Create atoms on a sphere

This example combines what is written in the Building section and demonstrates how to create a structural model populated with Carbon atoms placed on a sphere.

Example: create atoms on a sphere

import math

n = 100 # number of atoms
radius = SBQuantity.angstrom(4.2) # radius of the sphere

# generate positions on a sphere
golden_ratio = (1 + math.sqrt(5)) / 2
theta = 2 * math.pi * golden_ratio
increment = 2 / n
points = []
for i in range(n):
    y = ((i * increment) - 1) + (increment / 2)
    r = math.sqrt(1 - pow(y, 2))
    phi = (i % n) * theta
    x = math.cos(phi) * r
    z = math.sin(phi) * r
    position = SBPosition3(radius * x, radius * y, radius * z)
    points.append(position)

# create a structural model and add atoms to it

# instantiate a structural model
structuralModel = SBStructuralModel()

for i in range(n):
    atom = SBAtom(SBElement.Carbon)
    atom.setPosition(points[i])
    structuralModel.addChild(atom)

# create covalent bonds
structuralModel.createCovalentBonds()

# make the operation undoable
with SAMSON.holding('Add atoms'):
    # hold the structural model for undo/redo
    SAMSON.hold(structuralModel)
    # create the structural model
    structuralModel.create()
    # add the structural model to the active document
    SAMSON.getActiveDocument().addChild(structuralModel)