def Draw(self):
"""
Draw method for this temporary mode.
"""
_superclass_for_GM.Draw(self)
#This fixes NFR bug 2803
#Don't draw the Dna rubberband line if the cursor is over the confirmation
#corner. But make sure to call superclass.Draw method before doing this
#check because we need to draw the rest of the model in the graphics
#mode!. @see: DnaLineMode_GM.Draw() which does similar thing to not
#draw the rubberband line when the cursor is on the confirmation corner
handler = self.o.mouse_event_handler
if handler is not None and handler is self._ccinstance:
self.update_cursor()
return
if self.endPoint2 is not None:
if self.endPoint1:
drawsphere(self.endPoint1_sphereColor,
self.endPoint1,
STARTPOINT_SPHERE_RADIUS,
STARTPOINT_SPHERE_DRAWLEVEL,
opacity=self.endPoint1_sphereOpacity)
drawline(self.rubberband_line_color,
self.endPoint1,
self.endPoint2,
width=self.rubberband_line_width,
dashEnabled=True)
self._drawSnapReferenceLines()
if self._ok_to_render_cursor_text:
self._drawCursorText()
def drawDihedralDimension(color,
right,
up,
bpos,
p0,
p1,
p2,
p3,
text,
highlighted=False):
# Draw a frame of lines that shows how the four atoms are connected
# to the dihedral angle
csys = CylindricalCoordinates(p1, p2 - p1, up, right)
r1, theta1, z1 = csys.rtz(p0)
r2, theta2, z2 = csys.rtz(p3)
e0a = csys.xyz((r1, theta1, 0.5))
e1a = csys.xyz((r2, theta2, 0.5))
drawline(color, p1, p0)
drawline(color, p0, e0a)
drawline(color, p3, e1a)
drawline(color, p2, p3)
drawline(color, p1, p2)
# Use the existing angle drawing routine to finish up
drawAngleDimension(color,
right,
up,
bpos,
e0a, (p1 + p2) / 2,
e1a,
text,
minR1=r1,
minR2=r2,
highlighted=highlighted)
def drawPeptideTrace(alphaCarbonProteinChunk):
"""
Draws a protein backbone trace using atoms stored in
I{alphaCarbonProteinChunk}.
@param alphaCarbonProteinChunk: a special (temporary) chunk that contains
only the alpha carbon atoms in the peptide
backbone
@param alphaCarbonProteinChunk: Chunk
@see PeptideLine_GraphicsMode.Draw_other(), PeptideGenerator.make_aligned()
"""
if alphaCarbonProteinChunk and alphaCarbonProteinChunk.atoms:
last_pos = None
atomitems = alphaCarbonProteinChunk.atoms.items()
atomitems.sort()
alphaCarbonAtomsList = [atom for (key, atom) in atomitems]
for atom in alphaCarbonAtomsList:
drawsphere(blue, atom.posn(), 0.2, 1)
if last_pos:
drawline(gray, last_pos, atom.posn(), width=2)
last_pos = atom.posn()
pass
pass
return
def draw(self):
color = self.fix_color(self.color)
end1, end2 = self.end1, self.end2
width = self.width
dashed = self.dashed
drawline(color[:3], end1, end2, width=width,
dashEnabled=dashed) ###k dashEnabled untested here
def Draw_other(self):
"""
Do some custom drawing (in the model's abs coordsys),
as well as whatever the superclass does.
"""
#print "start ExampleCommand2E Draw_other"
super(ExampleCommand2E_GM, self).Draw_other()
drawline(red, V(1, 0, 1), V(1, 1, 1), width=2)
self.command._expr_instance.draw()
def Draw_other(self):
"""
Do some custom drawing (in the model's abs coordsys),
as well as whatever the superclass does.
"""
#print "start ExampleCommand2E Draw_other"
super(ExampleCommand2E_GM, self).Draw_other()
drawline(red, V(1,0,1), V(1,1,1), width = 2)
self.command._expr_instance.draw()
def Draw(self):
"""
Do some custom drawing (in the model's abs coordsys) after drawing the model.
"""
#print "start ExampleCommand2E Draw"
glpane = self.glpane
super(ExampleCommand2E_GM, self).Draw()
drawline(red, V(1, 0, 1), V(1, 1, 1), width=2)
self.command._expr_instance.draw()
def _draw_jig(self, glpane, color, highlighted=False):
"""
Draw a ESP Image jig as a plane with an edge and a bounding box.
"""
glPushMatrix()
glTranslatef(self.center[0], self.center[1], self.center[2])
q = self.quat
glRotatef(q.angle * 180.0 / math.pi, q.x, q.y, q.z)
#bruce 060207 extensively revised texture code re fixing bug 1059
if self.tex_name is not None and self.image_obj: # self.image_obj condition is needed, for clear_esp_image() to work
textureReady = True
glBindTexture(
GL_TEXTURE_2D, self.tex_name
) # maybe this belongs in draw_plane instead? Put it there later. ##e
self._initTextureEnv() # sets texture params the way we want them
else:
textureReady = False
drawPlane(self.fill_color,
self.width,
self.width,
textureReady,
self.opacity,
SOLID=True,
pickCheckOnly=self.pickCheckOnly)
hw = self.width / 2.0
corners_pos = [
V(-hw, hw, 0.0),
V(-hw, -hw, 0.0),
V(hw, -hw, 0.0),
V(hw, hw, 0.0)
]
drawLineLoop(color, corners_pos)
# Draw the ESP Image bbox.
if self.show_esp_bbox:
wo = self.image_offset
eo = self.edge_offset
drawwirecube(color, V(0.0, 0.0, 0.0), V(hw + eo, hw + eo, wo),
1.0) #drawwirebox
# This is for debugging purposes. This draws a green normal vector using
# local space coords. Mark 050930
if 0:
from graphics.drawing.CS_draw_primitives import drawline
drawline(green, V(0.0, 0.0, 0.0), V(0.0, 0.0, 1.0), 0, 3)
glPopMatrix()
# This is for debugging purposes. This draws a yellow normal vector using
# model space coords. Mark 050930
if 0:
from graphics.drawing.CS_draw_primitives import drawline
from utilities.constants import yellow
drawline(yellow, self.center, self.center + self.planeNorm, 0, 3)
def Draw(self):
"""
Do some custom drawing (in the model's abs coordsys) after drawing the model.
"""
#print "start ExampleCommand2E Draw"
glpane = self.glpane
super(ExampleCommand2E_GM, self).Draw()
drawline(red, V(1,0,1), V(1,1,1), width = 2)
self.command._expr_instance.draw()
def _draw_jig(self, glpane, color, highlighted = False):
"""
Draw an ESPImage jig (self) as a plane with an edge and a bounding box.
@note: this is not called during graphicsMode.Draw_model as with most
Jigs, but during graphicsMode.Draw_after_highlighting.
"""
glPushMatrix()
glTranslatef( self.center[0], self.center[1], self.center[2])
q = self.quat
glRotatef( q.angle*180.0/math.pi, q.x, q.y, q.z)
#bruce 060207 extensively revised texture code re fixing bug 1059
if self.tex_name is not None and self.image_obj:
# self.image_obj cond is needed, for clear_esp_image() to work
textureReady = True
glBindTexture(GL_TEXTURE_2D, self.tex_name)
# review: maybe this belongs in draw_plane instead?
self._initTextureEnv() # sets texture params the way we want them
else:
textureReady = False
drawPlane(self.fill_color, self.width, self.width, textureReady,
self.opacity, SOLID = True,
pickCheckOnly = self.pickCheckOnly )
hw = self.width/2.0
corners_pos = [V(-hw, hw, 0.0),
V(-hw, -hw, 0.0),
V( hw, -hw, 0.0),
V( hw, hw, 0.0)]
drawLineLoop(color, corners_pos)
# Draw the ESP Image bbox.
if self.show_esp_bbox:
wo = self.image_offset
eo = self.edge_offset
drawwirecube(color, V(0.0, 0.0, 0.0), V(hw + eo, hw + eo, wo), 1.0)
#drawwirebox
# This is for debugging purposes. This draws a green normal vector
# using local space coords. [Mark 050930]
if 0:
from graphics.drawing.CS_draw_primitives import drawline
drawline(green, V(0.0, 0.0, 0.0), V(0.0, 0.0, 1.0), 0, 3)
glpane.kluge_reset_texture_mode_to_work_around_renderText_bug()
glPopMatrix()
# This is for debugging purposes. This draws a yellow normal vector
# using model space coords. [Mark 050930]
if 0:
from graphics.drawing.CS_draw_primitives import drawline
from utilities.constants import yellow
drawline(yellow, self.center, self.center + self.planeNorm, 0, 3)
def Draw_other(self):
"""
"""
_superclass_for_GM.Draw_other(self)
if len(self.command.mouseClickPoints) >= 2:
#Draw reference vector.
drawline(env.prefs[DarkBackgroundContrastColor_prefs_key],
self.command.mouseClickPoints[0],
self.command.mouseClickPoints[1],
width = 4,
dashEnabled = True)
def draw(self):
"""
Draw two projections of the curve at the limits of the
thickness that defines the crystal volume.
The commented code is for debugging.
[bruce 041214 adds comment: the code looks like it
only draws one projection.]
"""
color = get_selCurve_color(self.selSense)
pl = zip(self.ptlist[:-1],self.ptlist[1:])
for p in pl:
drawline(color, p[0],p[1])
def Draw_other(self):
"""
"""
_superclass_for_GM.Draw_other(self)
if len(self.command.mouseClickPoints) >= 2:
#Draw reference vector.
drawline(env.prefs[DarkBackgroundContrastColor_prefs_key],
self.command.mouseClickPoints[0],
self.command.mouseClickPoints[1],
width=4,
dashEnabled=True)
def Draw_other(self):
"""
"""
_superclass_for_GM.Draw_other(self)
#This fixes NFR bug 2803
#Don't draw the Dna rubberband line if the cursor is over the confirmation
#corner. But make sure to call superclass.Draw_other method before doing this
#check because we need to draw the rest of the model in the graphics
#mode!. @see: DnaLineMode_GM.Draw_other() which does similar thing to not
#draw the rubberband line when the cursor is on the confirmation corner
handler = self.o.mouse_event_handler
if handler is not None and handler is self._ccinstance:
##### REVIEW:
#
# 1. This is probably incorrect in principle, as a way of
# deciding what to draw. The mouse event handling methods
# should set an attribute which directly specifies whether
# the next call of Draw_other (or other Draw methods)
# should draw the rubberband line or not.
# (Or which affects the value of an access method, e.g.
# something like self.should_draw_rubberband_lines().)
#
# 2. Why is update_cursor called here? Any call of update_cursor
# inside a specific Draw method seems suspicious.
#
# 3. This needs refactoring to merge with common code in its
# subclass DnaLineMode_GM, and to consider doing the same
# thing in its other 3 subclasses.
#
# [bruce 090310 comments]
self.update_cursor()
return
if self.endPoint2 is not None:
if self.endPoint1:
drawsphere(self.endPoint1_sphereColor,
self.endPoint1,
STARTPOINT_SPHERE_RADIUS,
STARTPOINT_SPHERE_DRAWLEVEL,
opacity = self.endPoint1_sphereOpacity
)
drawline(env.prefs[DarkBackgroundContrastColor_prefs_key],
self.endPoint1,
self.endPoint2,
width = self.rubberband_line_width,
dashEnabled = True)
self._drawSnapReferenceLines()
if self._ok_to_render_cursor_text:
self._drawCursorText()
def draw(self):
"""
Draw two projections of the curve at the limits of the
thickness that defines the cookie volume.
The commented code is for debugging.
[bruce 041214 adds comment: the code looks like it
only draws one projection.]
"""
color = get_selCurve_color(self.selSense)
pl = zip(self.ptlist[:-1],self.ptlist[1:])
for p in pl:
drawline(color, p[0],p[1])
def _draw_jig(self, glpane, color, highlighted = False):
length = glpane.scale # approx.
# print "%r got color = %r" % (self, color,) # it gets gray
for atom in self.atoms:
pos = atom.posn()
drawline(color, pos, - glpane.pov, width = 2)
# line from center of view, in case far off-screen
# lines in diagonal directions (more likely to hit screen if off-screen)
for direction in (glpane.up + glpane.right,
glpane.right + glpane.down,
glpane.down + glpane.left,
glpane.left + glpane.up):
endpoint = pos + direction * length
drawline( color, pos, endpoint, width = 2)
return
def _draw_jig(self, glpane, color, highlighted = False):
length = glpane.scale # approx.
# print "%r got color = %r" % (self, color,) # it gets gray
for atom in self.atoms:
pos = atom.posn()
drawline(color, pos, - glpane.pov, width = 2)
# line from center of view, in case far off-screen
# lines in diagonal directions (more likely to hit screen if off-screen)
for direction in (glpane.up + glpane.right,
glpane.right + glpane.down,
glpane.down + glpane.left,
glpane.left + glpane.up):
endpoint = pos + direction * length
drawline( color, pos, endpoint, width = 2)
return
def _bondDraw(self, color, p0, p1, carbonAt):
if self.dispMode == "Tubes":
drawcylinder(color, p0, p1, 0.2)
else:
if carbonAt < 0:
drawsphere(color, p0, 0.5, 1)
drawsphere(color, p1, 0.5, 1)
elif carbonAt == 0:
drawsphere(color, p0, 0.5, 1)
drawsphere(color, p1, 0.2, 1)
elif carbonAt == 1:
drawsphere(color, p0, 0.2, 1)
drawsphere(color, p1, 0.5, 1)
drawline(white, p0, p1)
def _bondDraw(self, color, p0, p1, carbonAt):
if self.dispMode == 'Tubes':
drawcylinder(color, p0, p1, 0.2)
else:
if carbonAt < 0:
drawsphere(color, p0, 0.5, 1)
drawsphere(color, p1, 0.5, 1)
elif carbonAt == 0:
drawsphere(color, p0, 0.5, 1)
drawsphere(color, p1, 0.2, 1)
elif carbonAt == 1:
drawsphere(color, p0, 0.2, 1)
drawsphere(color, p1, 0.5, 1)
drawline(white, p0, p1)
def xdraw(self):
"""
draw the actual grid of the matrix in 3-space.
Used for debugging only.
"""
col = (0.0, 0.0, 0.0)
dx = self.x/8.0
dy = self.y/8.0
for i in range(self.matrix.shape[0]):
for j in range(self.matrix.shape[1]):
if not self.matrix[i, j]:
p = (V(i, j)+self.matbase)/8.0
p = p[0]*self.x + p[1]*self.y + self.z
drawline(col, p, p + dx + dy)
drawline(col, p + dx, p + dy)
def xdraw(self):
"""
draw the actual grid of the matrix in 3-space.
Used for debugging only.
"""
col = (0.0, 0.0, 0.0)
dx = self.x/8.0
dy = self.y/8.0
for i in range(self.matrix.shape[0]):
for j in range(self.matrix.shape[1]):
if not self.matrix[i, j]:
p = (V(i, j)+self.matbase)/8.0
p = p[0]*self.x + p[1]*self.y + self.z
drawline(col, p, p + dx + dy)
drawline(col, p + dx, p + dy)
def draw_bondable_pairs(self):
"""
Draws bondable pairs of singlets and the bond lines between them.
Singlets in the selected chunk(s) are colored green.
Singlets in the unselected chunk(s) are colored blue.
Singlets with more than one way to bond are colored magenta.
"""
# Color of bond lines --
bondline_color = get_selCurve_color(0,self.o.backgroundColor)
for s1,s2 in self.command.bondable_pairs:
color = (self.command.ways_of_bonding[s1.key] > 1) and magenta or green
s1.overdraw_with_special_color(color)
color = (self.command.ways_of_bonding[s2.key] > 1) and magenta or blue
s2.overdraw_with_special_color(color)
# Draw bond lines between singlets --
drawline(bondline_color, s1.posn(), s2.posn())
def _cellDraw(self, color, p0, p1):
hasSinglet = False
if type(p1) == type((1,)):
v1 = p1[0]
hasSinglet = True
else:
v1 = p1
if self.dispMode == 'Tubes':
drawcylinder(color, p0, v1, 0.2)
else:
drawsphere(color, p0, 0.5, 1)
if hasSinglet:
drawsphere(color, v1, 0.2, 1)
else:
drawsphere(color, v1, 0.5, 1)
drawline(white, p0, v1)
def _cellDraw(self, color, p0, p1):
hasSinglet = False
if type(p1) == type((1,)):
v1 = p1[0]
hasSinglet = True
else:
v1 = p1
if self.dispMode == "Tubes":
drawcylinder(color, p0, v1, 0.2)
else:
drawsphere(color, p0, 0.5, 1)
if hasSinglet:
drawsphere(color, v1, 0.2, 1)
else:
drawsphere(color, v1, 0.5, 1)
drawline(white, p0, v1)
def drawDihedralDimension(color, right, up, bpos, p0, p1, p2, p3, text, highlighted=False):
# Draw a frame of lines that shows how the four atoms are connected
# to the dihedral angle
csys = CylindricalCoordinates(p1, p2 - p1, up, right)
r1, theta1, z1 = csys.rtz(p0)
r2, theta2, z2 = csys.rtz(p3)
e0a = csys.xyz((r1, theta1, 0.5))
e1a = csys.xyz((r2, theta2, 0.5))
drawline(color, p1, p0)
drawline(color, p0, e0a)
drawline(color, p3, e1a)
drawline(color, p2, p3)
drawline(color, p1, p2)
# Use the existing angle drawing routine to finish up
drawAngleDimension(
color, right, up, bpos, e0a, (p1 + p2) / 2, e1a, text, minR1=r1, minR2=r2, highlighted=highlighted
)
def draw_debug_text(glpane, point, text): #bruce 080422, should refile
"""
"""
from geometry.VQT import V
from utilities.constants import white, red
if point is None:
point = - glpane.pov
# todo: randomize offset using hash of text
offset = glpane.right * glpane.scale / 2.0 + \
glpane.up * glpane.scale / 2.0
# todo: correct for aspect ratio, use min scale in each dimension
offset2 = V( - offset[0], offset[1], 0.0 ) / 3.0
drawline( white, point, point + offset, width = 2)
drawline( white, point - offset2, point + offset2 )
point_size = 12
drawtext( text, red, point + offset, point_size, glpane )
return
def draw_debug_text(glpane, point, text): #bruce 080422, should refile
"""
"""
from geometry.VQT import V
from utilities.constants import white, red
if point is None:
point = - glpane.pov
# todo: randomize offset using hash of text
offset = glpane.right * glpane.scale / 2.0 + \
glpane.up * glpane.scale / 2.0
# todo: correct for aspect ratio, use min scale in each dimension
offset2 = V( - offset[0], offset[1], 0.0 ) / 3.0
drawline( white, point, point + offset, width = 2)
drawline( white, point - offset2, point + offset2 )
point_size = 12
drawtext( text, red, point + offset, point_size, glpane )
return
def _draw_jig(self, glpane, color, highlighted = False):
"""
[overrides superclass method]
"""
# note: kluge: called directly from a specialized Chunk, not from self.draw!
if self._should_draw():
sitepos = self.site_position() # or, should we assume the atom pos is up to date? yes, use that. ### FIX
colors = [red, orange, yellow]
for a in self.parent_atoms():
chunk = a.molecule
dispdef = chunk.get_dispdef(glpane)
disp, rad = a.howdraw(dispdef)
if self.picked:
rad *= 1.01
color = colors[0]
drawwirecube(color, a.posn(), rad) # useful??
drawline( color, a.posn(), sitepos)
# draw each atom in a different color (at least if there are no more than 3)
colors = colors[1:] + [color]
continue
return
def _drawSnapReferenceLines(self):
"""
Draw the snap reference lines as dottedt lines. Example, if the
moving end of the rubberband line is 'close enough' to a standard axis
vector, that point is 'snapped' soi that it lies on the axis. When this
is done, program draws a dotted line from origin to the endPoint2
indicating that the endpoint is snapped to that axis line.
This method is called inside the self.Draw method.
@see: self._snapEndPointToStandardAxis
@see: self.Draw
"""
if self.endPoint2 is None:
return
if self._standardAxisVectorForDrawingSnapReference:
drawline(blue,
V(0, 0, 0),
self.endPoint2,
dashEnabled=True,
stipleFactor=4,
width=2)
def _drawSnapReferenceLines(self):
"""
Draw the snap reference lines as dottedt lines. Example, if the
moving end of the rubberband line is 'close enough' to a standard axis
vector, that point is 'snapped' soi that it lies on the axis. When this
is done, program draws a dotted line from origin to the endPoint2
indicating that the endpoint is snapped to that axis line.
This method is called inside the self.Draw method.
@see: self._snapEndPointToStandardAxis
@see: self.Draw
"""
if self.endPoint2 is None:
return
if self._standardAxisVectorForDrawingSnapReference:
drawline(blue,
V(0, 0, 0),
self.endPoint2,
dashEnabled = True,
stipleFactor = 4,
width = 2)
def _draw_jig(self, glpane, color, highlighted=False):
"""
[overrides superclass method]
"""
# note: kluge: called directly from a specialized Chunk, not from self.draw!
if self._should_draw():
sitepos = self.site_position(
) # or, should we assume the atom pos is up to date? yes, use that. ### FIX
colors = [red, orange, yellow]
for a in self.parent_atoms():
chunk = a.molecule
dispdef = chunk.get_dispdef(glpane)
disp, rad = a.howdraw(dispdef)
if self.picked:
rad *= 1.01
color = colors[0]
drawwirecube(color, a.posn(), rad) # useful??
drawline(color, a.posn(), sitepos)
# draw each atom in a different color (at least if there are no more than 3)
colors = colors[1:] + [color]
continue
return
def drawSequence(seq, tfm=tfmgen(i)):
if len(seq) == 0:
return # a space character has an empty sequence
if type(seq[0][0]) is not types.IntType:
# handle multi-stroke characters
for x in seq:
drawSequence(x)
return
seq = map(lambda tpl: apply(tfm,tpl), seq)
for i in range(len(seq) - 1):
pos1, pos2 = seq[i], seq[i+1]
if self.glBegin:
# This is what we do for grid planes, where "somebody"
# is drawGPGrid in drawers.py.
# Somebody has already taken care of glBegin(GL_LINES).
# TODO: explain this in docstring.
glVertex(pos1[0], pos1[1], pos1[2])
glVertex(pos2[0], pos2[1], pos2[2])
# Somebody has already taken care of glEnd().
else:
# This is what we do for dimensions.
drawline(color, seq[i], seq[i+1])
def drawSequence(seq, tfm=tfmgen(i)):
if len(seq) == 0:
return # a space character has an empty sequence
if type(seq[0][0]) is not types.IntType:
# handle multi-stroke characters
for x in seq:
drawSequence(x)
return
seq = map(lambda tpl: apply(tfm, tpl), seq)
for i in range(len(seq) - 1):
pos1, pos2 = seq[i], seq[i + 1]
if self.glBegin:
# This is what we do for grid planes, where "somebody"
# is drawGPGrid in drawers.py.
# Somebody has already taken care of glBegin(GL_LINES).
# TODO: explain this in docstring.
glVertex(pos1[0], pos1[1], pos1[2])
glVertex(pos2[0], pos2[1], pos2[2])
# Somebody has already taken care of glEnd().
else:
# This is what we do for dimensions.
drawline(color, seq[i], seq[i + 1])
def Draw(self):
"""
Draw method for this temporary mode.
"""
_superclass_for_GM.Draw(self)
#This fixes NFR bug 2803
#Don't draw the Dna rubberband line if the cursor is over the confirmation
#corner. But make sure to call superclass.Draw method before doing this
#check because we need to draw the rest of the model in the graphics
#mode!. @see: DnaLineMode_GM.Draw() which does similar thing to not
#draw the rubberband line when the cursor is on the confirmation corner
handler = self.o.mouse_event_handler
if handler is not None and handler is self._ccinstance:
self.update_cursor()
return
if self.endPoint2 is not None:
if self.endPoint1:
drawsphere(self.endPoint1_sphereColor,
self.endPoint1,
STARTPOINT_SPHERE_RADIUS,
STARTPOINT_SPHERE_DRAWLEVEL,
opacity = self.endPoint1_sphereOpacity
)
drawline(self.rubberband_line_color,
self.endPoint1,
self.endPoint2,
width = self.rubberband_line_width,
dashEnabled = True)
self._drawSnapReferenceLines()
if self._ok_to_render_cursor_text:
self._drawCursorText()
def drawLinearDimension(color, # what color are we drawing this in
right, up, # screen directions mapped to xyz coords
bpos, # position of the handle for moving the text
p0, p1, # positions of the ends of the dimension
text, highlighted=False):
outOfScreen = cross(right, up)
bdiff = bpos - 0.5 * (p0 + p1)
csys = CylindricalCoordinates(p0, p1 - p0, bdiff, right)
# This works OK until we want to keep the text right side up, then the
# criterion for right-side-up-ness changes because we've changed 'up'.
br, bt, bz = csys.rtz(bpos)
e0 = csys.xyz((br + 0.5, 0, 0))
e1 = csys.xyz((br + 0.5, 0, 1))
drawline(color, p0, e0)
drawline(color, p1, e1)
v0 = csys.xyz((br, 0, 0))
v1 = csys.xyz((br, 0, 1))
if highlighted:
drawline(color, v0, v1, width=THICKLINEWIDTH)
else:
drawline(color, v0, v1)
# draw arrowheads at the ends
a1, a2 = 0.25, 1.0 * csys.zinv
arrow00 = csys.xyz((br + a1, 0, a2))
arrow01 = csys.xyz((br - a1, 0, a2))
drawline(color, v0, arrow00)
drawline(color, v0, arrow01)
arrow10 = csys.xyz((br + a1, 0, 1-a2))
arrow11 = csys.xyz((br - a1, 0, 1-a2))
drawline(color, v1, arrow10)
drawline(color, v1, arrow11)
# draw the text for the numerical measurement, make
# sure it goes from left to right
xflip = dot(csys.z, right) < 0
# then make sure it's right side up
theoreticalRight = (xflip and -csys.z) or csys.z
theoreticalOutOfScreen = cross(theoreticalRight, bdiff)
yflip = dot(theoreticalOutOfScreen, outOfScreen) < 0
if debug_flags.atom_debug:
print "DEBUG INFO FROM drawLinearDimension"
print csys
print theoreticalRight, theoreticalOutOfScreen
print xflip, yflip
if yflip:
def fx(y):
return br + 1.5 - y / (1. * HEIGHT)
else:
def fx(y):
return br + 0.5 + y / (1. * HEIGHT)
if xflip:
def fz(x):
return 0.9 - csys.zinv * x / (1. * WIDTH)
else:
def fz(x):
return 0.1 + csys.zinv * x / (1. * WIDTH)
def tfm(x, y, fx=fx, fz=fz):
return csys.xyz((fx(y), 0, fz(x)))
f3d = Font3D()
f3d.drawString(text, tfm=tfm, color=color)
def drawAngleDimension(color, right, up, bpos, p0, p1, p2, text,
minR1=0.0, minR2=0.0, highlighted=False):
z = cross(p0 - p1, p2 - p1)
try:
csys = CylindricalCoordinates(p1, z, up, right)
except ZeroLengthCylinder:
len0 = vlen(p1 - p0)
len2 = vlen(p1 - p2)
# make sure it's really a zero-degree angle
assert len0 > 1.0e-6
assert len2 > 1.0e-6
assert vlen(cross(p1 - p2, p1 - p0)) < 1.0e-6
# For an angle of zero degrees, there is no correct way to
# orient the text, so just draw a line segment
if len0 > len2:
L = len0
end = p0
else:
L = len2
end = p2
Lb = vlen(bpos - p1)
if Lb > L:
L = Lb
end = p1 + (Lb / L) * (end - p1)
drawline(color, p1, end)
return
br, bt, bz = csys.rtz(bpos)
theta1 = csys.rtz(p0)[1]
theta2 = csys.rtz(p2)[1]
if theta2 < theta1 - math.pi:
theta2 += 2 * math.pi
elif theta2 > theta1 + math.pi:
theta2 -= 2 * math.pi
if theta2 < theta1:
theta1, theta2 = theta2, theta1
e0 = csys.xyz((max(vlen(p0 - p1), br, minR1) + 0.5, theta1, 0))
e1 = csys.xyz((max(vlen(p2 - p1), br, minR2) + 0.5, theta2, 0))
drawline(color, p1, e0)
drawline(color, p1, e1)
if highlighted:
csys.drawArc(color, br, theta1, theta2, 0, width=THICKLINEWIDTH)
else:
csys.drawArc(color, br, theta1, theta2, 0)
# draw some arrowheads
e00 = csys.xyz((br, theta1, 0))
e10 = csys.xyz((br, theta2, 0))
dr = 0.25
dtheta = 1 / br
e0a = csys.xyz((br + dr, theta1 + dtheta, 0))
e0b = csys.xyz((br - dr, theta1 + dtheta, 0))
e1a = csys.xyz((br + dr, theta2 - dtheta, 0))
e1b = csys.xyz((br - dr, theta2 - dtheta, 0))
drawline(color, e00, e0a)
drawline(color, e00, e0b)
drawline(color, e10, e1a)
drawline(color, e10, e1b)
midangle = (theta1 + theta2) / 2
tmidpoint = csys.xyz((br + 0.5, midangle, 0))
h = 1.0e-3
textx = norm(csys.xyz((br + 0.5, midangle + h, 0)) - tmidpoint)
texty = norm(csys.xyz((br + 0.5 + h, midangle, 0)) - tmidpoint)
# make sure the text runs from left to right
if dot(textx, right) < 0:
textx = -textx
# make sure the text isn't upside-down
outOfScreen = cross(right, up)
textForward = cross(textx, texty)
if dot(outOfScreen, textForward) < 0:
tmidpoint = csys.xyz((br + 1.5, midangle, 0))
texty = -texty
textxyz = tmidpoint - (0.5 * len(text)) * textx
def tfm(x, y):
x = (x / (1. * WIDTH)) * textx
y = (y / (1. * HEIGHT)) * texty
return textxyz + x + y
f3d = Font3D()
f3d.drawString(text, tfm=tfm, color=color)
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 _DEBUG_draw_avg_centerpairs_of_potential_crossovers(self):
pairs = self._crossoverSite_marker.get_avg_center_pairs_of_potential_crossovers
for pair in pairs:
drawline(yellow, pair[0], pair[1], width=2)
def drawchunk(self, glpane, chunk, memo, highlighted):
"""
Draws reduced representation of a protein chunk.
"""
structure, total_length, ca_list, n_sec = memo
style = self.proteinStyle
scaleFactor = self.proteinStyleScaleFactor
resolution = self.proteinStyleQuality
scaling = self.proteinStyleScaling
smooth = self.proteinStyleSmooth
gleSetJoinStyle(TUBE_JN_ANGLE | TUBE_NORM_PATH_EDGE | TUBE_JN_CAP | TUBE_CONTOUR_CLOSED )
current_sec = 0
for sec, secondary in structure:
# Number of atoms in SS element including dummy atoms.
n_atoms = len(sec)
# The length should be at least 3.
if n_atoms >= 3:
# Alpha carbon trace styles. Simple but fast.
if style == PROTEIN_STYLE_CA_WIRE or \
style == PROTEIN_STYLE_CA_CYLINDER or \
style == PROTEIN_STYLE_CA_BALL_STICK:
for n in range( 1, n_atoms-2 ):
pos0, ss0, aa0, idx0, dpos0, cbpos0 = sec[n - 1]
pos1, ss1, aa1, idx1, dpos1, cbpos1 = sec[n]
pos2, ss2, aa2, idx2, dpos2, cbpos2 = sec[n + 1]
color = self._get_aa_color(chunk,
idx1,
total_length,
ss1,
aa1,
current_sec,
n_sec)
if style == PROTEIN_STYLE_CA_WIRE:
if pos0:
drawline(color,
pos1 + 0.5 * (pos0 - pos1),
pos1,
width=5,
isSmooth=True)
if pos2:
drawline(color,
pos1,
pos1 + 0.5 * (pos2 - pos1),
width=5,
isSmooth=True)
else:
if pos0:
drawcylinder(color,
pos1 + 0.5 * (pos0 - pos1),
pos1,
0.25 * scaleFactor,
capped=1)
if style == PROTEIN_STYLE_CA_BALL_STICK:
drawsphere(color, pos1, 0.5 * scaleFactor, 2)
else:
drawsphere(color, pos1, 0.25 * scaleFactor, 2)
if pos2:
drawcylinder(color,
pos1,
pos1 + 0.5 * (pos2 - pos1),
0.25 * scaleFactor,
capped=1)
elif style == PROTEIN_STYLE_PEPTIDE_TILES:
for n in range( 1, n_atoms-2 ):
pos0, ss0, aa0, idx0, dpos0, cbpos0 = sec[n - 1]
pos1, ss1, aa1, idx1, dpos1, cbpos1 = sec[n]
color = self._get_aa_color(chunk,
idx1,
total_length,
ss1,
aa1,
current_sec,
n_sec)
tri = []
nor = []
col = []
elif style == PROTEIN_STYLE_TUBE or \
style == PROTEIN_STYLE_LADDER or \
style == PROTEIN_STYLE_ZIGZAG or \
style == PROTEIN_STYLE_FLAT_RIBBON or \
style == PROTEIN_STYLE_SOLID_RIBBON or \
style == PROTEIN_STYLE_SIMPLE_CARTOONS or \
style == PROTEIN_STYLE_FANCY_CARTOONS:
tube_pos = []
tube_col = []
tube_rad = []
tube_dpos = []
for n in range( 2, n_atoms-2 ):
pos00, ss00, a00, idx00, dpos00, cbpos00 = sec[n - 2]
pos0, ss0, aa0, idx0, dpos0, cbpos0 = sec[n - 1]
pos1, ss1, aa1, idx1, dpos1, cbpos1 = sec[n]
pos2, ss2, aa2, idx2, dpos2, cbpos2 = sec[n + 1]
pos22, ss22, aa22, idx22, dpos22, cbpos22 = sec[n + 2]
color = self._get_aa_color(chunk,
idx1,
total_length,
ss1,
aa1,
current_sec,
n_sec)
rad = 0.25 * scaleFactor
if style == PROTEIN_STYLE_TUBE and \
scaling == 1:
if secondary > 0:
rad *= 2.0
if n == 2:
if pos0:
tube_pos.append(pos00)
tube_col.append(V(color))
tube_rad.append(rad)
tube_dpos.append(dpos1)
tube_pos.append(pos0)
tube_col.append(V(color))
tube_rad.append(rad)
tube_dpos.append(dpos1)
if style == PROTEIN_STYLE_LADDER:
drawcylinder(color, pos1, cbpos1, rad * 0.75)
drawsphere(color, cbpos1, rad * 1.5, 2)
if pos1:
tube_pos.append(pos1)
tube_col.append(V(color))
tube_rad.append(rad)
tube_dpos.append(dpos1)
if n == n_atoms - 3:
if pos2:
tube_pos.append(pos2)
tube_col.append(V(color))
tube_rad.append(rad)
tube_dpos.append(dpos1)
tube_pos.append(pos22)
tube_col.append(V(color))
tube_rad.append(rad)
tube_dpos.append(dpos1)
# For smoothed helices we need to add virtual atoms
# located approximately at the centers of peptide bonds
# but slightly moved away from the helix axis.
new_tube_pos = []
new_tube_col = []
new_tube_rad = []
new_tube_dpos = []
if smooth and \
secondary == 1:
for p in range(len(tube_pos)):
new_tube_pos.append(tube_pos[p])
new_tube_col.append(tube_col[p])
new_tube_rad.append(tube_rad[p])
new_tube_dpos.append(tube_dpos[p])
if p > 1 and p < len(tube_pos) - 3:
pv = tube_pos[p-1] - tube_pos[p]
nv = tube_pos[p+2] - tube_pos[p+1]
mi = 0.5 * (tube_pos[p+1] + tube_pos[p])
# The coefficient below was handpicked to make
# the helices approximately round.
mi -= 0.75 * norm(nv+pv)
new_tube_pos.append(mi)
new_tube_col.append(0.5*(tube_col[p]+tube_col[p+1]))
new_tube_rad.append(0.5*(tube_rad[p]+tube_rad[p+1]))
new_tube_dpos.append(0.5*(tube_dpos[p]+tube_dpos[p+1]))
tube_pos = new_tube_pos
tube_col = new_tube_col
tube_rad = new_tube_rad
tube_dpos = new_tube_dpos
if secondary != 1 or \
style != PROTEIN_STYLE_SIMPLE_CARTOONS:
tube_pos, tube_col, tube_rad, tube_dpos = make_tube(
tube_pos,
tube_col,
tube_rad,
tube_dpos,
resolution=resolution)
if style == PROTEIN_STYLE_ZIGZAG or \
style == PROTEIN_STYLE_FLAT_RIBBON or \
style == PROTEIN_STYLE_SOLID_RIBBON or \
style == PROTEIN_STYLE_SIMPLE_CARTOONS or \
style == PROTEIN_STYLE_FANCY_CARTOONS:
last_pos = None
last_width = 1.0
reset = False
# Find SS element widths and determine width increment.
if secondary == 0:
# Coils have a constant width.
width = scaleFactor * 0.1
dw = 0.0
elif secondary == 1:
# Helices expand and shrink at the ends.
width = scaleFactor * 0.1
dw = (1.0 * scaleFactor) / (resolution - 3)
else:
# Strands just shrink at the C-terminal end.
width = scaleFactor * 1.0
dw = (1.6 * scaleFactor) / (1.5 * resolution - 3)
if style == PROTEIN_STYLE_FLAT_RIBBON or \
style == PROTEIN_STYLE_SOLID_RIBBON or \
style == PROTEIN_STYLE_SIMPLE_CARTOONS or \
style == PROTEIN_STYLE_FANCY_CARTOONS:
tri_arr0 = []
nor_arr0 = []
col_arr0 = []
if style == PROTEIN_STYLE_SOLID_RIBBON or \
style == PROTEIN_STYLE_SIMPLE_CARTOONS or \
style == PROTEIN_STYLE_FANCY_CARTOONS:
tri_arr1 = []
nor_arr1 = []
col_arr1 = []
tri_arr2 = []
nor_arr2 = []
col_arr2 = []
tri_arr3 = []
nor_arr3 = []
col_arr3 = []
from copy import copy
new_tube_dpos = copy(tube_dpos)
for n in range(1, len(tube_pos)-1):
pos = tube_pos[n]
col = tube_col[n][0]
col2 = tube_col[n+1][0]
if last_pos:
next_pos = tube_pos[n+1]
dpos1 = last_width * tube_dpos[n-1]
dpos2 = width * tube_dpos[n]
ddpos = dpos1-dpos2
if reset:
dpos1 = dpos2
reset = False
if self.proteinStyle == PROTEIN_STYLE_ZIGZAG:
drawline(col, last_pos-dpos1, pos-dpos2, width=3)
drawline(col, last_pos+dpos1, pos+dpos2, width=3)
drawline(col, last_pos-dpos1, pos+dpos2, width=1)
drawline(col, pos-dpos2, pos+dpos2, width=1)
drawline(col, last_pos-dpos1, last_pos+dpos1, width=1)
if self.proteinStyle == PROTEIN_STYLE_FLAT_RIBBON:
if pos != last_pos:
nvec1 = norm(cross(dpos1, pos-last_pos))
if next_pos != pos:
nvec2 = norm(cross(dpos2, next_pos-pos))
else:
nvec2 = nvec1
nor_arr0.append(nvec1)
nor_arr0.append(nvec1)
nor_arr0.append(nvec2)
nor_arr0.append(nvec2)
tri_arr0.append(last_pos-dpos1)
tri_arr0.append(last_pos+dpos1)
tri_arr0.append(pos-dpos2)
tri_arr0.append(pos+dpos2)
col_arr0.append(col)
col_arr0.append(col)
col_arr0.append(col2)
col_arr0.append(col2)
if self.proteinStyle == PROTEIN_STYLE_SOLID_RIBBON or \
self.proteinStyle == PROTEIN_STYLE_SIMPLE_CARTOONS or \
self.proteinStyle == PROTEIN_STYLE_FANCY_CARTOONS:
if secondary > 0:
col3 = col4 = V(gray)
if pos != last_pos:
nvec1 = norm(cross(dpos1, pos-last_pos))
if next_pos != pos:
nvec2 = norm(cross(dpos2, next_pos-pos))
else:
nvec2 = nvec1
nor_arr0.append(nvec1)
nor_arr0.append(nvec1)
nor_arr0.append(nvec2)
nor_arr0.append(nvec2)
if self.proteinStyle == PROTEIN_STYLE_FANCY_CARTOONS:
dn1 = 0.15 * nvec1 * scaleFactor
dn2 = 0.15 * nvec2 * scaleFactor
else:
dn1 = 0.15 * nvec1 * scaleFactor
dn2 = 0.15 * nvec2 * scaleFactor
tri_arr0.append(last_pos - dpos1 - dn1)
tri_arr0.append(last_pos + dpos1 - dn1)
tri_arr0.append(pos - dpos2 - dn2)
tri_arr0.append(pos + dpos2 - dn2)
col_arr0.append(col)
col_arr0.append(col)
col_arr0.append(col2)
col_arr0.append(col2)
nor_arr1.append(nvec1)
nor_arr1.append(nvec1)
nor_arr1.append(nvec2)
nor_arr1.append(nvec2)
tri_arr1.append(last_pos - dpos1 + dn1)
tri_arr1.append(last_pos + dpos1 + dn1)
tri_arr1.append(pos - dpos2 + dn2)
tri_arr1.append(pos + dpos2 + dn2)
if secondary == 1:
col_arr1.append(0.5 * col + 0.5 * V(white))
col_arr1.append(0.5 * col + 0.5 * V(white))
col_arr1.append(0.5 * col2 + 0.5 * V(white))
col_arr1.append(0.5 * col2 + 0.5 * V(white))
else:
col_arr1.append(col)
col_arr1.append(col)
col_arr1.append(col2)
col_arr1.append(col2)
nor_arr2.append(-dpos1)
nor_arr2.append(-dpos1)
nor_arr2.append(-dpos2)
nor_arr2.append(-dpos2)
tri_arr2.append(last_pos - dpos1 - dn1)
tri_arr2.append(last_pos - dpos1 + dn1)
tri_arr2.append(pos - dpos2 - dn2)
tri_arr2.append(pos - dpos2 + dn2)
col_arr2.append(col3)
col_arr2.append(col3)
col_arr2.append(col4)
col_arr2.append(col4)
nor_arr3.append(-dpos1)
nor_arr3.append(-dpos1)
nor_arr3.append(-dpos2)
nor_arr3.append(-dpos2)
tri_arr3.append(last_pos + dpos1 - dn1)
tri_arr3.append(last_pos + dpos1 + dn1)
tri_arr3.append(pos + dpos2 - dn2)
tri_arr3.append(pos + dpos2 + dn2)
col_arr3.append(col3)
col_arr3.append(col3)
col_arr3.append(col4)
col_arr3.append(col4)
last_pos = pos
last_width = width
if secondary == 1:
if n > len(tube_pos) - resolution:
width -= dw
elif width < 1.0 * scaleFactor:
width += dw
if secondary == 2:
if n == len(tube_pos) - 1.5 * resolution:
width = scaleFactor * 1.6
reset = True
if n > len(tube_pos) - 1.5 * resolution:
width -= dw
new_tube_dpos[n] = width * tube_dpos[n]
###drawcylinder(white, tube_pos[0], tube_pos[10], 1.0)
if self.proteinStyle == PROTEIN_STYLE_FLAT_RIBBON:
drawtriangle_strip([1.0,1.0,0.0,-2.0], tri_arr0, nor_arr0, col_arr0)
if self.proteinStyle == PROTEIN_STYLE_SOLID_RIBBON or \
self.proteinStyle == PROTEIN_STYLE_SIMPLE_CARTOONS or \
self.proteinStyle == PROTEIN_STYLE_FANCY_CARTOONS:
if secondary == 0:
drawpolycone_multicolor([0,0,0,-2], tube_pos, tube_col, tube_rad)
else:
if (secondary == 1 and self.proteinStyle == PROTEIN_STYLE_SOLID_RIBBON) or \
secondary == 2:
drawtriangle_strip([1.0,1.0,0.0,-2.0], tri_arr0, nor_arr0, col_arr0)
drawtriangle_strip([1.0,1.0,0.0,-2.0], tri_arr1, nor_arr1, col_arr1)
drawtriangle_strip([1.0,1.0,0.0,-2.0], tri_arr2, nor_arr2, col_arr2)
drawtriangle_strip([1.0,1.0,0.0,-2.0], tri_arr3, nor_arr3, col_arr3)
# Fill in the strand N-terminal end.
quad_tri = []
quad_nor = []
quad_col = []
quad_tri.append(tri_arr2[0])
quad_tri.append(tri_arr3[0])
quad_tri.append(tri_arr2[1])
quad_tri.append(tri_arr3[1])
quad_nor.append(nor_arr2[0])
quad_nor.append(nor_arr3[0])
quad_nor.append(nor_arr2[1])
quad_nor.append(nor_arr3[1])
quad_col.append(col_arr2[0])
quad_col.append(col_arr3[0])
quad_col.append(col_arr2[1])
quad_col.append(col_arr3[1])
drawtriangle_strip([1.0,1.0,1.0,-2.0],quad_tri,quad_nor,quad_col)
if (secondary == 1 and self.proteinStyle == PROTEIN_STYLE_FANCY_CARTOONS):
drawtriangle_strip([1.0,1.0,0.0,-2.0], tri_arr0, nor_arr0, col_arr0)
drawtriangle_strip([1.0,1.0,0.0,-2.0], tri_arr1, nor_arr1, col_arr1)
tube_pos_left = []
tube_pos_right = []
new_tube_dpos[0] *= 0.1
new_tube_dpos[1] *= 0.2
new_tube_dpos[-1] *= 0.1
new_tube_dpos[-2] *= 0.2
for p in range(len(tube_pos)):
tube_pos_left.append(tube_pos[p] - new_tube_dpos[p])
tube_pos_right.append(tube_pos[p] + new_tube_dpos[p])
tube_rad[p] *= 0.75
drawpolycone_multicolor([0,0,0,-2], tube_pos_left, tube_col, tube_rad)
drawpolycone_multicolor([0,0,0,-2], tube_pos_right, tube_col, tube_rad)
# else:
if (secondary == 1 and style == PROTEIN_STYLE_SIMPLE_CARTOONS):
drawcylinder(tube_col[0][0], tube_pos[1], tube_pos[-3], 2.5, capped=1)
#print "hopsa"
if style == PROTEIN_STYLE_LADDER or \
style == PROTEIN_STYLE_TUBE:
# Draw tube.
drawpolycone_multicolor([0,0,0,-2], tube_pos, tube_col, tube_rad)
# increase Sec. Str. element counter
current_sec += 1
def drawLinearDimension(
color, # what color are we drawing this in
right,
up, # screen directions mapped to xyz coords
bpos, # position of the handle for moving the text
p0,
p1, # positions of the ends of the dimension
text,
highlighted=False):
outOfScreen = cross(right, up)
bdiff = bpos - 0.5 * (p0 + p1)
csys = CylindricalCoordinates(p0, p1 - p0, bdiff, right)
# This works OK until we want to keep the text right side up, then the
# criterion for right-side-up-ness changes because we've changed 'up'.
br, bt, bz = csys.rtz(bpos)
e0 = csys.xyz((br + 0.5, 0, 0))
e1 = csys.xyz((br + 0.5, 0, 1))
drawline(color, p0, e0)
drawline(color, p1, e1)
v0 = csys.xyz((br, 0, 0))
v1 = csys.xyz((br, 0, 1))
if highlighted:
drawline(color, v0, v1, width=THICKLINEWIDTH)
else:
drawline(color, v0, v1)
# draw arrowheads at the ends
a1, a2 = 0.25, 1.0 * csys.zinv
arrow00 = csys.xyz((br + a1, 0, a2))
arrow01 = csys.xyz((br - a1, 0, a2))
drawline(color, v0, arrow00)
drawline(color, v0, arrow01)
arrow10 = csys.xyz((br + a1, 0, 1 - a2))
arrow11 = csys.xyz((br - a1, 0, 1 - a2))
drawline(color, v1, arrow10)
drawline(color, v1, arrow11)
# draw the text for the numerical measurement, make
# sure it goes from left to right
xflip = dot(csys.z, right) < 0
# then make sure it's right side up
theoreticalRight = (xflip and -csys.z) or csys.z
theoreticalOutOfScreen = cross(theoreticalRight, bdiff)
yflip = dot(theoreticalOutOfScreen, outOfScreen) < 0
if debug_flags.atom_debug:
print "DEBUG INFO FROM drawLinearDimension"
print csys
print theoreticalRight, theoreticalOutOfScreen
print xflip, yflip
if yflip:
def fx(y):
return br + 1.5 - y / (1. * HEIGHT)
else:
def fx(y):
return br + 0.5 + y / (1. * HEIGHT)
if xflip:
def fz(x):
return 0.9 - csys.zinv * x / (1. * WIDTH)
else:
def fz(x):
return 0.1 + csys.zinv * x / (1. * WIDTH)
def tfm(x, y, fx=fx, fz=fz):
return csys.xyz((fx(y), 0, fz(x)))
f3d = Font3D()
f3d.drawString(text, tfm=tfm, color=color)
def drawLine(self, color, rtz1, rtz2, width=1):
drawline(color, self.xyz(rtz1), self.xyz(rtz2), width=width)
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 drawAngleDimension(color,
right,
up,
bpos,
p0,
p1,
p2,
text,
minR1=0.0,
minR2=0.0,
highlighted=False):
z = cross(p0 - p1, p2 - p1)
try:
csys = CylindricalCoordinates(p1, z, up, right)
except ZeroLengthCylinder:
len0 = vlen(p1 - p0)
len2 = vlen(p1 - p2)
# make sure it's really a zero-degree angle
assert len0 > 1.0e-6
assert len2 > 1.0e-6
assert vlen(cross(p1 - p2, p1 - p0)) < 1.0e-6
# For an angle of zero degrees, there is no correct way to
# orient the text, so just draw a line segment
if len0 > len2:
L = len0
end = p0
else:
L = len2
end = p2
Lb = vlen(bpos - p1)
if Lb > L:
L = Lb
end = p1 + (Lb / L) * (end - p1)
drawline(color, p1, end)
return
br, bt, bz = csys.rtz(bpos)
theta1 = csys.rtz(p0)[1]
theta2 = csys.rtz(p2)[1]
if theta2 < theta1 - math.pi:
theta2 += 2 * math.pi
elif theta2 > theta1 + math.pi:
theta2 -= 2 * math.pi
if theta2 < theta1:
theta1, theta2 = theta2, theta1
e0 = csys.xyz((max(vlen(p0 - p1), br, minR1) + 0.5, theta1, 0))
e1 = csys.xyz((max(vlen(p2 - p1), br, minR2) + 0.5, theta2, 0))
drawline(color, p1, e0)
drawline(color, p1, e1)
if highlighted:
csys.drawArc(color, br, theta1, theta2, 0, width=THICKLINEWIDTH)
else:
csys.drawArc(color, br, theta1, theta2, 0)
# draw some arrowheads
e00 = csys.xyz((br, theta1, 0))
e10 = csys.xyz((br, theta2, 0))
dr = 0.25
dtheta = 1 / br
e0a = csys.xyz((br + dr, theta1 + dtheta, 0))
e0b = csys.xyz((br - dr, theta1 + dtheta, 0))
e1a = csys.xyz((br + dr, theta2 - dtheta, 0))
e1b = csys.xyz((br - dr, theta2 - dtheta, 0))
drawline(color, e00, e0a)
drawline(color, e00, e0b)
drawline(color, e10, e1a)
drawline(color, e10, e1b)
midangle = (theta1 + theta2) / 2
tmidpoint = csys.xyz((br + 0.5, midangle, 0))
h = 1.0e-3
textx = norm(csys.xyz((br + 0.5, midangle + h, 0)) - tmidpoint)
texty = norm(csys.xyz((br + 0.5 + h, midangle, 0)) - tmidpoint)
# make sure the text runs from left to right
if dot(textx, right) < 0:
textx = -textx
# make sure the text isn't upside-down
outOfScreen = cross(right, up)
textForward = cross(textx, texty)
if dot(outOfScreen, textForward) < 0:
tmidpoint = csys.xyz((br + 1.5, midangle, 0))
texty = -texty
textxyz = tmidpoint - (0.5 * len(text)) * textx
def tfm(x, y):
x = (x / (1. * WIDTH)) * textx
y = (y / (1. * HEIGHT)) * texty
return textxyz + x + y
f3d = Font3D()
f3d.drawString(text, tfm=tfm, color=color)
def drawLine(self, color, rtz1, rtz2, width=1):
drawline(color, self.xyz(rtz1), self.xyz(rtz2), width=width)
def _DEBUG_draw_avg_centerpairs_of_potential_crossovers(self):
pairs = self._crossoverSite_marker.get_avg_center_pairs_of_potential_crossovers
for pair in pairs:
drawline(yellow, pair[0], pair[1], width = 2)
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 draw(self):
color = self.fix_color(self.color)
end1, end2 = self.end1, self.end2
width = self.width
dashed = self.dashed
drawline(color[:3], end1, end2, width = width, dashEnabled = dashed) ###k dashEnabled untested here
