Python class to handle PDB records

contrib/marat/nwchem-python/pdbrecord.py

@@ -0,0 +1,103 @@
+'''
+Created on Feb 7, 2012
+
+@author: marat
+'''
+import string 
+from array import *
+class PDBRecord:
+    '''
+    classdocs
+    '''
+    irecord=[0,6]
+    inum=[6,11]
+    iname=[12,16]
+    iresname=[17,20]
+    iresid=[22,26]
+    ix=[30,38]
+    iy=[38,46]
+    iz=[46,54]
+    iel=[76,78]
+    
+
+#     1 -  6      Record name      "ATOM    "
+#     7 - 11      Integer          serial     Atom serial number.
+#    13 - 16      Atom             name       Atom name.
+#    17           Character        altLoc     Alternate location indicator.
+#    18 - 20      Residue name     resName    Residue name.
+#    22           Character        chainID    Chain identifier.
+#    23 - 26      Integer          resSeq     Residue sequence number.
+#    27           AChar            iCode      Code for insertion of residues.
+#    31 - 38      Real(8.3)        x          Orthogonal coordinates for X in 
+#                                             Angstroms
+#    39 - 46      Real(8.3)        y          Orthogonal coordinates for Y in 
+#                                             Angstroms
+#    47 - 54      Real(8.3)        z          Orthogonal coordinates for Z in 
+#                                             Angstroms
+#    55 - 60      Real(6.2)        occupancy  Occupancy.
+#    61 - 66      Real(6.2)        tempFactor Temperature factor.
+#    77 - 78      LString(2)       element    Element symbol, right-justified.
+#    79 - 80      LString(2)       charge     Charge on the atom.
+
+    def __init__(self,line):
+        '''
+        Constructor
+        '''
+        self.buf=line
+
+
+    def recordName(self):
+        return PDBRecord.genrecord(self.buf,self.irecord)
+
+    def atomName(self):
+        return PDBRecord.genrecord(self.buf,self.iname)
+
+    def resName(self):
+        return PDBRecord.genrecord(self.buf,self.iresname)
+
+    def elemName(self):
+        return PDBRecord.genrecord(self.buf,self.iel)
+    
+    def resId(self):
+        return int(PDBRecord.genrecord(self.buf,self.iresid))
+    
+    def atomCoord(self):
+        return [float(PDBRecord.genrecord(self.buf,self.ix)),
+                float(PDBRecord.genrecord(self.buf,self.iy)),
+                float(PDBRecord.genrecord(self.buf,self.iz))]
+
+              
+                            
+    @staticmethod     
+    def genrecord(buf,ir):
+        return buf[ir[0]:ir[1]] 
+
+        
+    def __str__(self):
+        return self.buf
+    
+
+if __name__ == '__main__':
+    aline1="ATOM    588 1HG  GLU    18     -13.363  -4.163  -2.372  1.00  0.00           H"
+    pdb1 = PDBRecord(aline1)
+    print aline1
+    print pdb1.recordName()
+    print pdb1.atomName()    
+    print pdb1.resName() 
+    print pdb1.resId()
+    print pdb1.elemName()     
+    print pdb1.atomCoord()          
+
+#    Example
+#             1         2         3         4         5         6         7         8
+#    12345678901234567890123456789012345678901234567890123456789012345678901234567890
+#    MODEL        1
+#    ATOM      1  N   ALA     1      11.104   6.134  -6.504  1.00  0.00           N
+#    ATOM      2  CA  ALA     1      11.639   6.071  -5.147  1.00  0.00           C
+#    ...
+#    ...
+#    ATOM    293 1HG  GLU    18     -14.861  -4.847   0.361  1.00  0.00           H
+#    ATOM    294 2HG  GLU    18     -13.518  -3.769   0.084  1.00  0.00           H
+                                          
+
+