From a83baf1b52d3fea9eda5703e3d938f9dcc3ff25c Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Wed, 29 Aug 2018 16:43:36 -0500
Subject: [PATCH] polygon_mesh: Changed bead positions at crossovers to fix
issue with single-nt polymers
---
bin/dnarbd | 9 ++++---
dnarbd/readers/__init__.py | 2 +-
dnarbd/readers/polygon_mesh.py | 48 +++++++++++++++++++++++++---------
3 files changed, 42 insertions(+), 17 deletions(-)
mode change 100644 => 100755 bin/dnarbd
diff --git a/bin/dnarbd b/bin/dnarbd
old mode 100644
new mode 100755
index 703c3d8..cf16d9c
--- a/bin/dnarbd
+++ b/bin/dnarbd
@@ -50,10 +50,13 @@ if __name__ == '__main__':
model = read_model( infile )
+ if args.output_prefix is not None:
+ prefix = args.output_prefix
+
run_args = dict(
model = model,
- output_name = args.output_prefix,
- job_id = "job-"+args.output_prefix,
+ output_name = prefix,
+ job_id = "job-" + prefix,
directory = args.directory,
gpu = args.gpu,
coarse_steps = args.coarse_steps,
@@ -61,7 +64,5 @@ if __name__ == '__main__':
backbone_scale = args.backbone_scale
)
- if args.output_prefix == None:
- run_args['output_name'] = prefix
simulate( **run_args )
diff --git a/dnarbd/readers/__init__.py b/dnarbd/readers/__init__.py
index b846d72..2d1323c 100644
--- a/dnarbd/readers/__init__.py
+++ b/dnarbd/readers/__init__.py
@@ -13,7 +13,7 @@ from .segmentmodel_from_pdb import SegmentModelFromPdb
## TODO: make module this package conform to a single style for input/output
def read_cadnano(json_file, **model_parameters):
- data = read_json_file
+ data = read_json_file(json_file)
return model_from_cadnano_json(data)
def read_vhelix(maya_file, **model_parameters):
diff --git a/dnarbd/readers/polygon_mesh.py b/dnarbd/readers/polygon_mesh.py
index 15c4c88..f7bcc3a 100644
--- a/dnarbd/readers/polygon_mesh.py
+++ b/dnarbd/readers/polygon_mesh.py
@@ -326,9 +326,15 @@ def convert_maya_to_segments(helices):
if top not in connectionToSingleStrand:
ssSeg = get_end3_ssDNA(top)
if len(ssSeg) > 0:
- seg2 = SingleStrandedSegment("strand",
- start_position = ssSeg[0].get_position(),
- end_position = ssSeg[-1].get_position(),
+ r0 = ssSeg[0].get_position()
+ if ssSeg[0].end5 is not None:
+ r0 = 0.75*r0 + 0.25*ssSeg[0].end5.get_position()
+ r1 = ssSeg[-1].get_position()
+ if ssSeg[-1].end3 is not None:
+ r1 = 0.75*r1 + 0.25*ssSeg[-1].end3.get_position()
+ seg2 = SingleStrandedSegment("S{:03d}".format(len(ss_segments)),
+ start_position = r0,
+ end_position = r1,
num_nt = len(ssSeg))
seg.connect_end3(seg2)
connectionToSingleStrand[top] = seg2
@@ -354,9 +360,15 @@ def convert_maya_to_segments(helices):
if top.basepair not in connectionToSingleStrand:
ssSeg = get_end5_ssDNA(top.basepair)[::-1]
if len(ssSeg) > 0:
- seg2 = SingleStrandedSegment("strand",
- start_position = ssSeg[-1].get_position(),
- end_position = ssSeg[0].get_position(),
+ r0 = ssSeg[-1].get_position()
+ if ssSeg[-1].end5 is not None:
+ r0 = 0.75*r0 + 0.25*ssSeg[-1].end5.get_position()
+ r1 = ssSeg[0].get_position()
+ if ssSeg[0].end3 is not None:
+ r1 = 0.75*r1 + 0.25*ssSeg[0].end3.get_position()
+ seg2 = SingleStrandedSegment("S{:03d}".format(len(ss_segments)),
+ start_position = r0,
+ end_position = r1,
num_nt = len(ssSeg))
seg.connect_end5(seg2)
connectionToSingleStrand[top.basepair] = seg2
@@ -382,9 +394,15 @@ def convert_maya_to_segments(helices):
if bot not in connectionToSingleStrand:
ssSeg = get_end3_ssDNA(bot)
if len(ssSeg) > 0:
- seg2 = SingleStrandedSegment("strand",
- start_position = ssSeg[0].get_position(),
- end_position = ssSeg[-1].get_position(),
+ r0 = ssSeg[0].get_position()
+ if ssSeg[0].end5 is not None:
+ r0 = 0.75*r0 + 0.25*ssSeg[0].end5.get_position()
+ r1 = ssSeg[-1].get_position()
+ if ssSeg[-1].end3 is not None:
+ r1 = 0.75*r1 + 0.25*ssSeg[-1].end3.get_position()
+ seg2 = SingleStrandedSegment("S{:03d}".format(len(ss_segments)),
+ start_position = r0,
+ end_position = r1,
num_nt = len(ssSeg))
seg.connect_start3(seg2)
connectionToSingleStrand[bot] = seg2
@@ -406,9 +424,15 @@ def convert_maya_to_segments(helices):
if bot.basepair not in connectionToSingleStrand:
ssSeg = get_end5_ssDNA(bot.basepair)[::-1]
if len(ssSeg) > 0:
- seg2 = SingleStrandedSegment("strand",
- start_position = ssSeg[-1].get_position(),
- end_position = ssSeg[0].get_position(),
+ r0 = ssSeg[-1].get_position()
+ if ssSeg[-1].end5 is not None:
+ r0 = 0.75*r0 + 0.25*ssSeg[-1].end5.get_position()
+ r1 = ssSeg[0].get_position()
+ if ssSeg[0].end3 is not None:
+ r1 = 0.75*r1 + 0.25*ssSeg[0].end3.get_position()
+ seg2 = SingleStrandedSegment("S{:03d}".format(len(ss_segments)),
+ start_position = r0,
+ end_position = r1,
num_nt = len(ssSeg))
seg.connect_start5(seg2)
connectionToSingleStrand[bot.basepair] = seg2
--
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