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tbgl
tools
mrdna
Commits
cf915a07
Commit
cf915a07
authored
May 16, 2018
by
cmaffeo2
Browse files
Likely fixed most backmapping bugs
parent
b670c7f0
Changes
4
Expand all
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arbdmodel.py
View file @
cf915a07
...
...
@@ -710,7 +710,7 @@ class ArbdModel(PdbModel):
def
_writeArbdParticleFile
(
self
,
filename
):
with
open
(
filename
,
'w'
)
as
fh
:
for
p
in
self
.
particles
:
data
=
tuple
([
p
.
idx
,
p
.
name
]
+
[
x
for
x
in
p
.
collapsedPosition
()])
data
=
tuple
([
p
.
idx
,
p
.
type_
.
name
]
+
[
x
for
x
in
p
.
collapsedPosition
()])
fh
.
write
(
"ATOM %d %s %f %f %f
\n
"
%
data
)
...
...
cadnano_segments.py
View file @
cf915a07
...
...
@@ -199,7 +199,8 @@ class cadnano_part(SegmentModel):
self
.
part
=
part
self
.
_cadnano_part_to_segments
(
part
)
# SegmentModel.__init__(self,...)
self
.
segments
=
[
seg
for
hid
,
segs
in
self
.
helices
.
items
()
for
seg
in
segs
]
# self.segments = [seg for hid,segs in self.helices.items() for seg in segs]
self
.
segments
=
[
seg
for
hid
,
segs
in
sorted
(
self
.
helices
.
items
())
for
seg
in
segs
]
self
.
_add_intrahelical_connections
()
self
.
_add_crossovers
()
self
.
_add_prime_ends
()
...
...
@@ -227,7 +228,10 @@ class cadnano_part(SegmentModel):
vh_list
=
[]
strand_list
=
[]
self
.
xover_list
=
xover_list
=
[]
numHID
=
part
.
getIdNumMax
()
+
1
try
:
numHID
=
part
.
getMaxIdNum
()
+
1
except
:
numHID
=
part
.
getIdNumMax
()
+
1
for
id_num
in
range
(
numHID
):
offset_and_size
=
part
.
getOffsetAndSize
(
id_num
)
...
...
@@ -527,14 +531,13 @@ def run_simulation_protocol( output_name, job_id, json_data,
remove_long_bonds
=
False
,
gpu
=
0
,
directory
=
None
,
coarse_steps
=
1e
6
,
fine_steps
=
1e
6
coarse_steps
=
1e
5
+
1
,
fine_steps
=
1e
5
+
1
):
ret
=
None
d_orig
=
os
.
getcwd
()
try
:
directory
=
"/dev/shm/origami-job-robot_v1.9_bent--0f4axf4k"
if
directory
is
None
:
import
tempfile
directory
=
tempfile
.
mkdtemp
(
prefix
=
'origami-%s-'
%
job_id
,
dir
=
'/dev/shm/'
)
...
...
@@ -594,7 +597,7 @@ def run_simulation_protocol( output_name, job_id, json_data,
else
:
output_prefix
=
"%s-1"
%
output_name
full_output_prefix
=
"%s/%s"
%
(
output_directory
,
output_prefix
)
#
model.simulate( outputPrefix = output_prefix, numSteps=coarse_steps, **simargs )
model
.
simulate
(
outputPrefix
=
output_prefix
,
numSteps
=
coarse_steps
,
**
simargs
)
coordinates
=
readArbdCoords
(
'%s.0.restart'
%
full_output_prefix
)
...
...
@@ -605,7 +608,7 @@ def run_simulation_protocol( output_name, job_id, json_data,
model
.
_update_segment_positions
(
coordinates
)
model
.
_clear_beads
()
model
.
_generate_bead_model
(
1
,
1
,
local_twist
=
True
,
escapable_twist
=
True
)
#
model.simulate( outputPrefix = output_prefix, numSteps=fine_steps, **simargs )
model
.
simulate
(
outputPrefix
=
output_prefix
,
numSteps
=
fine_steps
,
**
simargs
)
coordinates
=
readAvgArbdCoords
(
'%s.psf'
%
output_prefix
,
'%s.pdb'
%
output_prefix
,
'%s.0.dcd'
%
full_output_prefix
,
rmsdThreshold
=
1
)
...
...
run.py
View file @
cf915a07
...
...
@@ -19,7 +19,7 @@ if __name__ == '__main__':
print
(
"WARNING: skipping unreadable json file {}"
.
format
(
f
))
continue
run_simulation_protocol
(
out
,
"job-"
+
out
+
"-"
,
data
,
gpu
=
0
)
run_simulation_protocol
(
out
,
"job-"
+
out
+
"-"
,
data
,
gpu
=
1
)
# try:
# run_simulation_protocol( out, "job-"+out+"-", data, gpu=0 )
# except:
...
...
segmentmodel.py
View file @
cf915a07
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