class VRMLChargeFile(VRMLWireframeFile):
color_scale = VRML.SymmetricColorScale(1.)
def writeAtom(self, atom, configuration):
p = atom.position(configuration)
c = atom.charge()
c = max(min(c, 1.), -1.)
if p is None:
self.warning = 1
else:
s = VRML.Sphere(p, 0.1*Units.Ang,
material = VRML.Material(diffuse_color =
self.color_scale(c)))
s.writeToFile(self)
bond_material = VRML.DiffuseMaterial('black')
def writeBond(self, bond, configuration, distance):
p1 = bond.a1.position(configuration)
p2 = bond.a2.position(configuration)
if p1 is not None and p2 is not None:
bond_vector = 0.5*distance(bond.a1, bond.a2, configuration)
cut = bond_vector != 0.5*(p2-p1)
if not cut:
c = VRML.Line(p1, p2, material = self.bond_material)
c.writeToFile(self)
else:
c = VRML.Line(p1, p1+bond_vector, material = self.bond_material)
c.writeToFile(self)
c = VRML.Line(p2, p2-bond_vector, material = self.bond_material)
c.writeToFile(self)
def writeAtom(self, atom, configuration):
p = atom.position(configuration)
if p is None:
self.warning = 1
else:
color = self.atomColor(atom)
s = VRML.Sphere(p, 0.1*Units.Ang,
material = VRML.DiffuseMaterial(color),
reuse = 1)
s.writeToFile(self)
def writeAtom(self, atom, configuration):
p = atom.position(configuration)
c = atom.charge()
c = max(min(c, 1.), -1.)
if p is None:
self.warning = 1
else:
s = VRML.Sphere(p, 0.1*Units.Ang,
material = VRML.Material(diffuse_color =
self.color_scale(c)))
s.writeToFile(self)
def writeBond(self, bond, configuration, distance):
p1 = bond.a1.position(configuration)
p2 = bond.a2.position(configuration)
if p1 is not None and p2 is not None:
bond_vector = 0.5*distance(bond.a1, bond.a2, configuration)
cut = bond_vector != 0.5*(p2-p1)
if not cut:
c = VRML.Line(p1, p2, material = self.bond_material)
c.writeToFile(self)
else:
c = VRML.Line(p1, p1+bond_vector, material = self.bond_material)
c.writeToFile(self)
c = VRML.Line(p2, p2-bond_vector, material = self.bond_material)
c.writeToFile(self)
def writeAtom(self, atom, configuration):
try:
highlight = atom.highlight
except AttributeError:
highlight = 0
if highlight:
p = atom.position(configuration)
if p is None:
self.warning = 1
else:
s = VRML.Sphere(p, 0.1*Units.Ang,
material = VRML.DiffuseMaterial(atom.color),
reuse = 1)
s.writeToFile(self)
def __init__(self, filename, color_values=None):
VRML.VRMLFile.__init__(self, filename, 'w')
self.warning = 0
self.color_values = color_values
if self.color_values is not None:
lower = N.minimum.reduce(color_values.array)
upper = N.maximum.reduce(color_values.array)
self.color_scale = VRML.ColorScale((lower, upper))
def view(self, scale=1., color=None):
"""Shows a graphical representation of the field using
a VRML viewer. All values are multiplied by |scale|. |color|
permits the choice of a color for the graphics objects."""
from Scientific.Visualization import VRML
objects = self.graphicsObjects(scale=scale,
color=color,
graphics_module=VRML)
VRML.Scene(objects).view()
def writeBond(self, bond, configuration, distance):
p1 = bond.a1.position(configuration)
p2 = bond.a2.position(configuration)
if p1 is not None and p2 is not None:
bond_vector = 0.5 * distance(bond.a1, bond.a2, configuration)
cut = bond_vector != 0.5 * (p2 - p1)
color1 = self.atomColor(bond.a1)
color2 = self.atomColor(bond.a2)
material1 = VRML.EmissiveMaterial(color1)
material2 = VRML.EmissiveMaterial(color2)
if color1 == color2 and not cut:
c = VRML.Line(p1, p2, material=material1)
c.writeToFile(self)
else:
c = VRML.Line(p1, p1 + bond_vector, material=material1)
c.writeToFile(self)
c = VRML.Line(p2, p2 - bond_vector, material=material2)
c.writeToFile(self)
def writeToFile(self, filename, scale=1., color=None):
"""Writes a graphical representation of the field
to the VRML file named by |filename|, multiplying
all values by |scale|. |color| permits the choice
of a color for the graphics objects."""
from Scientific.Visualization import VRML
objects = self.graphicsObjects(scale=scale,
color=color,
graphics_module=VRML)
VRML.Scene(objects).writeToFile(filename)
chain.applyTransformation(transformation)
# Let's calculate the local deformation due to the change in conformation
# for each atom. Small values indicate rigid regions and large values
# indicate flexible regions. The visualization requires a VRML viewer.
# Reference: K. Hinsen, A. Thomas, M.J. Field: Proteins 34, 369 (1999)
from MMTK.Deformation import FiniteDeformationFunction
from Scientific.Visualization import VRML
difference = monomer_configuration - universe.configuration()
deformation_function = FiniteDeformationFunction(universe, 0.3, 0.6)
deformation = deformation_function(difference)
graphics = universe.graphicsObjects(color_values=deformation,
graphics_module=VRML)
VRML.Scene(graphics).view()
# The deformation shows a small rigid region and a much larger
# more flexible region.
# Action: We show an animation of the two configurations. This requires
# an animation-capable external viewer, e.g. VMD.
from MMTK.Visualization import viewSequence
viewSequence(chain, [universe.configuration(), monomer_configuration])
# Interesting: there's a floppy loop with residues Gln61, Glu62, and Glu63
# at the tip. It seems to do a funny rotation relative to a closeby helix
# (His94-Lys101) when switching between the two configurations. Let's
# find out what this rotation is!
