just renamed it

contrib/marat/nwchem-python/pdbparser.py

@@ -0,0 +1,146 @@
+'''
+Created on Feb 7, 2012
+
+@author: marat
+'''
+import string 
+from array import *
+import inspect
+
+class PDBRecord:
+    '''
+    class PDBRecord parses line in PDB file.
+    It can only properly handle ATOM or HETATM records.
+    Before getting individual fields one should test
+    whether the record is atom based using PDBRecord.isAtomType() method.
+    Perhaps the best way to use this class at this point is to generate 
+    dictionary using PDBRecord.getDict(aline1)
+    
+    '''
+    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]
+    
+#    dictPDB=dict(record=[0,6],
+#                 )
+
+
+
+#     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
+#        '''
+#        pass
+
+    @staticmethod   
+    def recordName(buf):
+#        print inspect.getsource(PDBRecord.recordName)
+        return PDBRecord.genrecord(buf,PDBRecord.irecord)
+
+    @staticmethod     
+    def atomId(buf):
+        return int(PDBRecord.genrecord(buf,PDBRecord.inum))
+        
+    @staticmethod   
+    def atomName(buf):
+        return PDBRecord.genrecord(buf,PDBRecord.iname)
+    
+    @staticmethod   
+    def resName(buf):
+        return PDBRecord.genrecord(buf,PDBRecord.iresname)
+    
+    @staticmethod   
+    def elemName(buf):
+        return PDBRecord.genrecord(buf,PDBRecord.iel)
+    
+    @staticmethod     
+    def resId(buf):
+        return int(PDBRecord.genrecord(buf,PDBRecord.iresid))
+    
+    @staticmethod     
+    def atomCoord(buf):
+        return [float(PDBRecord.genrecord(buf,PDBRecord.ix)),
+                float(PDBRecord.genrecord(buf,PDBRecord.iy)),
+                float(PDBRecord.genrecord(buf,PDBRecord.iz))]
+
+    @staticmethod              
+    def getDict(buf):
+        d = {}
+        d["record"]=PDBRecord.recordName(buf)
+        if d["record"] not in ("ATOM  ", "HETATM"):
+            print d["record"]
+            return d  
+        d["element"]=PDBRecord.elemName(buf)  
+        d["coords"]=PDBRecord.atomCoord(buf) 
+        d["name"]=PDBRecord.atomName(buf)
+        d["resid"]=PDBRecord.resId(buf)
+        d["atomid"]=PDBRecord.atomId(buf)
+        d["resname"]=PDBRecord.resName(buf)
+
+        return d   
+                          
+    @staticmethod     
+    def genrecord(buf,ir):
+        return buf[ir[0]:ir[1]] 
+    
+    @staticmethod     
+    def isAtomType(buf):
+        return buf[0:4]!="ATOM" or buf[0:6]!="HETATM"
+              
+        
+    def __str__(self):
+        return self.buf
+    
+
+if __name__ == '__main__':
+    aline1="AAOM    588 1HG  GLU    18     -13.363  -4.163  -2.372  1.00  0.00           H"
+
+    print aline1
+#    print PDBRecord.recordName(aline1)
+#    print PDBRecord.atomName(aline1)    
+#    print PDBRecord.resName(aline1) 
+#    print PDBRecord.resId(aline1)
+#    print PDBRecord.elemName(aline1)     
+#    print PDBRecord.atomCoord(aline1)        
+#    print PDBRecord.isAtomType(aline1)    
+    print PDBRecord.getDict(aline1)
+
+    
+#    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
+                                          
+
+