new function sphere cut

examples/01_cut_a_sphere/README

@@ -0,0 +1,6 @@
+Generate a sphere from the pdb file
+
+run:
+python /home/tao/Nutstore/code/simupy/tools/build/sphere.py
+
+The details can be set in "inp" file

examples/01_cut_a_sphere/inp

@@ -0,0 +1,7 @@
+[SPHERE]
+pdbfile = ca12.pdb                ; input pdb file
+center = 23.978 23.978 23.978     ; center of the sphere, usually we use the center of the box
+radius = 12.8                     ; radius of the sphere (in A)
+atoms = Ca Al O                   ; Atom names in the pdb file
+natoms = 12 14 33                 ; Desired ratio
+outfile = caalo_128.pdb           ; Output pdb file

lib/mytype.py

@@ -178,6 +178,14 @@ def assignEleTypes(self,):
             match = pattern.match(b)
             if match:
                 i.element= match.group(1)
+
+    def assignAtomTypes2(self,):
+        """ assign atomtypes according to the element types
+        specially designed for lammps data file
+        """
+        self.assignEleTypes()
+        for i in self.atoms:
+            i.name = i.element
 
     def assignAtomTypes(self,):
         """ assign atomtypes according to the element types

lib/utilities.py

@@ -103,8 +103,6 @@ def get_angle(a1, a2, a3):
     theta = np.arccos(cost)/np.pi * 180.0
     return theta
 
-def cut_circle():
-    pass
 
 if __name__ == "__main__":
     a =  [3.4199999522999995 ,  0.0000000000000000  , 0.0000000000000000]