From 17f8c66ac653887fb9d96b3b149710f46b02cc74 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 23 Jul 2019 13:19:55 -0500
Subject: [PATCH] Fixed error in ssDNA model where the terminal dihedral angle
was not applied.
Added PointerParticle.duplicate()
---
arbdmodel/__init__.py | 3 +++
arbdmodel/ssdna_two_bead.py | 2 +-
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/arbdmodel/__init__.py b/arbdmodel/__init__.py
index bf34913..de77ac9 100644
--- a/arbdmodel/__init__.py
+++ b/arbdmodel/__init__.py
@@ -408,6 +408,9 @@ class PointParticle(Transformable, Child):
def get_restraints(self):
return [(self,r) for r in self.restraints]
+ def duplicate(self):
+ new = deepcopy(self)
+ return new
def __getattr__(self, name):
"""
diff --git a/arbdmodel/ssdna_two_bead.py b/arbdmodel/ssdna_two_bead.py
index b077e91..40fb40e 100644
--- a/arbdmodel/ssdna_two_bead.py
+++ b/arbdmodel/ssdna_two_bead.py
@@ -76,7 +76,7 @@ class DnaStrandFromPolymer(Group):
self.add_exclusion( i=b1, j=p3 )
## Four consecutive nts
- for i in range(len(nts)-4):
+ for i in range(len(nts)-3):
p1,b1 = nts[i].children
p2,b2 = nts[i+1].children
p3,b3 = nts[i+2].children
--
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