Bounding Box - Revision history

Pyadmin: 6 revisions

2014-03-28T01:49:04Z

6 revisions

New page

<source lang="python">
import math
from pymol import querying
from pymol.cgo import *
from pymol import cmd

#NOTE!! : These packages (numarray, Scientific) must be present in pymol's
#'$PYMOLDIR/py23/lib/python2.3/site-packages/' directory!!
# OR..if you are using Mac PyMOL 0.99beta19 or later then the system installs will be used
from numarray import *
from numarray.ma import average
from numarray import linear_algebra as la

from Scientific.Geometry import Vector, Tensor, Transformation

def boundingBox(selectionName, colourRGB=[1,1,1]):
"""
The main function to call :

run "box.py"
boundingBox("peptide")

Should make a box around "peptide" (assuming it exists!). For a different colour use:

boundingBox("peptide", colourRGB=[1, 0, 1])

Or whatever. The box should be a cgo called 'peptide-box' (for this example).
"""
model = querying.get_model(selectionName)
coords = model.get_coord_list()

#find the least square plane through the coordinates
eigenvalues, eigenvectors, centroid = findPlaneWithEigenVectors(coords)
normal = eigenvectors[eigenvalues.argmin()]
eigenvectors.remove(normal)

#orient the axes correctly
x, y, normal = orientAxes(eigenvectors[0], eigenvectors[1], normal)

#determine the dimensions and the structure's orientation wrt the origin
minDimensions, rotation = findMinDimensionsAndRotation(coords, centroid, x, y, normal)

#'create' the box(IE: make the corners) and 'draw' it (IE: make a cgo)
box = makeBox(minDimensions, rotation, centroid)
drawBox(box, selectionName, colourRGB)

def findPlaneWithEigenVectors(coords):
centroid = average(coords)
coords -= centroid
B = matrixmultiply(transpose(coords), coords)
eigenvalues, eigenvectors = la.eigenvectors(B)
#return eigenvalues, [Vector(e) for e in eigenvectors], Vector(centroid)
return eigenvalues, [Vector([i for i in e]) for e in eigenvectors], Vector(centroid) #not sure why I had to make this change!

def orientAxes(x, y, z):
XcrossY = x.cross(y)
#ZXY = around(math.degrees(z.angle(XcrossY)))
ZXY = int(around(math.degrees(z.angle(XcrossY)))) #again, a bit of a hack!
if (ZXY == 180): x, y = y, x
return x, y, z

def makeBox(dimensions, rotation, centroid):
x, y, z = dimensions
v = [[]] * 8

#make a cuboid with the lower corner on the origin
v[0] = [0, 0, 0] # [0, 0, 0]
v[1] = [x, 0, 0] # [1, 0, 0]
v[2] = [x, y, 0] # [1, 1, 0]
v[3] = [x, 0, z] # [1, 0, 1]
v[4] = [0, y, 0] # [0, 1, 0]
v[5] = [0, 0, z] # [0, 0, 1]
v[6] = [0, y, z] # [0, 1, 1]
v[7] = [x, y, z] # [1, 1, 1]

#move to the origin, THEN move to the centroid of the points, then rotate
translationToOrigin = Transformation.Translation(-Vector(x/2, y/2, z/2))
translationToCentroid = Transformation.Translation(centroid)
transform = translationToCentroid * rotation * translationToOrigin

#use the Transformation to transform the corners of the box
v = [transform(Vector(i)) for i in v]

bot = [v[0], v[1], v[2], v[4]] # O, x, xy, y
top = [v[7], v[3], v[5], v[6]] # xyz, xz, z, yz
minL = [v[0], v[4], v[6], v[5]] # O, y, yz, z
minR = [v[0], v[5], v[3], v[1]] # O, z, xz, x
maxL = [v[4], v[2], v[7], v[6]] # y, xy, xyz, yz
maxR = [v[3], v[1], v[2], v[7]] # xz, x, xy, xyz
box = [bot, minR, minL, maxR, maxL, top]

return box

def drawBox(box, name, colourRGB):
boxObj = []
for side in box:
boxObj.append(BEGIN)
boxObj.append(LINE_STRIP)
boxObj.append(COLOR)
boxObj.extend(colourRGB)
for point in side:
boxObj.append(VERTEX)
boxObj.extend(point)
boxObj.append(END)

cmd.set('auto_zoom', 0)
cmd.load_cgo(boxObj, "%s-box" % name)
cmd.set('auto_zoom', 1)

def findMinDimensionsAndRotation(coords, centroid, x, y, z):
O = Vector(0, 0, 0)
X = Vector(1, 0, 0)
Y = Vector(0, 1, 0)
Z = Vector(0, 0, 1)

#Create a Transformation t = |x, y, z| . |X, Y, Z| ^ -1
mfinal = array([array(X), array(Y), array(Z)])
morig = array([array(x), array(y), array(z)])
rotmatrix = matrixmultiply(morig, transpose(mfinal))
tTotal = Transformation.Rotation(Tensor(rotmatrix))

#Transform the coordinates and find the min, max dimensions
coordArray = array([array(tTotal(Vector(c))) for c in coords])
minDimensions = [max(coordArray[:,i]) - min(coordArray[:,i]) for i in range(3)]

#Now, compose the inverse rotation used to move the bounding box to the right place
tForward = Transformation.Rotation(Tensor(matrixmultiply(mfinal, transpose(morig))))

return minDimensions, tForward
</source>

[[Category:Script_Library|Bounding Box]]
[[Category:Math_Scripts]]

Gilleain: fixed to work again. not sure what has changed!

2005-10-20T04:25:20Z

fixed to work again. not sure what has changed!

New page

Tree at 22:15, 8 March 2005

2005-03-08T22:15:44Z

Tree at 22:14, 8 March 2005

2005-03-08T22:14:57Z

Gilleain at 19:46, 8 March 2005

2005-03-08T19:46:07Z

New page

<source lang="python">
import math
from pymol import querying
from pymol.cgo import *
from pymol import cmd

#NOTE!! : These packages (numarray, Scientific) must be present in pymol's
#'$PYMOLDIR/py23/lib/python2.3/site-packages/' directory!!
from numarray import *
from numarray.ma import average
from numarray import linear_algebra as la

from Scientific.Geometry import Vector, Tensor, Transformation

def boundingBox(selectionName, colourRGB=[1,1,1]):
"""
The main function to call :

run "box.py"
boundingBox("peptide")

Should make a box around "peptide" (assuming it exists!). For a different colour use:

boundingBox("peptide", colourRGB=[1, 0, 1])

Or whatever. The box should be a cgo called 'peptide-box' (for this example).
"""
model = querying.get_model(selectionName)
coords = model.get_coord_list()

#find the least square plane through the coordinates
eigenvalues, eigenvectors, centroid = findPlaneWithEigenVectors(coords)
normal = eigenvectors[eigenvalues.argmin()]
eigenvectors.remove(normal)

#orient the axes correctly
x, y, normal = orientAxes(eigenvectors[0], eigenvectors[1], normal)

#determine the dimensions and the structure's orientation wrt the origin
minDimensions, rotation = findMinDimensionsAndRotation(coords, centroid, x, y, normal)

#'create' the box(IE: make the corners) and 'draw' it (IE: make a cgo)
box = makeBox(minDimensions, rotation, centroid)
drawBox(box, selectionName, colourRGB)

def findPlaneWithEigenVectors(coords):
centroid = average(coords)
coords -= centroid
B = matrixmultiply(transpose(coords), coords)
eigenvalues, eigenvectors = la.eigenvectors(B)
return eigenvalues, [Vector(e) for e in eigenvectors], Vector(centroid)

def orientAxes(x, y, z):
XcrossY = x.cross(y)
ZXY = around(math.degrees(z.angle(XcrossY)))
if (ZXY == 180): x, y = y, x
return x, y, z

def makeBox(dimensions, rotation, centroid):
x, y, z = dimensions
v = [[]] * 8

#make a cuboid with the lower corner on the origin
v[0] = [0, 0, 0] # [0, 0, 0]
v[1] = [x, 0, 0] # [1, 0, 0]
v[2] = [x, y, 0] # [1, 1, 0]
v[3] = [x, 0, z] # [1, 0, 1]
v[4] = [0, y, 0] # [0, 1, 0]
v[5] = [0, 0, z] # [0, 0, 1]
v[6] = [0, y, z] # [0, 1, 1]
v[7] = [x, y, z] # [1, 1, 1]

#move to the origin, THEN move to the centroid of the points, then rotate
translationToOrigin = Transformation.Translation(-Vector(x/2, y/2, z/2))
translationToCentroid = Transformation.Translation(centroid)
transform = translationToCentroid * rotation * translationToOrigin

#use the Transformation to transform the corners of the box
v = [transform(Vector(i)) for i in v]

bot = [v[0], v[1], v[2], v[4]] # O, x, xy, y
top = [v[7], v[3], v[5], v[6]] # xyz, xz, z, yz
minL = [v[0], v[4], v[6], v[5]] # O, y, yz, z
minR = [v[0], v[5], v[3], v[1]] # O, z, xz, x
maxL = [v[4], v[2], v[7], v[6]] # y, xy, xyz, yz
maxR = [v[3], v[1], v[2], v[7]] # xz, x, xy, xyz
box = [bot, minR, minL, maxR, maxL, top]

return box

def drawBox(box, name, colourRGB):
boxObj = []
for side in box:
boxObj.append(BEGIN)
boxObj.append(LINE_STRIP)
boxObj.append(COLOR)
boxObj.extend(colourRGB)
for point in side:
boxObj.append(VERTEX)
boxObj.extend(point)
boxObj.append(END)

cmd.set('auto_zoom', 0)
cmd.load_cgo(boxObj, "%s-box" % name)
cmd.set('auto_zoom', 1)

def findMinDimensionsAndRotation(coords, centroid, x, y, z):
O = Vector(0, 0, 0)
X = Vector(1, 0, 0)
Y = Vector(0, 1, 0)
Z = Vector(0, 0, 1)

#Create a Transformation t = |x, y, z| . |X, Y, Z| ^ -1
mfinal = array([array(X), array(Y), array(Z)])
morig = array([array(x), array(y), array(z)])
rotmatrix = matrixmultiply(morig, transpose(mfinal))
tTotal = Transformation.Rotation(Tensor(rotmatrix))

#Transform the coordinates and find the min, max dimensions
coordArray = array([array(tTotal(Vector(c))) for c in coords])
minDimensions = [max(coordArray[:,i]) - min(coordArray[:,i]) for i in range(3)]

#Now, compose the inverse rotation used to move the bounding box to the right place
tForward = Transformation.Rotation(Tensor(matrixmultiply(mfinal, transpose(morig))))

return minDimensions, tForward
</source>

← Older revision		Revision as of 22:15, 8 March 2005
Line 127:		Line 127:
	</source>		</source>

−	[[Category:Scripting_Script_Library\|~~Measure Distance~~]]	+	[[Category:Scripting_Script_Library\|Bounding Box]]

← Older revision		Revision as of 22:14, 8 March 2005
Line 126:		Line 126:
	return minDimensions, tForward		return minDimensions, tForward
	</source>		</source>
		+
		+	[[Category:Scripting_Script_Library\|Measure Distance]]