def add_deletions(design: sc.Design):
for helix in range(3, maxhelix):
if not design.strands_starting_on_helix(helix):
pass
else:
hel1 = helix #first starting helix
break
for helix in range(hel1, maxhelix, 2):
for offset in range(block * cmax):
if design.domains_at(helix, offset) and offset % 48 == 0:
design.add_deletion(helix, offset)
def add_angle_inducing_insertions_deletions(design: sc.Design):
# insertion followed by deletion
start = 59
end = start + (32 * 12)
for helix in [1, 5, 7, 11, 13]:
for offset in range(start, end, 32):
design.add_insertion(helix, offset, 1)
design.add_deletion(helix, offset + 16)
# deletion followed by insertion
for helix in [2, 4, 8, 10, 14]:
for offset in range(start, end, 32):
design.add_deletion(helix, offset)
design.add_insertion(helix, offset + 16, 1)
def add_deletion_in_range(design: sc.Design, helix: int, start: int, end: int,
deletion_offset: int) -> None:
# Inserts deletion somewhere in given range.
# `offset` is the relative offset within a column at which to put the deletions.
# If negative, chooses first available offset.
candidate_offsets = []
for candidate_deletion_offset in range(start, end):
if valid_deletion_offset(design, helix, candidate_deletion_offset):
candidate_offsets.append(candidate_deletion_offset)
if len(candidate_offsets) == 0:
raise ValueError(f"no pair of Substrands found on Helix {helix} "
f"overlapping interval [{start},{end})")
if deletion_offset < 0:
# pick offset furthest from edges of interval
candidate_offsets.sort(
key=lambda offset: min(offset - start, end - offset))
deletion_absolute_offset = candidate_offsets[0]
else:
deletion_absolute_offset = start + deletion_offset
design.add_deletion(helix, deletion_absolute_offset)
def add_twist_correct_deletions(design: sc.Design) -> None:
# I choose between 3 and 4 offset arbitrarily for twist-correction deletions for some reason,
# so they have to be hard-coded.
for col, offset in zip(range(4, 29, 3), [4, 3, 3, 4, 3, 3, 3, 3, 3]):
for helix in range(2, 18):
design.add_deletion(helix, 16 * col + offset)
def add_deletions(design: sc.Design):
for helix in range(24):
for offset in range(27, 294, 48):
design.add_deletion(helix, offset)
def add_twist_correction_deletions(design: sc.Design) -> None:
for helix in range(24):
for offset in range(19, 286, 48):
design.add_deletion(helix, offset)
