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)
def applyTwist(self):
""" Using self.base_idxs, twist bases relative to one another
"""
new_coords = self.atom_group._getCoords()
tidxs = self.twists
sidxs = self.start_idxs
# print("checker", len(tidxs), len(sidxs))
assert(len(tidxs) == len(sidxs))
start = 0
lim = len(sidxs) - 1
for i in range(lim+1):
if i < lim:
next = sidxs[i+1]
else:
next = len(new_coords)
# print("twists", i, len(tidxs))
theta = tidxs[i]
m = matrix.makeRotationX(theta)
new_coords[start:next] = matrix.applyTransform(new_coords[start:next], m)
start = next
# end for
self.atom_group.setCoords(new_coords)
def applyTransformQueue(self):
new_coords = self.atom_group._getCoords()
for item in self.transform_queue:
m, start, end = item
new_coords[start:end] = matrix.applyTransform(new_coords[start:end], m)
self.transform_queue = []