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mrdna
Commits
22534586
Commit
22534586
authored
Mar 03, 2020
by
cmaffeo2
Browse files
Slightly updated routine for circular DNA in case beads overlap
parent
6f40a20c
Changes
1
Hide whitespace changes
Inline
Side-by-side
mrdna/segmentmodel.py
View file @
22534586
...
...
@@ -359,6 +359,30 @@ given context, provide the position
# nt_pos = self.get_nt_position(seg)
# return seg.nt_pos_to_contour(nt_pos)
def
combine
(
self
,
other
):
assert
(
other
in
self
.
intrahelical_neighbors
)
assert
(
self
in
other
.
intrahelical_neighbors
)
self
.
intrahelical_neighbors
.
remove
(
other
)
other
.
intrahelical_neighbors
.
remove
(
self
)
for
b
in
other
.
intrahelical_neighbors
:
b
.
intrahelical_neighbors
.
remove
(
other
)
b
.
intrahelical_neighbors
.
append
(
self
)
self
.
intrahelical_neighbors
.
append
(
b
)
for
l
in
other
.
locations
:
self
.
locations
.
append
(
l
)
l
.
particle
=
self
## Remove bead
other
.
parent
.
children
.
remove
(
other
)
if
other
in
other
.
parent
.
beads
:
other
.
parent
.
beads
.
remove
(
other
)
if
'orientation_bead'
in
other
.
__dict__
:
other
.
parent
.
children
.
remove
(
other
.
orientation_bead
)
for
b
in
list
(
other
.
parent
.
bonds
):
if
other
in
b
[:
2
]:
other
.
parent
.
bonds
.
remove
(
b
)
def
update_position
(
self
,
contour_position
):
self
.
contour_position
=
contour_position
self
.
position
=
self
.
parent
.
contour_to_position
(
contour_position
)
...
...
@@ -2285,6 +2309,32 @@ class SegmentModel(ArbdModel):
for
b
in
(
b1
,
b2
):
assert
(
b
is
not
None
)
b1
.
make_intrahelical_neighbor
(
b2
)
def
_combine_zero_sep_beads
():
skip_keys
=
[]
for
b1
,
b2
in
[
k
for
k
,
v
in
special_seps
.
items
()
if
v
==
0
]:
if
(
b1
,
b2
)
in
skip_keys
:
continue
del
special_seps
[(
b1
,
b2
)]
del
special_seps
[(
b2
,
b1
)]
skip_keys
.
append
((
b2
,
b1
))
for
b
in
b2
.
intrahelical_neighbors
:
if
b
is
b1
:
continue
if
b
is
not
b1
and
b
.
parent
is
b2
.
parent
:
sep
=
np
.
abs
(
b2
.
contour_position
-
b
.
contour_position
)
*
b
.
parent
.
num_nt
special_seps
[(
b
,
b1
)]
=
sep
special_seps
[(
b1
,
b
)]
=
sep
b1
.
combine
(
b2
)
for
k
in
list
(
special_seps
.
keys
()):
if
b2
in
k
:
if
b2
==
k
[
0
]:
newkey
=
(
b1
,
k
[
1
])
else
:
newkey
=
(
k
[
0
],
b2
)
special_seps
[
newkey
]
=
special_seps
[
k
]
del
special_seps
[
k
]
_combine_zero_sep_beads
()
""" Reassign bead types """
if
self
.
DEBUG
:
print
(
"Assigning bead types"
)
beadtype_s
=
dict
()
...
...
@@ -3267,8 +3317,8 @@ class SegmentModel(ArbdModel):
ntsJ1
,
ntsJ2
=
[
segJ
.
contour_to_nt_pos
(
B
.
address
)
for
B
in
(
B1
,
B2
)]
ntsI
=
ntsI2
-
ntsI1
+
1
ntsJ
=
ntsJ2
-
ntsJ1
+
1
assert
(
np
.
isclose
(
ntsI
,
int
(
round
(
ntsI
))
)
)
assert
(
np
.
isclose
(
ntsJ
,
int
(
round
(
ntsJ
))
)
)
#
assert( np.isclose( ntsI, int(round(ntsI)) ) )
#
assert( np.isclose( ntsJ, int(round(ntsJ)) ) )
ntsI
,
ntsJ
=
[
int
(
round
(
i
))
for
i
in
(
ntsI
,
ntsJ
)]
## Find if dsDNA "segments" are pointing in same direction
...
...
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