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# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
# usage:
#
# python Generate.py adenine > adenine.mmp
import sys
import math
zSpacing = 3180 # 0.1 pm
minorGroveDegrees = 133
baseTwistDegrees = 33.75
sugarRadius = 6760 # pm -- Value from EricD's pdb: 6760
sugarPhosphateDistance = 3640 # Value from EricD's pdb: 3574
baseTwist = math.pi * baseTwistDegrees / 180
if (len(sys.argv) < 2):
print >>sys.stderr, "must specify base name"
sys.exit(1)
baseName = sys.argv[1]
prefix = """mmpformat 050920 required; 060421 preferred
kelvin 300
group (View Data)
info opengroup open = True
csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000)
csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000)
egroup (View Data)
group (%s)
info opengroup open = True
mol (%s) def""" % (baseName, baseName)
postfix = """egroup (%s)
end1
group (Clipboard)
info opengroup open = False
egroup (Clipboard)
end molecular machine part %s""" % (baseName, baseName)
def printAtom(index, type, position, bondedTo):
print "atom %d (%d) (%d, %d, %d) def" % (index, type, position[0], position[1], position[2])
if (bondedTo):
print "bond1 %d" % bondedTo
def rotate(x, y, theta):
sinTheta = math.sin(theta)
cosTheta = math.cos(theta)
return (x * cosTheta - y * sinTheta, x * sinTheta + y * cosTheta)
def midpoint(position1, position2):
x = (position1[0] + position2[0]) / 2
y = (position1[1] + position2[1]) / 2
z = (position1[2] + position2[2]) / 2
return (x, y, z)
def extendToRadius(position, radius):
oldR = math.sqrt(position[0] * position[0] + position[1] * position[1])
factor = radius / oldR
return (position[0] * factor, position[1] * factor, position[2])
# given the position of a pseudo atom in strand1, return the position
# of the same pseudo atom in strand2
def strand2(position):
x = position[0]
y = position[1]
z = position[2]
theta = math.pi * (180 - minorGroveDegrees) / 180
newX, newY = rotate(-x, y, theta)
return (newX, newY, -z)
sugar = (sugarRadius, 0, 0)
sugar2xy = rotate(sugarRadius, 0, baseTwist)
sugar2 = (sugar2xy[0], sugar2xy[1], zSpacing)
def distance(xyz):
return math.sqrt(xyz[0] * xyz[0] + xyz[1] * xyz[1] + xyz[2] * xyz[2])
dist = 0
phosphateRadius = sugarRadius
while (dist < sugarPhosphateDistance):
phosphate = extendToRadius(midpoint(sugar, sugar2), phosphateRadius)
dist = distance((sugar[0] - phosphate[0], sugar[1] - phosphate[1], sugar[2] - phosphate[2]))
phosphateRadius += 1
print >>sys.stderr, "phosphateRadius %d" % phosphateRadius
print >>sys.stderr, "dist %d" % dist
phosphate0xy = rotate(phosphate[0], phosphate[1], -baseTwist)
phosphate0 = (phosphate0xy[0], phosphate0xy[1], phosphate[2] - zSpacing)
bondpoint1 = midpoint(phosphate, sugar2)
bondpoint2 = midpoint(phosphate0, sugar)
print prefix
if (baseName == 'end1'):
# Axis
printAtom(1, 200, (0, 0, 0), 0) # Ax
printAtom(2, 204, (0, 0, zSpacing/2), 1) # Ae
printAtom(3, 0, (0, 0, -zSpacing/2), 1) # Axis bondpoint
# Strand1
printAtom(4, 201, sugar, 1) # Ss
printAtom(5, 205, phosphate, 4) # Pe
printAtom(6, 0, bondpoint2, 4)
# Strand2
printAtom(7, 201, strand2(sugar), 1) # Ss
printAtom(8, 202, strand2(phosphate), 7) # Pl
printAtom(9, 0, strand2(bondpoint1), 8)
printAtom(10, 206, strand2(bondpoint2), 7) # Sh
elif (baseName == 'end2'):
# Axis
printAtom(1, 200, (0, 0, 0), 0) # Ax
printAtom(2, 204, (0, 0, -zSpacing/2), 1) # Ae
printAtom(3, 0, (0, 0, zSpacing/2), 1) # Axis bondpoint
# Strand1
printAtom(4, 201, sugar, 1) # Ss
printAtom(5, 202, phosphate, 4) # Pl
printAtom(6, 0, bondpoint1, 5)
printAtom(7, 206, bondpoint2, 4) # Sh
# Strand2
printAtom(8, 201, strand2(sugar), 1) # Ss
printAtom(9, 205, strand2(phosphate), 8) # Pe
printAtom(10, 0, strand2(bondpoint2), 8)
else:
# Axis
printAtom(1, 200, (0, 0, 0), 0) # Ax
printAtom(2, 0, (0, 0, zSpacing/2), 1) # Axis bondpoint
printAtom(3, 0, (0, 0, -zSpacing/2), 1) # Axis bondpoint
# Strand1
printAtom(4, 201, sugar, 1) # Ss
printAtom(5, 202, phosphate, 4) # Pl
printAtom(6, 0, bondpoint1, 5)
printAtom(7, 0, bondpoint2, 4)
# Strand2
printAtom(8, 201, strand2(sugar), 1) # Ss
printAtom(9, 202, strand2(phosphate), 8) # Pl
printAtom(10, 0, strand2(bondpoint1), 9)
printAtom(11, 0, strand2(bondpoint2), 8)
print postfix
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