# Overview

Can display multiple copies of the unit cell.

# Example

```run supercell.py
fetch 2x19, async=0
supercell 2,1,1, 2x19, green
supercell 1,1,2, 2x19, orange, name=super2
```

# The Code

```'''
(c) 2010 Thomas Holder

PyMOL python script (load with `run supercell.py`)
Usage: See "help supercell"
'''

from pymol import cmd, cgo
from math import cos, sin, radians, sqrt
import numpy

def cellbasis(angles, edges):
'''
For the unit cell with given angles and edge lengths calculate the basis
transformation (vectors) as a 4x4 numpy.array
'''
rad = [radians(i) for i in angles]
basis = numpy.identity(4)
basis[1][2] = (cos(rad[0]) - basis[0][1]*basis[0][2])/basis[1][1]
basis[2][2] = sqrt(1 - basis[0][2]**2 - basis[1][2]**2)
edges.append(1.0)
return basis * edges # numpy.array multiplication!

def supercell(a=1, b=1, c=1, object=None, color='blue', name='supercell'):
'''
DESCRIPTION

Draw a supercell, as requested by Nicolas Bock on the pymol-users
mailing list (Subject: [PyMOL] feature request: supercell construction
Date: 04/12/2010 10:12:17 PM (Mon, 12 Apr 2010 14:12:17 -0600))

USAGE

supercell a, b, c [, object [, color [, name]]]

ARGUMENTS

a, b, c = integer: repeat cell in x,y,z direction a,b,c times
{default: 1,1,1}

object = string: name of object to take cell definition from

color = string: color of cell {default: blue}

name = string: name of the cgo object to create {default: supercell}

show cell

'''
if object is None:
object = cmd.get_object_list()[0]

sym = cmd.get_symmetry(object)
cell_edges = sym[0:3]
cell_angles = sym[3:6]

basis = cellbasis(cell_angles, cell_edges)
assert isinstance(basis, numpy.ndarray)

ts = list()
for i in range(int(a)):
for j in range(int(b)):
for k in range(int(c)):
ts.append([i,j,k])

obj = [
cgo.BEGIN,
cgo.LINES,
cgo.COLOR,
]
obj.extend(cmd.get_color_tuple(color))

for t in ts:
shift = basis[0:3,0:3] * t
shift = shift[:,0] + shift[:,1] + shift[:,2]

for i in range(3):
vi = basis[0:3,i]
vj = [
numpy.array([0.,0.,0.]),
basis[0:3,(i+1)%3],
basis[0:3,(i+2)%3],
basis[0:3,(i+1)%3] + basis[0:3,(i+2)%3]
]
for j in range(4):
obj.append(cgo.VERTEX)
obj.extend((shift + vj[j]).tolist())
obj.append(cgo.VERTEX)
obj.extend((shift + vj[j] + vi).tolist())

cmd.delete(name)