From 548aee18db14512c2bd73165a43b17f5d58685b4 Mon Sep 17 00:00:00 2001
From: Marat Valiev <marat.valiev@pnnl.gov>
Date: Thu, 9 Feb 2012 03:30:02 +0000
Subject: [PATCH] connected to pdbrecord

---
 contrib/marat/nwchem-python/GenericAtom.py | 48 +++++++++++++++++-----
 1 file changed, 38 insertions(+), 10 deletions(-)

diff --git a/contrib/marat/nwchem-python/GenericAtom.py b/contrib/marat/nwchem-python/GenericAtom.py
index cd04051253..39d099c833 100644
--- a/contrib/marat/nwchem-python/GenericAtom.py
+++ b/contrib/marat/nwchem-python/GenericAtom.py
@@ -5,28 +5,56 @@ Created on Feb 7, 2012
 '''
 import sys
 from types import *
+from pdbrecord import PDBAtomRecord 
+from numpy import *
 
-class GenericAtom:
+class GenericAtom(object):
     '''
     classdocs
     '''
 
-
-    def __init__(self,d=None):
+    def __init__(self,d):
         '''
         Constructor
         '''
-        if d is None:
-            self.dict  = {}
-        else:
+        self.dct = d
+
+        if d:
             if type(d) is not type({}):
                 print "wrong type ", type(d)
                 print "expecting", type({})
                 sys.exit(1)
             else:
-                self.dict  = d
+                self.dct  = d
+        try:
+            self.coord=array(self.dct.pop("coord"))
+        except:
+            self.coord=None
+                
+    @classmethod                
+    def fromPDBrecord(cls,buf):
+        '''
+        alternative constructor from PDB record
+        '''
+        d=PDBAtomRecord.dct(buf)
+        if d:
+            return cls(d)
+        return None
+    @staticmethod
+    def bondlength(a1,a2):
+        dr=a1.coord-a2.coord
+        return linalg.norm(dr)
+
             
 if __name__ == '__main__':
-    a=GenericAtom({})
-    print a
-        
\ No newline at end of file
+    aline1="ATOM    588 1HG  GLU    18     -13.363  -4.163  -2.372  1.00  0.00           H"
+    aline2="ATOM      1  I1  IO3     1      -1.555  -0.350   0.333        1.39           I"
+    aline3="ATOM      2  O1  IO3     1      -0.985  -1.156   1.840       -0.80           O"
+
+    a=GenericAtom.fromPDBrecord(aline2)   
+    print a.coord
+    print a.dct     
+    b=GenericAtom.fromPDBrecord(aline3)
+    print b.coord
+    print b.dct         
+    print GenericAtom.bondlength(a,b)
\ No newline at end of file