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Before go back to bridges and ladders methods

Thomas Forest 4 years ago
parent
commit
182fee3f7a
2 changed files with 100 additions and 15 deletions
  1. 96 10
      src/atom.py
  2. 4 5
      src/dssp.py

+ 96 - 10
src/atom.py View File

@@ -52,17 +52,23 @@ class Residue:
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         E = q1*q2*(1/r_ON + 1/r_CH - 1/r_OH - 1/r_CN)*f
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         return(E)
54 54
 
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-    def get_turns(self, residues, turns):
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+    def get_turns(self, residues):
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         """
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         Get all the turns from a specific residue.
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         """
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+        turns = {}
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         i = residues.index(self)
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+        k = 0
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         for j in range(3,6):
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                 if(i+j<len(residues)):
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                     if(self.h_bond(residues[i+j])<-0.5):
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-                        print(j,"TURN", residues[i].resid, residues[i+j].resid)
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-                        turns[i] = Turn(j,residues[i].resid)
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+                        k = j
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+        if k != 0:    
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+            #print(k,"TURN", residues[i].resid, residues[i+k].resid)
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+            return Turn(k,residues[i].resid)
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+        return False
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+    
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     def get_bridges(self, residues):
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         bridges = {}
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         bridge = {}
@@ -124,22 +130,38 @@ class Residue:
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         else:
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             return(False)
126 132
 
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-    def get_helix(self, residues, turns):
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+    def get_helix(self, residues):
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         """
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         Return if there is an helix at a given residue,
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         as well as its type.
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         """
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         i = residues.index(self)
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         # if there are no turns or it is the first residue, skip
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-        if not turns or i == 0:
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+        if i == 0:
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             return False
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-        if (i <= len(residues)):
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-            if(i in turns.keys() and i-1 in turns.keys()):
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-                print(turns[i].turn_type,"- HELIX at", residues[i].resid)
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-                return(turns[i].turn_type, residues[i].resid)
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+        
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+        if(self.get_turns(residues) and residues[i-1].get_turns(residues)):
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+            print(self.get_turns(residues).turn_type,"- HELIX at", residues[i].resid)
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+            return(self.get_turns(residues).turn_type, residues[i].resid)
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+        return(False)
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+
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+    def get_helix2(self, residues):
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+        """
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+        Return if there is an helix at a given residue,
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+        as well as its type.
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+        """
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+        i = residues.index(self)
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+        # if there are no turns or it is the first residue, skip
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+        if i == 0:
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+            return False
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+        
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+        if(i in turns.keys() and i-1 in turns.keys()):
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+            print(turns[i].turn_type,"- HELIX at", residues[i].resid)
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+            return(turns[i].turn_type, residues[i].resid)
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         return(False)
141 162
     
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-    def get_ladders(self, residues, ladders):
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+    def get_ladders(self, residues, ladders={}):
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+        #ladders = {}
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         i = residues.index(self)
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         if i != 0:
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             if self.get_bridges(residues):
@@ -151,6 +173,70 @@ class Residue:
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                         ladders[i] = {'start':i-1,
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                                       'end':i,
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                                       'bridges':[consec_bridge, local_bridge]}
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+        return ladders
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+
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+    def get_ladder(self, residues):
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+        #ladders = {}
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+        i = residues.index(self)
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+        if i != 0:
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+            if self.get_bridges(residues):
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+                if (residues[i-1].get_bridges(residues)):
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+                    local_bridge = self.get_bridges(residues)
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+                    consec_bridge = residues[i-1].get_bridges(residues)
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+                    if local_bridge.bridge_type == consec_bridge.bridge_type:
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+                        #print("ladder", consec_bridge.res_num, local_bridge.res_num)
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+                        ladder = {'start':consec_bridge.res_num,
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+                                  'end':local_bridge.res_num,
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+                                  'bridges':[consec_bridge, local_bridge]}
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+                        return ladder
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+        return False
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+
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+    def get_sheets(self, residues):
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+        """
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+        Bridges between ladders.
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+        Check if 1 bridge between one ladder and one or more other ladders.
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+        Iterate over all residues of one ladder and check if bridge with other residues
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+        of the other ladders.
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+        """
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+        sheets = {}
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+        sheet_start = residues.index(self)
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+        j=sheet_start
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+        k=2
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+        if(self.get_ladder(residues)):
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+            local_ladder = self.get_ladder(residues)
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+            while j < len(residues)-2:
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+                k = 2
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+                while residues[j+k].get_ladder(residues):
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+                    if(residues[j+k].get_bridges(residues)):
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+                        j = j+k     
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+                    k+=1
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+                if(k>):
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+                    last = j
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+                j+=1
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+                print(j)
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+        if(k>2):                
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+            sheet_end = last      
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+                        
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+            print("SHEET", sheet_start, sheet_end)       
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+
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+    def get_sheets2(self):
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+        """
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+        Bridges between ladders.
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+        Check if 1 bridge between one ladder and one or more other ladders.
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+        Iterate over all residues of one ladder and check if bridge with other residues
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+        of the other ladders.
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+        """
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+        sheets = {}
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+        for ladder in ladders:
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+            for ladd2 in ladders:
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+                for bridge in ladders[ladder]['bridges']:
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+                    if bridge.res_partner in res_list(ladders[ladd2]):
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+                        print("ladder",ladders[ladder]['start'], ladders[ladder]['end'],"bridge",bridge.res_num, bridge.res_partner,
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+                        "ladder 2",ladders[ladd2]['start'], ladders[ladd2]['end'])
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+                #print("stop ladder 2")
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+            print("stop ladder 1")            
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+
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+            
154 240
 
155 241
     def get_ladders2(self, bridges, residues):
156 242
         ladders = {}

+ 4 - 5
src/dssp.py View File

@@ -49,12 +49,11 @@ else:
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     #print(residues[2].atoms, residues[0].resid, residues[1].resid)
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     print(get_TCO(residues[2],residues[3]))
51 51
 
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-    turns = {}
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+    #turns = {}
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     ladders = {}
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     for i,res in enumerate(residues):
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         # res.get_turns(residues, turns)
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-        # res.get_helix(residues, turns)
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-        res.get_bridges(residues)
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+        #res.get_helix(residues)
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+        #res.get_bridges(residues)
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         res.get_ladders(residues, ladders)
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-        
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- 
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+        #res.get_sheets(residues)