def drawTag(color, basePoint, endPoint, pointSize = 20.0):
"""
Draw a tag (or a 'flag') as a line ending with a circle (like a balloon
with a string). Note: The word 'Flag' is intentionally not used in the
method nameto avoid potential confusion with a boolean flag.
@param color: color of the tag
@type color: A
@param basePoint: The base point of the tag
@type basePoint: V
@param endPoint: The end point of the tag
@type endPoint: V
@param pointSize: The pointSize of the point to be drawin at the <endPoint>
@type pointSize: float
@see: GraphicsMode._drawTags where it is called (an example)
"""
drawline(color, basePoint, endPoint)
drawPoint(color, endPoint, pointSize = 20.0)
def drawTag(color, basePoint, endPoint, pointSize = 20.0):
"""
Draw a tag (or a 'flag') as a line ending with a circle (like a balloon
with a string). Note: The word 'Flag' is intentionally not used in the
method nameto avoid potential confusion with a boolean flag.
@param color: color of the tag
@type color: A
@param basePoint: The base point of the tag
@type basePoint: V
@param endPoint: The end point of the tag
@type endPoint: V
@param pointSize: The pointSize of the point to be drawin at the <endPoint>
@type pointSize: float
@see: GraphicsMode._drawTags where it is called (an example)
"""
drawline(color, basePoint, endPoint)
drawPoint(color, endPoint, pointSize = 20.0)
def drawNanotubeLadder(endCenter1,
endCenter2,
cntRise,
glpaneScale,
lineOfSightVector,
ladderWidth = 6.8, # default diameter for 5x5 CNT
beamThickness = 2.0,
beam1Color = None,
beam2Color = None,
stepColor = None
):
"""
Draws the CNT in a ladder display.
@param endCenter1: Nanotube center at end 1
@type endCenter1: B{V}
@param endCenter2: Nanotube center at end 2
@type endCenter2: B{V}
@param cntRise: Center to center distance between consecutive steps
@type cntRise: float
@param glpaneScale: GLPane scale used in scaling arrow head drawing
@type glpaneScale: float
@param lineOfSightVector: Glpane lineOfSight vector, used to compute the
the vector along the ladder step.
@type: B{V}
@param ladderWidth: width of the ladder
@type ladderWidth: float
@param beamThickness: Thickness of the two ladder beams
@type beamThickness: float
@param beam1Color: Color of beam1
@param beam2Color: Color of beam2
@see: B{DnaLineMode.Draw } (where it is used) for comments on color
convention
"""
ladderLength = vlen(endCenter1 - endCenter2)
# Don't draw the vertical line (step) passing through the startpoint unless
# the ladderLength is atleast equal to the cntRise.
# i.e. do the drawing only when there are atleast two ladder steps.
# This prevents a 'revolving line' effect due to the single ladder step at
# the first endpoint
if ladderLength < cntRise:
return
unitVector = norm(endCenter2 - endCenter1)
if beam1Color is None:
beam1Color = env.prefs[DarkBackgroundContrastColor_prefs_key]
if beam2Color is None:
beam2Color = env.prefs[DarkBackgroundContrastColor_prefs_key]
if stepColor is None:
stepColor = env.prefs[DarkBackgroundContrastColor_prefs_key]
glDisable(GL_LIGHTING)
glPushMatrix()
glTranslatef(endCenter1[0], endCenter1[1], endCenter1[2])
pointOnAxis = V(0, 0, 0)
vectorAlongLadderStep = cross(-lineOfSightVector, unitVector)
unitVectorAlongLadderStep = norm(vectorAlongLadderStep)
ladderBeam1Point = pointOnAxis + \
unitVectorAlongLadderStep * 0.5 * ladderWidth
ladderBeam2Point = pointOnAxis - \
unitVectorAlongLadderStep * 0.5 * ladderWidth
# Following limits the arrowHead Size to the given value. When you zoom out,
# the rest of ladder drawing becomes smaller (expected) and the following
# check ensures that the arrowheads are drawn proportinately. (Not using a
# 'constant' to do this as using glpaneScale gives better results)
if glpaneScale > 40:
arrowDrawingScale = 40
else:
arrowDrawingScale = glpaneScale
x = 0.0
while x < ladderLength:
drawPoint(stepColor, pointOnAxis)
drawCircle(stepColor, pointOnAxis, ladderWidth * 0.5, unitVector)
previousPoint = pointOnAxis
previousLadderBeam1Point = ladderBeam1Point
previousLadderBeam2Point = ladderBeam2Point
pointOnAxis = pointOnAxis + unitVector * cntRise
x += cntRise
ladderBeam1Point = previousPoint + \
unitVectorAlongLadderStep * 0.5 * ladderWidth
ladderBeam2Point = previousPoint - \
unitVectorAlongLadderStep * 0.5 * ladderWidth
if previousLadderBeam1Point:
drawline(beam1Color,
previousLadderBeam1Point,
ladderBeam1Point,
width = beamThickness,
isSmooth = True )
drawline(beam2Color,
previousLadderBeam2Point,
ladderBeam2Point,
width = beamThickness,
isSmooth = True )
#drawline(stepColor, ladderBeam1Point, ladderBeam2Point)
glPopMatrix()
glEnable(GL_LIGHTING)
def drawDnaSingleRibbon(glpane,
endCenter1,
endCenter2,
basesPerTurn,
duplexRise,
# maybe: don't pass these three args, get from glpane
# instead? [bruce 080422 comment]
glpaneScale,
lineOfSightVector,
displayStyle,
ribbon1_start_point = None,
ribbon1_direction = None,
peakDeviationFromCenter = 9.5,
ribbonThickness = 2.0,
ribbon1Color = None,
stepColor = None):
"""
@see: drawDnaRibbons (method in this file)
@see: DnaStrand_GraphicsMode._drawHandles()
"""
if 0:
# debug code, useful to see where the argument points are located
# [bruce 080422]
draw_debug_text(glpane, endCenter1, "endCenter1")
draw_debug_text(glpane, endCenter2, "endCenter2")
draw_debug_text(glpane, ribbon1_start_point, "ribbon1_start_point")
#Try to match the rubberband display style as closely as possible to
#either the glpane's current display or the chunk display of the segment
#being edited. The caller should do the job of specifying the display style
#it desires. As of 2008-02-20, this method only supports following display
#styles --Tubes, Ball and Stick, CPK and lines. the sphere radius
#for ball and stick or CPK is calculated approximately.
if displayStyle == diTrueCPK:
SPHERE_RADIUS = 3.5
ribbonThickness = 2.0
elif displayStyle == diTUBES:
SPHERE_RADIUS = 0.01
ribbonThickness = 5.0
elif displayStyle == diLINES:
#Lines display and all other unsupported display styles
SPHERE_RADIUS = 0.01
ribbonThickness = 1.0
else:
#ball and stick display style. All other unsupported displays
#will be rendered in ball and stick display style
SPHERE_RADIUS = 1.0
ribbonThickness = 3.0
if stepColor is None:
stepColor = env.prefs[DarkBackgroundContrastColor_prefs_key]
ribbonLength = vlen(endCenter1 - endCenter2)
#Don't draw the vertical line (step) passing through the startpoint unless
#the ribbonLength is at least equal to the duplexRise.
# i.e. do the drawing only when there are at least two ladder steps.
# This prevents a 'revolving line' effect due to the single ladder step at
# the first endpoint. It also means the dna duplex axis can be determined
# below from the two endpoints.
if ribbonLength < duplexRise:
return
unitVectorAlongLength = norm(endCenter2 - endCenter1)
glDisable(GL_LIGHTING)
##glPushMatrix()
##glTranslatef(endCenter1[0], endCenter1[1], endCenter1[2])
##pointOnAxis = V(0, 0, 0)
pointOnAxis = endCenter1
axial_shift = V(0.0, 0.0, 0.0) # might be changed below
# [these might be discarded and recomputed just below;
# the case where they aren't is (and I think was) untested.
# -- bruce 080422 comment]
vectorAlongLadderStep = cross(-lineOfSightVector, unitVectorAlongLength)
unitVectorAlongLadderStep = norm(vectorAlongLadderStep)
unitDepthVector = cross(unitVectorAlongLength, unitVectorAlongLadderStep)
## * -1
if ribbon1_start_point is not None:
# [revise the meaning of these values to give the coordinate system
# with the right phase in which to draw the ribbon.
# bruce 080422 bugfix]
vectorAlongLadderStep0 = ribbon1_start_point - endCenter1
# note: this might not be perpendicular to duplex axis.
# fix by subtracting off the parallel component.
# but add the difference back to every point below.
vectorAlongLadderStep = vectorAlongLadderStep0 - \
dot( unitVectorAlongLength,
vectorAlongLadderStep0 ) * unitVectorAlongLength
axial_shift = (vectorAlongLadderStep0 - vectorAlongLadderStep)
# note: even using this, there is still a small glitch in the
# location of the first drawn sphere vs. the ribbon point... don't
# know why. [bruce 080422]
unitVectorAlongLadderStep = norm(vectorAlongLadderStep)
unitDepthVector = cross(unitVectorAlongLength,
unitVectorAlongLadderStep) ## * -1
pass
del vectorAlongLadderStep
###===
#Following limits the arrowHead Size to the given value. When you zoom out,
#the rest of ladder drawing becomes smaller (expected) and the following
#check ensures that the arrowheads are drawn proportionately.
# (Not using a 'constant' to do this as using glpaneScale gives better
#results)
if glpaneScale > 40:
arrowDrawingScale = 40
else:
arrowDrawingScale = glpaneScale
#Formula .. Its a Sine Wave.
# y(x) = A.sin(2*pi*f*x + phase_angle) ------[1]
# where --
# f = 1/T
# A = Amplitude of the sine wave (or 'peak deviation from center')
# y = y coordinate of the sine wave -- distance is in Angstroms
# x = the x coordinate
# phase_angle is computed for each wave. We know y at x =0. For example,
# for ribbon_1, , at x = 0, y = A. Putting these values in equation [1]
# we get the phase_angle.
x = 0.0
T = duplexRise * basesPerTurn
# The 'Period' of the sine wave
# (i.e. peak to peak distance between consecutive crests)
numberOfBasesDrawn = 0
theta_offset = 0
## phase_angle_ribbon_1 = HALF_PI
## theta_ribbon_1 = (TWICE_PI * x / T) + phase_angle_ribbon_1
#Initialize ribbon1_point
# [note: might not be needed, since identical to first point
# computed during loop, but present code uses it to initialize
# previous_ribbon1_point during loop [bruce 080422 comment]]
ribbon1_point = _compute_ribbon_point(pointOnAxis + axial_shift,
basesPerTurn,
duplexRise,
unitVectorAlongLength,
unitVectorAlongLadderStep,
unitDepthVector,
peakDeviationFromCenter,
numberOfBasesDrawn,
theta_offset
)
while x < ribbonLength:
#Draw the axis point.
drawPoint(stepColor, pointOnAxis)
previousPointOnAxis = pointOnAxis
previous_ribbon1_point = ribbon1_point
ribbon1_point = _compute_ribbon_point(pointOnAxis + axial_shift,
basesPerTurn,
duplexRise,
unitVectorAlongLength,
unitVectorAlongLadderStep,
unitDepthVector,
peakDeviationFromCenter,
numberOfBasesDrawn,
theta_offset
)
if x == duplexRise and ribbon1_direction == -1:
# For ribbon_2 we need to draw an arrow head for y at x = 0.
# To do this, we need the 'next ribbon_2' point in order to
# compute the appropriate vectors. So when x = duplexRise, the
# previous_ribbon2_point is nothing but y at x = 0.
arrowLengthVector2 = norm(ribbon1_point -
previous_ribbon1_point )
arrowHeightVector2 = cross(-lineOfSightVector,
arrowLengthVector2)
drawArrowHead( ribbon1Color,
previous_ribbon1_point,
arrowDrawingScale,
-arrowHeightVector2,
-arrowLengthVector2)
# Draw sphere over previous_ribbon1_point and not ribbon1_point.
# This is so we don't draw a sphere over the last point on ribbon1
# (instead, it is drawn as an arrowhead after the while loop).
drawsphere(ribbon1Color,
previous_ribbon1_point,
SPHERE_RADIUS,
SPHERE_DRAWLEVEL,
opacity = SPHERE_OPACITY)
drawline(stepColor, pointOnAxis, ribbon1_point)
#Increment the pointOnAxis and x
pointOnAxis = pointOnAxis + unitVectorAlongLength * duplexRise
x += duplexRise
numberOfBasesDrawn += 1
if previous_ribbon1_point:
drawline(ribbon1Color,
previous_ribbon1_point,
ribbon1_point,
width = ribbonThickness,
isSmooth = True )
arrowLengthVector1 = norm(ribbon1_point - previous_ribbon1_point)
arrowHeightVector1 = cross(-lineOfSightVector, arrowLengthVector1)
pass
continue # while x < ribbonLength
if ribbon1_direction == 1:
#Arrow head for endpoint of ribbon_1.
drawArrowHead(ribbon1Color,
ribbon1_point,
arrowDrawingScale,
arrowHeightVector1,
arrowLengthVector1)
#The second axis endpoint of the dna is drawn as a transparent sphere.
#Note that the second axis endpoint is NOT NECESSARILY endCenter2 . In fact
# those two are equal only at the ladder steps. In other case (when the
# ladder step is not completed), the endCenter1 is ahead of the
#'second axis endpoint of the dna'
drawsphere(AXIS_ENDPOINT_SPHERE_COLOR,
previousPointOnAxis,
AXIS_ENDPOINT_SPHERE_RADIUS,
AXIS_ENDPOINT_SPHERE_DRAWLEVEL,
opacity = AXIS_ENDPOINT_SPHERE_OPACITY)
##glPopMatrix()
glEnable(GL_LIGHTING)
return # from drawDnaSingleRibbon
def drawDnaSingleRibbon(glpane,
endCenter1,
endCenter2,
basesPerTurn,
duplexRise,
# maybe: don't pass these three args, get from glpane
# instead? [bruce 080422 comment]
glpaneScale,
lineOfSightVector,
displayStyle,
ribbon1_start_point = None,
ribbon1_direction = None,
peakDeviationFromCenter = 9.5,
ribbonThickness = 2.0,
ribbon1Color = None,
stepColor = None):
"""
@see: drawDnaRibbons (method in this file)
@see: DnaStrand_GraphicsMode._drawHandles()
"""
if 0:
# debug code, useful to see where the argument points are located
# [bruce 080422]
draw_debug_text(glpane, endCenter1, "endCenter1")
draw_debug_text(glpane, endCenter2, "endCenter2")
draw_debug_text(glpane, ribbon1_start_point, "ribbon1_start_point")
#Try to match the rubberband display style as closely as possible to
#either the glpane's current display or the chunk display of the segment
#being edited. The caller should do the job of specifying the display style
#it desires. As of 2008-02-20, this method only supports following display
#styles --Tubes, Ball and Stick, CPK and lines. the sphere radius
#for ball and stick or CPK is calculated approximately.
if displayStyle == diTrueCPK:
SPHERE_RADIUS = 3.5
ribbonThickness = 2.0
elif displayStyle == diTUBES:
SPHERE_RADIUS = 0.01
ribbonThickness = 5.0
elif displayStyle == diLINES:
#Lines display and all other unsupported display styles
SPHERE_RADIUS = 0.01
ribbonThickness = 1.0
else:
#ball and stick display style. All other unsupported displays
#will be rendered in ball and stick display style
SPHERE_RADIUS = 1.0
ribbonThickness = 3.0
if stepColor is None:
stepColor = env.prefs[DarkBackgroundContrastColor_prefs_key]
ribbonLength = vlen(endCenter1 - endCenter2)
#Don't draw the vertical line (step) passing through the startpoint unless
#the ribbonLength is at least equal to the duplexRise.
# i.e. do the drawing only when there are at least two ladder steps.
# This prevents a 'revolving line' effect due to the single ladder step at
# the first endpoint. It also means the dna duplex axis can be determined
# below from the two endpoints.
if ribbonLength < duplexRise:
return
unitVectorAlongLength = norm(endCenter2 - endCenter1)
glDisable(GL_LIGHTING)
##glPushMatrix()
##glTranslatef(endCenter1[0], endCenter1[1], endCenter1[2])
##pointOnAxis = V(0, 0, 0)
pointOnAxis = endCenter1
axial_shift = V(0.0, 0.0, 0.0) # might be changed below
# [these might be discarded and recomputed just below;
# the case where they aren't is (and I think was) untested.
# -- bruce 080422 comment]
vectorAlongLadderStep = cross(-lineOfSightVector, unitVectorAlongLength)
unitVectorAlongLadderStep = norm(vectorAlongLadderStep)
unitDepthVector = cross(unitVectorAlongLength, unitVectorAlongLadderStep)
## * -1
if ribbon1_start_point is not None:
# [revise the meaning of these values to give the coordinate system
# with the right phase in which to draw the ribbon.
# bruce 080422 bugfix]
vectorAlongLadderStep0 = ribbon1_start_point - endCenter1
# note: this might not be perpendicular to duplex axis.
# fix by subtracting off the parallel component.
# but add the difference back to every point below.
vectorAlongLadderStep = vectorAlongLadderStep0 - \
dot( unitVectorAlongLength,
vectorAlongLadderStep0 ) * unitVectorAlongLength
axial_shift = (vectorAlongLadderStep0 - vectorAlongLadderStep)
# note: even using this, there is still a small glitch in the
# location of the first drawn sphere vs. the ribbon point... don't
# know why. [bruce 080422]
unitVectorAlongLadderStep = norm(vectorAlongLadderStep)
unitDepthVector = cross(unitVectorAlongLength,
unitVectorAlongLadderStep) ## * -1
pass
del vectorAlongLadderStep
###===
#Following limits the arrowHead Size to the given value. When you zoom out,
#the rest of ladder drawing becomes smaller (expected) and the following
#check ensures that the arrowheads are drawn proportionately.
# (Not using a 'constant' to do this as using glpaneScale gives better
#results)
if glpaneScale > 40:
arrowDrawingScale = 40
else:
arrowDrawingScale = glpaneScale
#Formula .. Its a Sine Wave.
# y(x) = A.sin(2*pi*f*x + phase_angle) ------[1]
# where --
# f = 1/T
# A = Amplitude of the sine wave (or 'peak deviation from center')
# y = y coordinate of the sine wave -- distance is in Angstroms
# x = the x coordinate
# phase_angle is computed for each wave. We know y at x =0. For example,
# for ribbon_1, , at x = 0, y = A. Putting these values in equation [1]
# we get the phase_angle.
x = 0.0
T = duplexRise * basesPerTurn
# The 'Period' of the sine wave
# (i.e. peak to peak distance between consecutive crests)
numberOfBasesDrawn = 0
theta_offset = 0
## phase_angle_ribbon_1 = HALF_PI
## theta_ribbon_1 = (TWICE_PI * x / T) + phase_angle_ribbon_1
#Initialize ribbon1_point
# [note: might not be needed, since identical to first point
# computed during loop, but present code uses it to initialize
# previous_ribbon1_point during loop [bruce 080422 comment]]
ribbon1_point = _compute_ribbon_point(pointOnAxis + axial_shift,
basesPerTurn,
duplexRise,
unitVectorAlongLength,
unitVectorAlongLadderStep,
unitDepthVector,
peakDeviationFromCenter,
numberOfBasesDrawn,
theta_offset
)
while x < ribbonLength:
#Draw the axis point.
drawPoint(stepColor, pointOnAxis)
previousPointOnAxis = pointOnAxis
previous_ribbon1_point = ribbon1_point
ribbon1_point = _compute_ribbon_point(pointOnAxis + axial_shift,
basesPerTurn,
duplexRise,
unitVectorAlongLength,
unitVectorAlongLadderStep,
unitDepthVector,
peakDeviationFromCenter,
numberOfBasesDrawn,
theta_offset
)
if x == duplexRise and ribbon1_direction == -1:
# For ribbon_2 we need to draw an arrow head for y at x = 0.
# To do this, we need the 'next ribbon_2' point in order to
# compute the appropriate vectors. So when x = duplexRise, the
# previous_ribbon2_point is nothing but y at x = 0.
arrowLengthVector2 = norm(ribbon1_point -
previous_ribbon1_point )
arrowHeightVector2 = cross(-lineOfSightVector,
arrowLengthVector2)
drawArrowHead( ribbon1Color,
previous_ribbon1_point,
arrowDrawingScale,
-arrowHeightVector2,
-arrowLengthVector2)
# Draw sphere over previous_ribbon1_point and not ribbon1_point.
# This is so we don't draw a sphere over the last point on ribbon1
# (instead, it is drawn as an arrowhead after the while loop).
drawsphere(ribbon1Color,
previous_ribbon1_point,
SPHERE_RADIUS,
SPHERE_DRAWLEVEL,
opacity = SPHERE_OPACITY)
drawline(stepColor, pointOnAxis, ribbon1_point)
#Increment the pointOnAxis and x
pointOnAxis = pointOnAxis + unitVectorAlongLength * duplexRise
x += duplexRise
numberOfBasesDrawn += 1
if previous_ribbon1_point:
drawline(ribbon1Color,
previous_ribbon1_point,
ribbon1_point,
width = ribbonThickness,
isSmooth = True )
arrowLengthVector1 = norm(ribbon1_point - previous_ribbon1_point)
arrowHeightVector1 = cross(-lineOfSightVector, arrowLengthVector1)
pass
continue # while x < ribbonLength
if ribbon1_direction == 1:
#Arrow head for endpoint of ribbon_1.
drawArrowHead(ribbon1Color,
ribbon1_point,
arrowDrawingScale,
arrowHeightVector1,
arrowLengthVector1)
#The second axis endpoint of the dna is drawn as a transparent sphere.
#Note that the second axis endpoint is NOT NECESSARILY endCenter2 . In fact
# those two are equal only at the ladder steps. In other case (when the
# ladder step is not completed), the endCenter1 is ahead of the
#'second axis endpoint of the dna'
drawsphere(AXIS_ENDPOINT_SPHERE_COLOR,
previousPointOnAxis,
AXIS_ENDPOINT_SPHERE_RADIUS,
AXIS_ENDPOINT_SPHERE_DRAWLEVEL,
opacity = AXIS_ENDPOINT_SPHERE_OPACITY)
##glPopMatrix()
glEnable(GL_LIGHTING)
return # from drawDnaSingleRibbon
