def _neighborSegment_ok_for_crossover_search(
self,
neighborSegment,
reference_segment_end1,
reference_segment_axisVector):
ok_for_search = False
orthogonal_vector = None
neighbor_end1 , neighbor_end2 = neighborSegment.getAxisEndPoints()
#Use end1 of neighbor segment and find out the perpendicular
#distance (and the vector) between this atom and the
#axis vector of dnaSegment (whose neighbors are being
#searched). If this distance is less than a specified amount
#then 'neighbor' is an approved neighbor of 'dnaSegment'
if neighbor_end1 is not None:
p1 = reference_segment_end1
v1 = reference_segment_axisVector
p2 = neighbor_end1
dist, orthogonal_dist = orthodist(p1, v1, p2)
#Check if the orthogonal distance is withing the
#specified limit.
if orthogonal_dist <= MAX_PERPENDICULAR_DISTANCE_BET_SEGMENT_AXES:
ok_for_search = True
vec = p1 + dist*v1 - p2
orthogonal_vector = orthogonal_dist*norm(vec)
if self.graphicsMode.DEBUG_DRAW_PLANE_NORMALS:
self._DEBUG_plane_normals_ends_for_drawing.append(
(p2, (p2 + orthogonal_vector)) )
return ok_for_search, orthogonal_vector
def _mirrorChunk(self, chunkToMirror):
"""
Converts the given chunk into its own mirror.
@param chunkToMirror: The chunk that needs to be converted into its own
mirror chunk.
@type chunkToMirror: instance of class Chunk
@see: self.Mirror
"""
m = chunkToMirror
# ninad060813 Following gives an orthogonal distance between the
#chunk center and mirror plane.
self.mirrorDistance, self.wid = orthodist(m.center,
self.mirrorAxis,
self.mirrorJigs[0].center)
# @@@@ ninad060813 This moves the mirror chunk on the other side of
# the mirror plane. It surely moves the chunk along the axis of the
# mirror plane but I am still unsure if this *always* moves the
# chunk on the other side of the mirror.
#Probably the 'orthodist' function has helped me here??
m.move(2*(self.mirrorDistance)*self.mirrorAxis)
m.stretch(-1.0)
m.rot(Q(self.mirrorAxis, pi))
return
def _mirrorJig(self, jigToMirror):
"""
Converts the given jig into its own mirror. If the jig is a motor,
it also reverses its direction.
@param jigToMirror: The jig that needs to be converted into its own
mirror jig.
@type jigToMirror: instance of class Jig
@see: self.Mirror
"""
j = jigToMirror
# ninad060813 This gives an orthogonal distance between the chunk
# center and mirror plane.
#Fixed bug 2503.
if not (isinstance(j, Motor) or isinstance(j, ESPImage)):
return
self.mirrorDistance, self.wid = orthodist(j.center, self.mirrorAxis,
self.mirrorJigs[0].center)
j.move(2*(self.mirrorDistance)*self.mirrorAxis)
j.rot(Q(self.mirrorAxis, pi))
#Reverse the direction of Linear and Rotary motor for correct
#mirror operation
if isinstance(j, Motor):
j.reverse_direction()
return
def findHandles_exact(self, p1, p2, cutoff = 0.0, backs_ok = 1, offset = V(0,0,0)):
"""
return a list of (dist, handle) pairs, in arbitrary order,
which includes, for each handle (spherical surface) hit by the ray from p1 thru p2,
its front-surface intersection with the ray,
unless that has dist < cutoff and backs_ok,
in which case include its back-surface intersection
(unless *that* has dist < cutoff).
"""
#e For now, just be simple, don't worry about speed.
# Someday we can preprocess self.handlpos using Numeric functions,
# like in nearSinglets and/or findSinglets
# (I have untested prototype code for this in extrude-outs.py).
hh = self.handles
res = []
v = norm(p2-p1)
## is this modifying the vector in-place, causing a bug?? offset += self.origin # treat our handles' pos as relative to this
## I don't know, but one of the three instances of += was doing this!!! probably i was resetting the atom or mol pos....
offset = offset + self.origin # treat our handles' pos as relative to this
radius_multiplier = self.radius_multiplier
for (pos,radius,info) in hh:
## bug in this? pos += offset
pos = pos + offset
radius *= radius_multiplier
dist, wid = orthodist(p1, v, pos)
if radius >= wid: # the ray hits the sphere
delta = sqrt(radius*radius - wid*wid)
front = dist - delta # depth from p1 of front surface of sphere, where it's hit
if front >= cutoff:
res.append((front,(pos,radius,info)))
elif backs_ok:
back = dist + delta
if back >= cutoff:
res.append((back,(pos,radius,info)))
return res
def _mirrorJig(self, jigToMirror):
"""
Converts the given jig into its own mirror. If the jig is a motor,
it also reverses its direction.
@param jigToMirror: The jig that needs to be converted into its own
mirror jig.
@type jigToMirror: instance of class Jig
@see: self.Mirror
"""
j = jigToMirror
# ninad060813 This gives an orthogonal distance between the chunk
# center and mirror plane.
#Fixed bug 2503.
if not (isinstance(j, Motor) or isinstance(j, ESPImage)):
return
self.mirrorDistance, self.wid = orthodist(j.center, self.mirrorAxis,
self.mirrorJigs[0].center)
j.move(2*(self.mirrorDistance)*self.mirrorAxis)
j.rot(Q(self.mirrorAxis, pi))
#Reverse the direction of Linear and Rotary motor for correct
#mirror operation
if isinstance(j, Motor):
j.reverse_direction()
return
def _mirrorChunk(self, chunkToMirror):
"""
Converts the given chunk into its own mirror.
@param chunkToMirror: The chunk that needs to be converted into its own
mirror chunk.
@type chunkToMirror: instance of class Chunk
@see: self.Mirror
"""
m = chunkToMirror
# ninad060813 Following gives an orthogonal distance between the
#chunk center and mirror plane.
self.mirrorDistance, self.wid = orthodist(m.center,
self.mirrorAxis,
self.mirrorJigs[0].center)
# @@@@ ninad060813 This moves the mirror chunk on the other side of
# the mirror plane. It surely moves the chunk along the axis of the
# mirror plane but I am still unsure if this *always* moves the
# chunk on the other side of the mirror.
#Probably the 'orthodist' function has helped me here??
m.move(2*(self.mirrorDistance)*self.mirrorAxis)
m.stretch(-1.0)
m.rot(Q(self.mirrorAxis, pi))
return
def _neighborSegment_ok_for_crossover_search(self, neighborSegment,
reference_segment_end1,
reference_segment_axisVector):
ok_for_search = False
orthogonal_vector = None
neighbor_end1, neighbor_end2 = neighborSegment.getAxisEndPoints()
#Use end1 of neighbor segment and find out the perpendicular
#distance (and the vector) between this atom and the
#axis vector of dnaSegment (whose neighbors are being
#searched). If this distance is less than a specified amount
#then 'neighbor' is an approved neighbor of 'dnaSegment'
if neighbor_end1 is not None:
p1 = reference_segment_end1
v1 = reference_segment_axisVector
p2 = neighbor_end1
dist, orthogonal_dist = orthodist(p1, v1, p2)
#Check if the orthogonal distance is withing the
#specified limit.
if orthogonal_dist <= MAX_PERPENDICULAR_DISTANCE_BET_SEGMENT_AXES:
ok_for_search = True
vec = p1 + dist * v1 - p2
orthogonal_vector = orthogonal_dist * norm(vec)
if self.graphicsMode.DEBUG_DRAW_PLANE_NORMALS:
self._DEBUG_plane_normals_ends_for_drawing.append(
(p2, (p2 + orthogonal_vector)))
return ok_for_search, orthogonal_vector
def findHandles_exact(self,
p1,
p2,
cutoff=0.0,
backs_ok=1,
offset=V(0, 0, 0)):
"""
@return: a list of (dist, handle) pairs, in arbitrary order, which
includes, for each handle (spherical surface) hit by the ray from p1
thru p2, its front-surface intersection with the ray, unless that has
dist < cutoff and backs_ok, in which case include its back-surface
intersection (unless *that* has dist < cutoff).
"""
#e For now, just be simple, don't worry about speed.
# Someday we can preprocess self.handlpos using Numeric functions,
# like in nearSinglets and/or findSinglets
# (I have untested prototype code for this in extrude-outs.py).
hh = self.handles
res = []
v = norm(p2 - p1)
# is this modifying the vector in-place, causing a bug??
## offset += self.origin # treat our handles' pos as relative to this
# I don't know, but one of the three instances of += was doing this!!!
# probably i was resetting the atom or mol pos....
offset = offset + self.origin # treat our handles' pos as relative to this
radius_multiplier = self.radius_multiplier
for (pos, radius, info) in hh:
## bug in this? pos += offset
pos = pos + offset
radius *= radius_multiplier
dist, wid = orthodist(p1, v, pos)
if radius >= wid: # the ray hits the sphere
delta = sqrt(radius * radius - wid * wid)
front = dist - delta # depth from p1 of front surface of sphere, where it's hit
if front >= cutoff:
res.append((front, (pos, radius, info)))
elif backs_ok:
back = dist + delta
if back >= cutoff:
res.append((back, (pos, radius, info)))
return res
