From c62ac059d34de6fb551569c5074290f87959a149 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Fri, 4 Oct 2024 14:51:15 -0500
Subject: [PATCH] Add explicitly_unstacked argument to oxDNA reader to ensure
we get terminal_crossover connections
---
mrdna/readers/segmentmodel_from_lists.py | 9 +++++++++
mrdna/readers/segmentmodel_from_oxdna.py | 7 ++++---
2 files changed, 13 insertions(+), 3 deletions(-)
diff --git a/mrdna/readers/segmentmodel_from_lists.py b/mrdna/readers/segmentmodel_from_lists.py
index ef184a0..c07306c 100644
--- a/mrdna/readers/segmentmodel_from_lists.py
+++ b/mrdna/readers/segmentmodel_from_lists.py
@@ -253,6 +253,15 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
basepaired / stacked / phosphodiester-bonded nucleotide. If there
is no such nucleotide, the value should be -1.
+ By default, where there is a 3'-to-5' connection between
+ double-straned helices, they will be connected by an intrahelical
+ connection that makes the helical domain continue across the
+ connection, even if they do not stack in the stacking
+ array. Instead, a "terminal_crossover" representing a relatively
+ free (e.g. kinked) junction can be placed by including the index
+ of one of the participating bases in the optional
+ :explicitly_unstacked: tuple.
+
Args:
basepair: List of each nucleotide's basepair's index
stack: List containing index of the nucleotide stacked on the 3' of each nucleotide
diff --git a/mrdna/readers/segmentmodel_from_oxdna.py b/mrdna/readers/segmentmodel_from_oxdna.py
index e6ded48..d85002e 100644
--- a/mrdna/readers/segmentmodel_from_oxdna.py
+++ b/mrdna/readers/segmentmodel_from_oxdna.py
@@ -143,7 +143,7 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
orientation = [np.array(o).T.dot(_yrot) for o in zip(perp_dir,-base_dir,-normal_dir)]
seq=nt_prop["seq"]
bp=nt_prop["bp"]
- stack=nt_prop["stack"]
+ stack=np.array((list(nt_prop["stack"])))
three_prime=nt_prop["threeprime"]
nt_prop["orientation"]=orientation
nt_prop["r"]=list(r)
@@ -205,8 +205,9 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
## _debug_write_bonds()
logger.info(f'mrdna_model_from_oxdna: num_bp, num_ss_nt, num_stacked: {np.sum(bp>=0)//2} {np.sum(bp<0)} {np.sum(stack >= 0)}')
-
- model = model_from_basepair_stack_3prime( r, bp, stack, three_prime, seq, orientation, **model_parameters )
+ model = model_from_basepair_stack_3prime( r, bp, stack, three_prime, seq, orientation,
+ explicitly_unstacked = np.argwhere(stack == -1),
+ **model_parameters )
"""
model.DEBUG = True
--
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