def thickenate(prisms,
thicknessMap={
0: 1.4,
1: 1.3,
2: 1.2,
3: 1.1,
4: 1.0,
5: 0.9,
6: 0.8,
7: 0.7
},
minThickness=0.6):
for count, prism in enumerate(prisms):
thickness = minThickness
if count > 0:
layer_count = int(math.log(count, 2))
else:
layer_count = 0
if layer_count in thicknessMap.keys():
thickness = thicknessMap[layer_count]
bMinusA = geometry.getNormalVector(prism[1], prism[0])
cMinusA = geometry.getNormalVector(prism[2], prism[0])
normal = geometry.normalizeVector(geometry.cross(bMinusA, cMinusA))
for point in prism:
for coord in xrange(3):
point[coord] = point[coord] - normal[coord] * thickness / 2.0
newPoints = []
for point in prism:
newPoint = []
for coord in xrange(3):
newPoint.append(point[coord] + normal[coord] * thickness)
newPoints.append(newPoint)
prism.extend(newPoints)
u(ux + vy + wz )(1 - cos theta) + x cos theta + (- wy + vz) sin theta
v(ux + vy + wz )(1 - cos theta) + ycos theta + (wx - uz) sin theta
w(ux + vy + wz )(1 - cos theta) + z cos theta + (- vx + uy) sin theta
use normal vector UVW, rotate theta around this, use every point in pointList
'''
vecU, vecV, vecW = vector
cosTheta = math.cos(theta)
sinTheta = math.sin(theta)
newPts = []
for point in pointList:
ptX, ptY, ptZ = point
uxvywz = vecU * ptX + vecV * ptY + vecW * ptZ
newX = vecU * uxvywz * (1 - cosTheta) + ptX * cosTheta + (
-vecW * ptY + vecV * ptZ) * sinTheta
newY = vecV * uxvywz * (1 - cosTheta) + ptY * cosTheta + (
vecW * ptX - vecU * ptZ) * sinTheta
newZ = vecW * uxvywz * (1 - cosTheta) + ptZ * cosTheta + (
-vecV * ptX + vecU * ptY) * sinTheta
newPts.append((newX, newY, newZ))
return newPts
#following is for rudimentary testing
if __name__ == "__main__":
points = [[1., 2., 3.], [3., 2., 3.], [-2, 0., 1.]]
vecRot = geometry.normalizeVector(
(random.random(), random.random(), random.random()))
theta = random.random()
print projectPoints(points, vecRot, theta)
pdbCode = string.split(os.path.split(onePdb)[-1], '.')[0]
points = pdbD.coords
try:
os.mkdir(os.path.join(databaseDir, pdbCode))
except OSError:
pass # directory exists, fine
for vector in xrange(3):
for thetaTen in xrange(0, 62, 3):
vecX, vecY, vecZ = 0., 0., 0.
if vector == 0:
vecX = 1.
elif vector == 1:
vecY = 1.
elif vector == 2:
vecZ = 1.
normalVec = geometry.normalizeVector((vecX, vecY, vecZ))
theta = thetaTen / 10.
name = string.join(
[str(vecX), str(vecY),
str(vecZ), str(theta)], '.')
projectedPts = project.projectPointsOnto2D(points, normalVec,
theta)
mins, maxs = project.size2dSquare(projectedPts, radius)
matrix = project.make2dMap(projectedPts, radius, mins, maxs, size)
pngfile = open(
os.path.join(databaseDir, pdbCode,
pdbCode + '.' + name + '.png'), 'wb')
pngwriter = png.Writer(size, size, greyscale=True, bitdepth=1)
pngwriter.write(pngfile, matrix)
pngfile.close()
'''
pdbCode = string.split(os.path.split(onePdb)[-1], '.')[0]
points = pdbD.coords
try:
os.mkdir(os.path.join(databaseDir, pdbCode))
except OSError:
pass # directory exists, fine
for vector in xrange(3):
for thetaTen in xrange(0, 62, 3):
vecX, vecY, vecZ = 0., 0., 0.
if vector == 0:
vecX = 1.
elif vector == 1:
vecY = 1.
elif vector == 2:
vecZ = 1.
normalVec = geometry.normalizeVector((vecX, vecY, vecZ))
theta = thetaTen / 10.
name = string.join([str(vecX), str(vecY), str(vecZ), str(theta)], '.')
projectedPts = project.projectPointsOnto2D(points, normalVec, theta)
mins, maxs = project.size2dSquare(projectedPts, radius)
matrix = project.make2dMap(projectedPts, radius, mins, maxs, size)
pngfile = open(
os.path.join(
databaseDir, pdbCode, pdbCode + '.' + name + '.png'), 'wb')
pngwriter = png.Writer(size, size, greyscale=True, bitdepth=1)
pngwriter.write(pngfile, matrix)
pngfile.close()
'''
