From 843a09f8fa3fbb86f9b4b0ae698af258c1e6b5ff Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Fri, 21 Sep 2018 20:09:26 -0500
Subject: [PATCH] Improved readability of code for connection beads
---
mrdna/segmentmodel.py | 45 +++++++++++++++++++------------------------
1 file changed, 20 insertions(+), 25 deletions(-)
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 4101d4b..af50091 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -1891,31 +1891,26 @@ class SegmentModel(ArbdModel):
## TODO: offload the work here to s1/s2 (?)
a1,a2 = [l.address for l in (A,B)]
- if A.particle is None:
- b = s1.get_nearest_bead(a1)
- try:
- bead_is_far = s1.contour_to_nt_pos(np.abs(b.contour_position-a1)) >= min(max_basepairs_per_bead, max_nucleotides_per_bead)*0.5
- if bead_is_far or "is_intrahelical" in b.__dict__:
- raise Exception("not close")
- ## combine beads
- b.update_position( 0.5*(b.contour_position + a1) ) # avg position
- except:
- b = s1._generate_one_bead(a1,0)
- A.particle = b
- b.locations.append(A)
-
- if B.particle is None:
- b = s2.get_nearest_bead(a2)
- try:
- bead_is_far = s2.contour_to_nt_pos(np.abs(b.contour_position-a2)) >= min(max_basepairs_per_bead, max_nucleotides_per_bead)*0.5
- if bead_is_far or "is_intrahelical" in b.__dict__:
- raise Exception("not close")
- ## combine beads
- b.update_position( 0.5*(b.contour_position + a2) ) # avg position
- except:
- b = s2._generate_one_bead(a2,0)
- B.particle = b
- b.locations.append(B)
+ def maybe_add_bead(location, seg, address, ):
+ if location.particle is None:
+ b = seg.get_nearest_bead(address)
+ try:
+ distance = seg.contour_to_nt_pos(np.abs(b.contour_position-address))
+ max_distance = min(max_basepairs_per_bead, max_nucleotides_per_bead)*0.5
+ if "is_intrahelical" in b.__dict__:
+ max_distance = 0.5
+ if distance >= max_distance:
+ raise Exception("except")
+
+ ## combine beads
+ b.update_position( 0.5*(b.contour_position + address) ) # avg position
+ except:
+ b = seg._generate_one_bead(address,0)
+ location.particle = b
+ b.locations.append(location)
+
+ maybe_add_bead(A,s1,a1)
+ maybe_add_bead(B,s2,a2)
""" Some tests """
for c,A,B in self.get_connections("intrahelical"):
--
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