system definition

contrib/marat/nwchem-python/my_system.py

@@ -0,0 +1,87 @@
+'''
+Created on Feb 5, 2012
+
+@author: marat
+'''
+from atom_params import *
+from generic_atom import *
+from generic_residue import *
+
+class MySystem(object):
+    '''
+    classdocs
+    '''
+
+
+    def __init__(self, name=None,atoms=None):
+        '''
+        Constructor
+        '''
+        self.name  = "system" if name==None else name
+        self.atoms = [] if atoms==None else atoms
+        self.residues = {}
+        self.natoms=len(self.atoms)
+
+    def info1(self):
+        output = self.name +"\n"
+        for x in self.atoms:
+            output = output + str(x)+"\n"
+        return output
+    
+    @classmethod        
+    def fromPDBfile(cls,filename):
+        '''
+        alternative constructor from PDB file
+        '''
+        cls = MySystem()
+#        print cls
+#        print cls.atoms
+        fp = open(str(filename),'r')
+        
+        for line in fp.readlines():
+            if line.startswith('ATOM'):
+                a=GenericAtom.fromPDBrecord(line)
+                cls.AddAtom(a)
+        return cls
+    
+    def toPDBfile(self):
+        for residue in self.residues.itervalues():
+            print residue
+            
+    def AddAtom(self,a1):
+        self.atoms.append(a1)
+        rmap = self.residues
+        tag = a1.groupTag()
+#        print tag
+        if tag not in rmap:
+#            print "tag not found"
+            rmap[tag]=GenericResidue()
+        rmap[tag].AddAtom(a1)
+
+        
+    def info(self):
+        for residue in self.residues.itervalues():
+            print residue           
+    
+if __name__ == '__main__':
+#    sim0 = MySystem("test")
+#    sim1 = MySystem.fromPDBfile("test.pdb")  
+#    sys.exit()
+
+    aline1 = "ATOM      3  O2  IO3     1      -1.182   1.410   0.573       -0.80     O"
+    aline2 = "ATOM      1  I1  IO3     1      -1.555  -0.350   0.333        1.39     I"
+
+#    try:
+#        b = ResAtom.fromPDBrecord(aline1)
+#    except SystemExit:
+#        print "error reading PDB line"
+#        sys.exit(1)
+#    sim0.AddAtom(b)
+#    a = ResAtom.fromPDBrecord(aline2)
+#    sim0.AddAtom(a)
+#    
+    sim1 = MySystem.fromPDBfile("test.pdb")
+    sim1.info()
+#    sim1 = MySystem.fromPDBfile("test.pdb")
+# 
+#    sim1.toPDBfile()