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tools
mrdna
Commits
2191911b
Commit
2191911b
authored
Sep 04, 2018
by
cmaffeo2
Browse files
Added some code for debugging
parent
8d210e3b
Changes
1
Hide whitespace changes
Inline
Side-by-side
dnarbd/segmentmodel.py
View file @
2191911b
...
...
@@ -317,6 +317,9 @@ class SegmentParticle(PointParticle):
orientation
=
np
.
eye
(
3
)
o
.
position
=
self
.
position
+
orientation
.
dot
(
np
.
array
((
Segment
.
orientation_bond
.
r0
,
0
,
0
))
)
def
__repr__
(
self
):
return
"<SegmentParticle {} on {}[{:.2f}]>"
.
format
(
self
.
name
,
self
.
parent
,
self
.
contour_position
)
## TODO break this class into smaller, better encapsulated pieces
class
Segment
(
ConnectableElement
,
Group
):
...
...
@@ -724,14 +727,12 @@ class Segment(ConnectableElement, Group):
# conn_locs = self.get_contour_sorted_connections_and_locations()
# locs = [A for c,A,B in conn_locs]
# existing_beads = [l.particle for l in locs if l.particle is not None]
# if self.name == "
31-2
":
#
pdb.set_trace()
# if self.name == "
S001
":
#
pdb.set_trace()
existing_beads
=
{
l
.
particle
for
l
in
self
.
locations
if
l
.
particle
is
not
None
}
existing_beads
=
sorted
(
list
(
existing_beads
),
key
=
lambda
b
:
b
.
get_contour_position
(
self
)
)
existing_beads
0
=
{
l
.
particle
for
l
in
self
.
locations
if
l
.
particle
is
not
None
}
existing_beads
=
sorted
(
list
(
existing_beads
0
),
key
=
lambda
b
:
b
.
get_contour_position
(
self
)
)
if
len
(
existing_beads
)
!=
len
(
set
(
existing_beads
)):
pdb
.
set_trace
()
for
b
in
existing_beads
:
assert
(
b
.
parent
is
not
None
)
...
...
@@ -1329,6 +1330,7 @@ class SegmentModel(ArbdModel):
def
_get_potential
(
self
,
type_
,
kSpring
,
d
,
max_potential
=
None
):
key
=
(
type_
,
kSpring
,
d
,
max_potential
)
if
key
not
in
self
.
_bonded_potential
:
assert
(
kSpring
>=
0
)
if
type_
==
"bond"
:
self
.
_bonded_potential
[
key
]
=
HarmonicBond
(
kSpring
,
d
,
rRange
=
(
0
,
1200
),
max_potential
=
max_potential
)
elif
type_
==
"angle"
:
...
...
@@ -1484,9 +1486,15 @@ class SegmentModel(ArbdModel):
if
len
(
beads
)
<=
1
:
pdb
.
set_trace
()
""" Get positions """
positions
=
bead_coordinates
[
ids
,:].
T
# print("BEADS NOT IN {}:".format(s))
# for b,c in filter(lambda z: z[0] not in s.beads, zip(beads,contours)):
# print(" {}[{:03f}]: {:0.3f}".format(b.parent.name, b.contour_position, c) )
ret
=
interpolate
.
splprep
(
positions
,
u
=
contours
,
s
=
0
,
k
=
1
,
full_output
=
1
)
tck
=
ret
[
0
][
0
]
...
...
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