def transformBases(self, start, end, x, y, z, is_5to3):
"""
assumes start < end
start (int): the start index to transform
end (int): the end_idx to transform (use -1 for the end) (non-inclusive)
x (int): unit in bases from 0
y, z (float): units in multiple of RADIUS from 0,0
is_5to3 (bool): if the bases will be 5' to 3' in the x direction
or 3' to 5'
"""
old_coords = self.atom_group._getCoords() # points to source array
start_idxs = self.start_idxs
twist_per_segment = 2.*math.pi/self.bases_per_turn
theta0 = self.theta_offset
try:
start_idx = start_idxs[start]
except:
print("start idx problem:", len(start_idxs), start)
raise
if end == -1 or end > len(self.seq) - 1:
# print("doop", end)
end_idx = len(old_coords)
else:
# print("goop", end)
end_idx = start_idxs[end]
if not is_5to3:
# 1. Flip 180 degrees about Z to change direction
m_rev = matrix.makeRotationZ(math.pi)
self.reverse_queue.append((m_rev, start_idx, end_idx))
# 2. Translate as required
# print("translating", x + end - start )
m = matrix.makeTranslation((x + end - start)*DELTA_X + DELTA_X_REV_OFFSET,
y*RADIUS,
z*RADIUS)
if x + end - start - 1 < 1:
print("tb", len(self.twists), x, end, start, x + end - start - 1)
raise ValueError("transformBases: issue with start and end")
self.twists[start:end] = [(q*twist_per_segment + theta0 + THETA_REV_OFFSET)\
for q in range(x + end - start - 1, x - 1, -1)]
else:
m = matrix.makeTranslation(x*DELTA_X, y*RADIUS, z*RADIUS)
self.twists[start:end] = \
[(q*twist_per_segment + theta0) \
for q in range(x, x + end - start)]
self.base_idxs[start:end] = list(range(0, end - start))
self.transform_queue.append((m, start_idx, end_idx))
def linearize(self):
""" Using self.base_idxs, separate out bases relative to one another
"""
new_coords = self.atom_group._getCoords()
bidxs = self.base_idxs
sidxs = self.start_idxs
start = 0
lim = len(sidxs) - 1
for i in range(lim+1):
if i < lim:
next = sidxs[i+1]
else:
next = len(new_coords)
base_idx = bidxs[i]
m = matrix.makeTranslation(base_idx*DELTA_X, 0, 0)
new_coords[start:next] = matrix.applyTransform(new_coords[start:next], m)
start = next
# end for
self.atom_group.setCoords(new_coords)