diff --git a/dnarbd/examples/run.py b/dnarbd/examples/from_cadnano.py
similarity index 58%
rename from dnarbd/examples/run.py
rename to dnarbd/examples/from_cadnano.py
index 6d5f77d6977c24be6e9b61bf5e5e97e4b8adb546..8e0358671c228b42c16ccd92e5aafdcb78ecb042 100644
--- a/dnarbd/examples/run.py
+++ b/dnarbd/examples/from_cadnano.py
@@ -4,7 +4,7 @@ from glob import glob
import re
from dnarbd.readers import cadnano_reader()
-from dnarbd.simulate import run_simulation_protocol
+from dnarbd.simulate import run_multiresolution_simulation as simulate
if __name__ == '__main__':
if len(sys.argv) > 1:
@@ -22,13 +22,11 @@ if __name__ == '__main__':
print("WARNING: skipping unreadable json file {}".format(f))
continue
- gpu = 0
directory = "run.out.7bd92d9.twist-angles"
- run_simulation_protocol( out, "job-"+out+"-", model, gpu=gpu,
- directory = directory)
- # try:
- # run_simulation_protocol( out, "job-"+out+"-", model, gpu=gpu,
- # directory = directory)
- # except:
- # print("WARNING: failed to simulate json file {}".format(f))
- # continue
+ simulate( model,
+ output_name = out,
+ coarse_steps = 1e7,
+ fine_steps = 1e7,
+ gpu=1,
+ directory = directory
+ )
diff --git a/dnarbd/examples/segmentmodel_example.py b/dnarbd/examples/from_code.py
similarity index 61%
rename from dnarbd/examples/segmentmodel_example.py
rename to dnarbd/examples/from_code.py
index 4d22fc23d7747aa1f63021a67a84ebdecff38a88..557f4abb4ba9571848bba737bfd4dcbee2637ac9 100644
--- a/dnarbd/examples/segmentmodel_example.py
+++ b/dnarbd/examples/from_code.py
@@ -1,18 +1,15 @@
import numpy as np
from dnarbd import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
+from dnarbd.simulate import run_multiresolution_simulation as simulate
"""
-Example of using segmentmodel to construct a CG
-
-May need to update your shell PATH variable before running this script, e.g.:
-PATH=/home/cmaffeo2/miniconda3/bin:$PATH
+Example using segmentmodel API to construct a model
"""
-
-
if __name__ == "__main__":
-
+
+ """ First create the individual helices and strands """
seg1 = DoubleStrandedSegment("strand", num_bp = 46)
seg2 = SingleStrandedSegment("strand",
@@ -24,20 +21,37 @@ if __name__ == "__main__":
end_position = seg1.end_position + np.array((-5,0,5)),
num_nt = 128)
+ """ Each "Segment" will has a "start" and "end"
+ - start3 and end5 are an attribute for all Segments
+ - start5 and end3 are an attribute for only DoubleStrandedSegment
+ The 3/5 refers to 3' or 5' end of a DNA strand
+ """
+
seg1.start3
seg1.start5
seg1.end3
seg1.end5
+ """ Add intrahelical connections """
seg1.connect_end3(seg2) # equivalent for ssDNA to: seg1.connect_end3(seg2.end5)
seg1.connect_end5(seg3)
seg1.connect_start3(seg3)
+ """ Add crossover connections """
+ ...
+
+
+ """ Create a model """
model = SegmentModel( [seg1, seg2, seg3],
local_twist = True,
max_basepairs_per_bead = 5,
max_nucleotides_per_bead = 5,
dimensions=(5000,5000,5000),
)
-
- model.simulate( outputPrefix = 'strand-test', outputPeriod=1e4, numSteps=1e6, gpu=1 )
+
+ """ Simulate """
+ simulate( model,
+ output_name = "strand-test",
+ coarse_steps = 1e7,
+ fine_steps = 1e7,
+ gpu=1 )
diff --git a/dnarbd/simulate.py b/dnarbd/simulate.py
index fe8e0b0d42ced786b76dcd48b11cd45678eb3781..7805f08a03d97941e823868d65b597a64bd7fc2c 100644
--- a/dnarbd/simulate.py
+++ b/dnarbd/simulate.py
@@ -5,19 +5,28 @@ from .coords import readArbdCoords, readAvgArbdCoords
arbd="/home/cmaffeo2/development/cuda/arbd.dbg/src/arbd" # reduced the mem footprint cause vmd
namd="/home/cmaffeo2/development/namd-bin/NAMD_Git-2017-07-06_Linux-x86_64-multicore-CUDA/namd2"
-def multiresolution_simulation( output_name, job_id, model,
- remove_long_bonds=False,
+def multiresolution_simulation( model, output_name,
+ job_id=None,
gpu = 0,
directory=None,
- coarse_steps = 5e7+1,
- fine_steps = 5e7+1
+ coarse_steps = 5e7,
+ fine_steps = 5e7,
+ coarse_output_period = 1e5,
+ fine_output_period = 1e5,
+ remove_long_bonds=False,
+ backbone_scale=1.0,
):
+ ## Round steps up to nearest multiple of output_period, plus 1
+ coarse_steps = ((coarse_steps//coarse_output_period)+1)*coarse_output_period+1
+ fine_steps = ((fine_steps//fine_output_period)+1)*fine_output_period+1
+
ret = None
d_orig = os.getcwd()
try:
if directory is None:
- directory = tempfile.mkdtemp(prefix='origami-%s-' % job_id, dir='/dev/shm/')
+ tmp = job_id if job_id is not None else output_name
+ directory = tempfile.mkdtemp(prefix='origami-%s-' % tmp, dir='/dev/shm/')
elif not os.path.exists(directory):
os.makedirs(directory)
os.chdir(directory)
@@ -27,8 +36,7 @@ def multiresolution_simulation( output_name, job_id, model,
# TODO: add the output directory in to the readArbdCoords functions or make it an attribute of the model object
""" Coarse simulation """
- # simargs = dict(timestep=200e-6, outputPeriod=1e5, gpu=gpu )
- simargs = dict(timestep=200e-6, outputPeriod=1e5, gpu=gpu, arbd=arbd )
+ simargs = dict(timestep=200e-6, outputPeriod=coarse_output_period, gpu=gpu)
model._clear_beads()
model._generate_bead_model( 5, 5, local_twist=False )
@@ -53,6 +61,7 @@ def multiresolution_simulation( output_name, job_id, model,
output_prefix = "%s-2" % output_name
full_output_prefix = "%s/%s" % (output_directory,output_prefix)
simargs['timestep'] = 50e-6
+ simargs['outputPeriod'] = fine_output_period
model._update_segment_positions(coordinates)
model._clear_beads()
model._generate_bead_model( 1, 1, local_twist=True, escapable_twist=True )
@@ -75,8 +84,7 @@ def multiresolution_simulation( output_name, job_id, model,
full_output_prefix = "%s/%s" % (output_directory,output_prefix)
model._update_segment_positions(coordinates)
model._clear_beads()
- # model._generate_atomic_model(scale=0.25)
- model._generate_atomic_model(scale=1.0)
+ model._generate_atomic_model(scale=backbone_scale)
model.atomic_simulate( outputPrefix = output_prefix )
ret = directory