From b670c7f05d2ad4a2dba71efc471a46ffaa23491f Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Wed, 11 Apr 2018 11:12:14 -0500
Subject: [PATCH] Conditionally update coordinates using linear interpolation
when there are not many beads
---
cadnano_segments.py | 20 ++++++++++----------
run.py | 10 ++++++----
segmentmodel.py | 46 +++++++++++++++++++++++++++++++++++++++------
3 files changed, 56 insertions(+), 20 deletions(-)
diff --git a/cadnano_segments.py b/cadnano_segments.py
index 32c2104..626ceea 100644
--- a/cadnano_segments.py
+++ b/cadnano_segments.py
@@ -526,15 +526,15 @@ def run_simulation_protocol( output_name, job_id, json_data,
sequence=None,
remove_long_bonds=False,
gpu = 0,
- directory=None
+ directory=None,
+ coarse_steps = 1e6,
+ fine_steps = 1e6
):
- coarseSteps = 1e5+1
- fineSteps = 1e5+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/')
@@ -583,18 +583,18 @@ def run_simulation_protocol( output_name, job_id, json_data,
output_prefix = "%s-0" % output_name
full_output_prefix = "%s/%s" % (output_directory,output_prefix)
## TODO Remove long bonds
- model.simulate( outputPrefix = output_prefix, numSteps=0.05*coarseSteps, **simargs )
+ model.simulate( outputPrefix = output_prefix, numSteps=0.05*coarse_steps, **simargs )
coordinates = readArbdCoords('%s.0.restart' % full_output_prefix)
output_prefix = "%s-1" % output_name
model._update_segment_positions(coordinates)
# model._clear_beads()
# # model._generate_bead_model( 7, 4, False )
# model._generate_bead_model( 7, 4, False )
- model.simulate( outputPrefix = output_prefix, numSteps=0.95*coarseSteps, **simargs )
+ model.simulate( outputPrefix = output_prefix, numSteps=0.95*coarse_steps, **simargs )
else:
output_prefix = "%s-1" % output_name
full_output_prefix = "%s/%s" % (output_directory,output_prefix)
- model.simulate( outputPrefix = output_prefix, numSteps=coarseSteps, **simargs )
+ # model.simulate( outputPrefix = output_prefix, numSteps=coarse_steps, **simargs )
coordinates = readArbdCoords('%s.0.restart' % full_output_prefix)
@@ -605,7 +605,7 @@ 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=fineSteps, **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)
@@ -615,7 +615,7 @@ 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=False )
- model.simulate( outputPrefix = output_prefix, numSteps=fineSteps, **simargs )
+ model.simulate( outputPrefix = output_prefix, numSteps=fine_steps, **simargs )
coordinates = readAvgArbdCoords('%s.psf' % output_name,'%s.pdb' % output_prefix, '%s.0.dcd' % full_output_prefix )
@@ -625,7 +625,7 @@ def run_simulation_protocol( output_name, job_id, json_data,
model._update_segment_positions(coordinates)
model._clear_beads()
model._generate_atomic_model(scale=0.25)
- model.atomic_simulate( outputPrefix = full_output_prefix )
+ model.atomic_simulate( outputPrefix = output_prefix )
ret = directory
diff --git a/run.py b/run.py
index 03b1bb6..499f49c 100644
--- a/run.py
+++ b/run.py
@@ -18,7 +18,9 @@ if __name__ == '__main__':
except:
print("WARNING: skipping unreadable json file {}".format(f))
continue
- try:
- run_simulation_protocol( out, "job-"+out+"-", data, gpu=0 )
- except:
- print("ERROR: failed to simulate {}".format(f))
+
+ run_simulation_protocol( out, "job-"+out+"-", data, gpu=0 )
+ # try:
+ # run_simulation_protocol( out, "job-"+out+"-", data, gpu=0 )
+ # except:
+ # print("ERROR: failed to simulate {}".format(f))
diff --git a/segmentmodel.py b/segmentmodel.py
index 5875ecb..8ba4461 100644
--- a/segmentmodel.py
+++ b/segmentmodel.py
@@ -668,6 +668,9 @@ 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 == "51-2":
+ # 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) )
@@ -722,6 +725,8 @@ class Segment(ConnectableElement, Group):
last = eb1
for j in range(num_beads):
s = ds*(j+1) + s0
+ # if self.name in ("51-2","51-3"):
+ # print(" adding bead at {}".format(s))
b = self._generate_one_bead(s,nts)
last.make_intrahelical_neighbor(b)
@@ -732,6 +737,8 @@ class Segment(ConnectableElement, Group):
if eb2.parent == self:
tmp_children.append(eb2)
+ # if self.name in ("51-2","51-3"):
+ # pdb.set_trace()
self._rebuild_children(tmp_children)
def _regenerate_beads(self, max_nts_per_bead=4, ):
@@ -1292,7 +1299,11 @@ class SegmentModel(ArbdModel):
beads = list(beads)
## Skip beads that are None (some locations were not assigned a particle to avoid double-counting)
- beads = [b for b in beads if b is not None]
+ # beads = [b for b in beads if b is not None]
+ beads = list(filter(lambda x: x is not None, beads))
+ if isinstance(self, DoubleStrandedSegment):
+ beads = list(filter(lambda x: x.type_.name[0] == "D", beads))
+
contours = []
for b in beads:
try:
@@ -1316,10 +1327,31 @@ class SegmentModel(ArbdModel):
""" Get positions """
positions = bead_coordinates[ids,:].T
- try:
- tck, u = interpolate.splprep( positions, u=contours, s=0, k=3 )
- except:
- tck, u = interpolate.splprep( positions, u=contours, s=0, k=1 )
+ ret = interpolate.splprep( positions, u=contours, s=0, k=1, full_output=1 )
+ tck = ret[0][0]
+
+ ret = interpolate.splprep( positions, u=contours, s=0, k=1, full_output=1 )
+ tck2 = ret[0][0]
+
+ assert( tck[0][0] == tck2[0][0] )
+
+ # if len(beads) < 8:
+ # ret = interpolate.splprep( positions, u=contours, s=0, k=1, full_output=1 )
+ # tck = ret[0][0]
+ # if ret[2] > 0:
+ # pdb.set_trace()
+
+ # else:
+ # try:
+ # ret = interpolate.splprep( positions, u=contours, s=0, k=3, full_output=1 )
+ # tck = ret[0][0]
+ # if ret[2] > 0:
+ # pdb.set_trace()
+ # except:
+ # ret = interpolate.splprep( positions, u=contours, s=0, k=1, full_output=1 )
+ # tck = ret[0][0]
+ # if ret[2] > 0:
+ # pdb.set_trace()
s.position_spline_params = tck
@@ -1404,6 +1436,8 @@ class SegmentModel(ArbdModel):
## Loop through all connections, generating beads at appropriate locations
for c,A,B in self.get_connections("intrahelical"):
s1,s2 = [l.container for l in (A,B)]
+ # if s1.name in ("51-2","51-3") and s2.name in ("51-2","51-3"):
+ # pdb.set_trace()
print("Working on {}".format(c))
## TODO be more elegant!
# if isinstance(s1, DoubleStrandedSegment) and isinstance(s2, DoubleStrandedSegment) and A.on_fwd_strand == False: continue
@@ -1498,7 +1532,7 @@ class SegmentModel(ArbdModel):
b1,b2 = [l.particle for l in (A,B)]
if b1 is b2:
## already handled by Segment._generate_beads
- continue
+ pass
else:
for b in (b1,b2): assert( b is not None )
b1.make_intrahelical_neighbor(b2)
--
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