From 00443f9d469456cc71e36f2b4178ad3c1fb1d54e Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Thu, 6 Sep 2018 13:25:39 -0500
Subject: [PATCH] Gave vHelix reader large default dimensions; removed some
print statements
---
mrdna/readers/__init__.py | 2 ++
mrdna/readers/polygon_mesh.py | 2 --
mrdna/segmentmodel.py | 9 ++++++---
3 files changed, 8 insertions(+), 5 deletions(-)
diff --git a/mrdna/readers/__init__.py b/mrdna/readers/__init__.py
index 8a6110c..e430d87 100644
--- a/mrdna/readers/__init__.py
+++ b/mrdna/readers/__init__.py
@@ -20,6 +20,8 @@ def read_cadnano(json_file, **model_parameters):
def read_vhelix(maya_file, **model_parameters):
data = parse_maya_file(maya_file)
segments, dsSegmentDict = convert_maya_to_segments( data )
+ if 'dimensions' not in model_parameters:
+ model_parameters['dimensions']=(5000,5000,5000)
model = SegmentModel( segments,**model_parameters )
model.set_sequence(m13seq*10)
return model
diff --git a/mrdna/readers/polygon_mesh.py b/mrdna/readers/polygon_mesh.py
index 2ab0a00..4e2027c 100644
--- a/mrdna/readers/polygon_mesh.py
+++ b/mrdna/readers/polygon_mesh.py
@@ -314,10 +314,8 @@ def convert_maya_to_segments(helices):
nt = 0
def add_primes(b,nt,fwd):
if b.end3 is None:
- if not fwd: print("3prime at {}[{},{}]".format(hn,nt,fwd))
segments[hn].add_3prime(nt,fwd)
if b.end5 is None:
- if not fwd: print("5prime at {}[{},{}]".format(hn,nt,fwd))
segments[hn].add_5prime(nt,fwd)
for b in ordered_fwd_bases:
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 7c7b47d..b2b4ef8 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -905,6 +905,7 @@ class DoubleStrandedSegment(Segment):
## Real work
def _connect_ends(self, end1, end2, type_, force_connection):
+ debug = False
## TODO remove self?
## validate the input
for end in (end1, end2):
@@ -914,10 +915,10 @@ class DoubleStrandedSegment(Segment):
## Remove other connections involving these points
if end1.connection is not None:
- print("WARNING: reconnecting {}".format(end1))
+ if debug: print("WARNING: reconnecting {}".format(end1))
end1.connection.delete()
if end2.connection is not None:
- print("WARNING: reconnecting {}".format(end2))
+ if debug: print("WARNING: reconnecting {}".format(end2))
end2.connection.delete()
## Create and add connection
@@ -1133,12 +1134,14 @@ class Strand(Group):
self.children = self.strand_segments = []
self.segname = segname
self.is_circular = is_circular
+ self.debug = False
## TODO disambiguate names of functions
def add_dna(self, segment, start, end, is_fwd):
""" start/end are given as nt """
if np.abs(start-end) <= 0.9:
- print( "WARNING: segment constructed with a very small number of nts ({})".format(np.abs(start-end)) )
+ if self.debug:
+ print( "WARNING: segment constructed with a very small number of nts ({})".format(np.abs(start-end)) )
# import pdb
# pdb.set_trace()
for s in self.strand_segments:
--
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