diff corebio/resource/stride.py @ 0:c55bdc2fb9fa

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/corebio/resource/stride.py	Thu Oct 27 12:09:09 2011 -0400
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+
+#  Copyright (c) 2003 Gavin E. Crooks
+#  Copyright (c) 2005 David D. Ding <[e-mail]>
+#
+#  This software is distributed under the MIT Open Source License.
+#  <http://www.opensource.org/licenses/mit-license.html>
+#
+#  Permission is hereby granted, free of charge, to any person obtaining a 
+#  copy of this software and associated documentation files (the "Software"),
+#  to deal in the Software without restriction, including without limitation
+#  the rights to use, copy, modify, merge, publish, distribute, sublicense,
+#  and/or sell copies of the Software, and to permit persons to whom the
+#  Software is furnished to do so, subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included
+#  in all copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
+#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 
+#  THE SOFTWARE.
+
+"""STRIDE: Protein secondary structure assignment from atomic coordinates.
+
+This module provides an interface to STRIDE, a c program used to recognize
+secondary structural elements in proteins from their atomic coordinates.
+
+"""
+
+from corebio.seq import Seq, protein_alphabet, Alphabet
+from corebio.resource.astral import to_one_letter_code
+
+# alphabet for stride secondary structure
+stride_alphabet = Alphabet("HGIEBC12345678@&T")
+
+# Dictionary for conversion between names and alphabet
+stride_alphabet_names  = ( 
+    "H", "AlphaHelix",
+    "G", "310Helix",
+    "I", "PiHelix",
+    "E", "Strand",
+    "b", "Bridge",
+    "B", "Bridge",
+    "C", "Coil",
+    "1", "TurnI",
+    "2", "TurnI'",
+    "3", "TurnII",
+    "4", "TurnII'",
+    "5", "TurnVIa",
+    "6", "TurnVIb",
+    "7", "TurnVIII",
+    "8", "TurnIV",
+    "@", "GammaClassic",
+    "&", "GammaInv",
+    "T", "Turn"
+    )
+
+
+class Stride(object) :
+    def __init__(self, stride_file) :
+        """ Read and parse a STRIDE output file.
+        
+        args:
+            - stride_file   : An open file handle
+        attributes :
+            - pdbid     : The PDB id.
+            - res       : A list of Res objects, one per PDB resiude
+        """     
+        res =[]
+        f=stride_file
+        self.pdbid = f.readline()[75:79]
+        for l in f:
+            if l[0:3] =="ASG":
+                res.append(Res(l)) 
+                
+        self.res = res # A list of Res objects
+        
+        self._res_dict = None
+
+    def total_area(self) :
+        """ Return the solvent accessible area """
+        area = 0
+        for i in self.res :
+            area += i.solvent_acc_area
+        return area
+    
+    def primary(self):
+        """ Return the protein primary sequence as a Seq object."""
+        return Seq(''.join([r.primary_seq for r in self.res]), protein_alphabet)
+        
+    def secondary(self):
+        """Return the secondary structure of the protien as a Seq object"""
+        return Seq(''.join([r.secondary_str for r in self.res]), stride_alphabet)
+        
+        
+    def get_res(self, chainid, resid) :
+        """ Return the given resiude """
+        if not self._res_dict :
+            d = {}
+            for r in self.res :
+                d[ (r.chainid, r.resid)] = r
+            self._res_dict =d
+        
+        return self._res_dict[(chainid, resid)]
+
+    
+    
+class Res(object):
+    """ Structural information of a single resiude. An ASG line from a stride
+        output file.
+        
+        Attributes :
+         - chainid 
+         - resid   
+         - primary_seq 
+         - secondary_str 
+         - solvent_acc_area 
+         - phi 
+         - psi
+    """
+         
+    def __init__(self, res_line) :
+        """ Eats a single 'ASG' line from a stride file, splits it up  
+        into parts and return a Res object."""
+            
+        if (len(res_line)<70): 
+            raise ValueError("Line not long enough")
+        try: 
+            self.chainid = res_line[9:10]
+            # STRIDE converts blank chain ids into dashes. Undo.
+            if self.chainid=="-" : self.chainid = " "
+                
+            # In rare cases STRIDE columns can be misaligned. Grab extra 
+            # white space to compensate.
+            self.resid = res_line[10:15].strip() 
+            self.primary_seq = to_one_letter_code[res_line[5:8].capitalize()]
+            self.secondary_str = res_line[24:25]
+            self.solvent_acc_area = float(res_line[64:71]) 
+            self.phi = float(res_line[42:49].strip())
+            self.psi = float(res_line[52:59].strip())
+        except FloatingPointError:
+            raise FloatingPointError("Can't float phi, psi, or area")
+        except KeyError:
+            raise KeyError("Can't find three letter code in dictionary")
+        except LookupError:
+            raise LookupError("One of the values is out of index of res_line")
+            
+                
+            
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