAB = b[0]-a[0]
     yAB = b[1]-a[1]