diff --git a/CodeExamples/Molecule.ipynb b/CodeExamples/Molecule.ipynb
index 93c48a34600eb48de13284315865b8764a52d05b..bfcd610ef83ca97295ec950f283b8afc2f9c75c2 100644
--- a/CodeExamples/Molecule.ipynb
+++ b/CodeExamples/Molecule.ipynb
@@ -33,71 +33,14 @@
" New concept of extending a class which inherits variable and method.\n",
" \"\"\"\n",
"\n",
- " def __init__(self,x,y,z,r):\n",
- " \"\"\"\n",
- " Constructor to form an atom with x,y,z,r parameters\n",
- " \"\"\"\n",
- " Vector3d.__init__(self,x,y,z) # set underlying Vector3d\n",
- " self.radius = float(r) # add radius of atom\n",
"\n",
- " def __str__(self):\n",
- " \"\"\"\n",
- " Implemnts str() (this overwrite the one in Vector3d)\n",
- " \"\"\"\n",
- " return \"Atom : r = \" + str(self.radius) + \" at \" + Vector3d.__str__(self)\n",
- "\n",
- " def isInside(self,v):\n",
- " \"\"\"\n",
- " isInside method, returns True if Vector3d v in inside atom.\n",
- " (Note distance() inherited from Vector3d)\n",
- " \"\"\"\n",
- " return self.distance(v) <= self.radius\n",
"\n",
"class Molecule(list):\n",
" \"\"\"\n",
" Molecule, being a list to hold Atoms\n",
" \"\"\"\n",
- " def __init__(self,*args):\n",
- " \"\"\"\n",
- " Constructor to form a Molecule with optional arguments each one assume to be an Atom\n",
- " Note *args syntax, new concept.\n",
- " \"\"\"\n",
- " list.__init__(self) # Init underlying list\n",
- " for a in args: # Append any args to list, note args will be a list\n",
- " self.append(a)\n",
- "\n",
- " def __str__(self):\n",
- " \"\"\"\n",
- " Format string of all atoms\n",
- " \"\"\"\n",
- " s = \"\"\n",
- " for a in self:\n",
- " s += str(a) + \"\\n\"\n",
- " return s\n",
- "\n",
- " def inInside(self, v):\n",
- " \"\"\"\n",
- " Method to check if vector is inside moleule.\n",
- " \"\"\"\n",
- " for a in self:\n",
- " if a.isInside(v):\n",
- " return True # Jump out as soon as inside an atom.\n",
+ " \n",
"\n",
- " return False # if here then outside\n",
- "\n",
- " def fromFile(self,file):\n",
- " \"\"\"\n",
- " Read Atoms from a file\n",
- " \"\"\"\n",
- " for line in file.readlines():\n",
- " if len(line) > 0 and not line.startswith(\"#\"): # Ignore blank lines and comments\n",
- " tokens = line.split(\",\")\n",
- " r = float(tokens[1]) # ignore first token with name\n",
- " x = float(tokens[2])\n",
- " y = float(tokens[3])\n",
- " z = float(tokens[4])\n",
- " self.append(Atom(x,y,z,r)) # Form Atom and append to self\n",
- " return self\n",
"\n",
"class BoundingBox(object):\n",
" \"\"\"\n",
@@ -105,51 +48,7 @@
" This class involves several new Python features.\n",
" (This is the most complex class in the whole program)\n",
" \"\"\"\n",
- " def __init__(self, m):\n",
- " \"\"\"\n",
- " The Conctructor, which takes molecule or an atom.\n",
- " This uses recursion to call itself if needed.\n",
- " \"\"\"\n",
- "\n",
- " if isinstance(m,list): # If a list given ,its a moleculte\n",
- " # Set initial box as two infinite vectors\n",
- " self.min = Vector3d(float(\"inf\"),float(\"inf\"),float(\"inf\"))\n",
- " self.max = Vector3d(float(\"-inf\"),float(\"-inf\"),float(\"-inf\"))\n",
- "\n",
- " # Now add it atoms one at a time\n",
- " for a in m:\n",
- " # Note recalling the BoundingBox for each atom (recursion)\n",
- " self.addBox(BoundingBox(a))\n",
- "\n",
- " else: # Assume its an atom\n",
- " self.min = m.subtract(m.radius)\n",
- " self.max = m.add(m.radius)\n",
- "\n",
- "\n",
- " def addBox(self,box):\n",
- " \"\"\"\n",
- " Method to add a box, used the min/max methods in Vector3d\n",
- " \"\"\"\n",
- " self.min = self.min.min(box.min)\n",
- " self.max = self.max.max(box.max)\n",
- "\n",
- "\n",
- "\n",
- " def volume(self):\n",
- " \"\"\"\n",
- " Get the volume of the box\n",
- " \"\"\"\n",
- " d = self.max.subtract(self.min)\n",
- " return d.x*d.y*d.z # Return the volume\n",
- "\n",
- " def getRandomPoint(self):\n",
- " \"\"\"\n",
- " Get a random point in the bounding box as a Vector3d.\n",
- " \"\"\"\n",
- " x = random.uniform(self.min.x,self.max.x)\n",
- " y = random.uniform(self.min.y,self.max.y)\n",
- " z = random.uniform(self.min.z,self.max.z)\n",
- " return Vector3d(x,y,z)\n",
+ " \n",
"\n",
"\n",
"def main():\n",
@@ -157,37 +56,8 @@
" \"\"\"\n",
"\n",
" file = open(str(input(\"File : \")),\"r\") # Open file\n",
- " mol = Molecule().fromFile(file) # Read in molecule\n",
- " print(\"Molecule is \\n\" + str(mol)) # Print out info\n",
- " box = BoundingBox(mol) # Form Bounding box\n",
- "\n",
- " maxpoint = float(input(\"Number of points : \")) # Max number of points\n",
- " plotInterval = maxpoint/100 # Plot internal for monitoring\n",
- " xData = [] # Data liost for graph\n",
- " yData = []\n",
- "\n",
- " # counters for number inside box total number of time round loop\n",
- " inside = 0\n",
- " p = 0\n",
- "\n",
- " while p < maxpoint: # Loop counting internal points\n",
- " p += 1\n",
- " # Test if a random point is inside the molecule\n",
- " if mol.inInside(box.getRandomPoint()):\n",
- " inside += 1\n",
- "\n",
- " if p % plotInterval == 0: # Store graphical data (100 point only)\n",
- " xData.append(p)\n",
- " yData.append(box.volume()*inside/p)\n",
- "\n",
- " estimate = box.volume()*inside/p # Print out final estimage\n",
- " print(\"Final estimate is : \" + str(estimate))\n",
- "\n",
- "\n",
- " plt.plot(xData,yData) # Draw graph (with default plot)\n",
- " plt.ylim(0.9*estimate,1.1*estimate)\n",
- " plt.title(\"Estimate of volume for \" + str(maxpoint) + \" points.\")\n",
- " plt.show()\n",
+ " \n",
+ " \n",
"\n",
"main()\n",
"\n"