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tbgl
tools
mrdna
Commits
b37c4817
Commit
b37c4817
authored
Jul 06, 2018
by
cmaffeo2
Browse files
Updated initial placement of orientation beads
parent
87fc5b22
Changes
1
Hide whitespace changes
Inline
Side-by-side
segmentmodel.py
View file @
b37c4817
...
...
@@ -394,15 +394,23 @@ class Segment(ConnectableElement, Group):
def
contour_to_orientation
(
self
,
s
):
assert
(
isinstance
(
s
,
float
)
or
isinstance
(
s
,
int
)
or
len
(
s
)
==
1
)
# TODO make vectorized version
orientation
=
None
if
self
.
start_orientation
is
not
None
:
# axis = self.start_orientation.dot( np.array((0,0,1)) )
if
self
.
quaternion_spline_params
is
None
:
axis
=
self
.
contour_to_tangent
(
s
)
orientation
=
rotationAboutAxis
(
axis
,
self
.
twist_per_nt
*
self
.
contour_to_nt_pos
(
s
),
normalizeAxis
=
True
)
if
self
.
quaternion_spline_params
is
None
:
axis
=
self
.
contour_to_tangent
(
s
)
axis
=
axis
/
np
.
linalg
.
norm
(
axis
)
rotAxis
=
np
.
cross
(
axis
,
np
.
array
((
0
,
0
,
1
)))
rotAxisL
=
np
.
linalg
.
norm
(
rotAxis
)
theta
=
np
.
arcsin
(
rotAxisL
)
if
rotAxisL
>
0.001
:
orientation0
=
rotationAboutAxis
(
rotAxis
/
rotAxisL
,
theta
*
180
/
np
.
pi
,
normalizeAxis
=
False
)
else
:
q
=
interpolate
.
splev
(
s
,
self
.
quaternion_spline_params
)
if
len
(
q
)
>
1
:
q
=
np
.
array
(
q
).
T
# TODO: is this needed?
orientation
=
quaternion_to_matrix
(
q
)
orientation0
=
np
.
eye
(
3
)
orientation
=
rotationAboutAxis
(
axis
,
self
.
twist_per_nt
*
self
.
contour_to_nt_pos
(
s
),
normalizeAxis
=
False
)
orientation
=
orientation
.
dot
(
orientation0
)
else
:
q
=
interpolate
.
splev
(
s
,
self
.
quaternion_spline_params
)
if
len
(
q
)
>
1
:
q
=
np
.
array
(
q
).
T
# TODO: is this needed?
orientation
=
quaternion_to_matrix
(
q
)
return
orientation
def
get_contour_sorted_connections_and_locations
(
self
,
type_
):
...
...
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