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mrdna
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c62ac059
Commit
c62ac059
authored
5 months ago
by
cmaffeo2
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Add explicitly_unstacked argument to oxDNA reader to ensure we get terminal_crossover connections
parent
f70fa502
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mrdna/readers/segmentmodel_from_lists.py
+9
-0
9 additions, 0 deletions
mrdna/readers/segmentmodel_from_lists.py
mrdna/readers/segmentmodel_from_oxdna.py
+4
-3
4 additions, 3 deletions
mrdna/readers/segmentmodel_from_oxdna.py
with
13 additions
and
3 deletions
mrdna/readers/segmentmodel_from_lists.py
+
9
−
0
View file @
c62ac059
...
...
@@ -253,6 +253,15 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
basepaired / stacked / phosphodiester-bonded nucleotide. If there
is no such nucleotide, the value should be -1.
By default, where there is a 3
'
-to-5
'
connection between
double-straned helices, they will be connected by an intrahelical
connection that makes the helical domain continue across the
connection, even if they do not stack in the stacking
array. Instead, a
"
terminal_crossover
"
representing a relatively
free (e.g. kinked) junction can be placed by including the index
of one of the participating bases in the optional
:explicitly_unstacked: tuple.
Args:
basepair: List of each nucleotide
'
s basepair
'
s index
stack: List containing index of the nucleotide stacked on the 3
'
of each nucleotide
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...
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mrdna/readers/segmentmodel_from_oxdna.py
+
4
−
3
View file @
c62ac059
...
...
@@ -143,7 +143,7 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
orientation
=
[
np
.
array
(
o
).
T
.
dot
(
_yrot
)
for
o
in
zip
(
perp_dir
,
-
base_dir
,
-
normal_dir
)]
seq
=
nt_prop
[
"
seq
"
]
bp
=
nt_prop
[
"
bp
"
]
stack
=
nt_prop
[
"
stack
"
]
stack
=
np
.
array
((
list
(
nt_prop
[
"
stack
"
]
)))
three_prime
=
nt_prop
[
"
threeprime
"
]
nt_prop
[
"
orientation
"
]
=
orientation
nt_prop
[
"
r
"
]
=
list
(
r
)
...
...
@@ -205,8 +205,9 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
## _debug_write_bonds()
logger
.
info
(
f
'
mrdna_model_from_oxdna: num_bp, num_ss_nt, num_stacked:
{
np
.
sum
(
bp
>=
0
)
//
2
}
{
np
.
sum
(
bp
<
0
)
}
{
np
.
sum
(
stack
>=
0
)
}
'
)
model
=
model_from_basepair_stack_3prime
(
r
,
bp
,
stack
,
three_prime
,
seq
,
orientation
,
**
model_parameters
)
model
=
model_from_basepair_stack_3prime
(
r
,
bp
,
stack
,
three_prime
,
seq
,
orientation
,
explicitly_unstacked
=
np
.
argwhere
(
stack
==
-
1
),
**
model_parameters
)
"""
model.DEBUG = True
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