# module name to make the example use that module.
from Scientific.Visualization import VRML2
module = VRML2
# Create the protein and find its center of mass and tensor of inertia.
protein = Protein('insulin')
center, inertia = protein.centerAndMomentOfInertia()
# Diagonalize the inertia tensor and scale the axes to a suitable length.
mass = protein.mass()
diagonal, directions = LA.eigenvectors(inertia.array)
diagonal = N.sqrt(diagonal / mass)
# Generate the backbone graphics objects.
graphics = protein.graphicsObjects(graphics_module=module,
model='backbone',
color='red')
# Add an atomic wireframe representation of all valine sidechains
valines = protein.residuesOfType('val')
sidechains = valines.map(lambda r: r.sidechain)
graphics = graphics + sidechains.graphicsObjects(
graphics_module=module, model='wireframe', color='blue')
# Add three arrows corresponding to the principal axes of inertia.
for length, axis in map(None, diagonal, directions):
graphics.append(
module.Arrow(center,
center + length * Vector(axis),
0.02,
material=module.EmissiveMaterial('green')))
orientation=(Vector(0, 1, 0),3.14159),
description="Back")
left_cam = visualization_module.Camera(position=[center[0]-distance_away,center[1],center[2]],
orientation=(Vector(0, 1, 0),3.14159*1.5),
description="Left")
#Other visualisation methods ("models") you might like to try:-
model_name = 'vdw'
#model_name = 'tube'
#model_name = 'ball_and_stick'
print "Creating " + model_name + " graphic of Protein"
#You can also specify colour for the whole molecule if you want,
#otherwise the individual atom colours are used (Oxygen = Red,
#Hydrogen = White, Sulphur = Yellow etc)
graphics = protein.graphicsObjects(graphics_module = visualization_module,
model = model_name)
print "Creating arrows below protein"
#In order to help visualise what the camera objects are doing, I
#am adding some arrows in the x-z planes above and below the molecule.
#
#The red arrows point towards the "front" camera, green towards the
#"right" camera, blue towards the "back" camera and yellow towards the
#"left" camera.
#
d = 2.0 #distance from centre of mass (above or below)
l = 2.0 #length of each arrow
graphics.append(visualization_module.Arrow(center + Vector(0,-d,0),
center + Vector(0,-d,l), 0.1,
material=visualization_module.DiffuseMaterial('red')))
graphics.append(visualization_module.Arrow(center + Vector(0,-d,0),
description="Back")
left_cam = visualization_module.Camera(
position=[center[0] - distance_away, center[1], center[2]],
orientation=(Vector(0, 1, 0), 3.14159 * 1.5),
description="Left")
#Other visualisation methods ("models") you might like to try:-
model_name = 'vdw'
#model_name = 'tube'
#model_name = 'ball_and_stick'
print "Creating " + model_name + " graphic of Protein"
#You can also specify colour for the whole molecule if you want,
#otherwise the individual atom colours are used (Oxygen = Red,
#Hydrogen = White, Sulphur = Yellow etc)
graphics = protein.graphicsObjects(graphics_module=visualization_module,
model=model_name)
print "Creating arrows below protein"
#In order to help visualise what the camera objects are doing, I
#am adding some arrows in the x-z planes above and below the molecule.
#
#The red arrows point towards the "front" camera, green towards the
#"right" camera, blue towards the "back" camera and yellow towards the
#"left" camera.
#
d = 2.0 #distance from centre of mass (above or below)
l = 2.0 #length of each arrow
graphics.append(
visualization_module.Arrow(
center + Vector(0, -d, 0),
center + Vector(0, -d, l),