From 3cb7829aade3db0c47ff7e47e909cd061dae6626 Mon Sep 17 00:00:00 2001
From: pinyili2 <pinyili2@illinois.edu>
Date: Thu, 22 Aug 2024 10:49:04 -0500
Subject: [PATCH] fix some bugs
---
mrdna/readers/segmentmodel_from_oxdna_pinyi.py | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/mrdna/readers/segmentmodel_from_oxdna_pinyi.py b/mrdna/readers/segmentmodel_from_oxdna_pinyi.py
index bf50368..7846dde 100644
--- a/mrdna/readers/segmentmodel_from_oxdna_pinyi.py
+++ b/mrdna/readers/segmentmodel_from_oxdna_pinyi.py
@@ -140,7 +140,7 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
basepair_pos = r + base_dir*10.0
normal_dir = -conf_data[:,6:9]
perp_dir = np.cross(base_dir, normal_dir)
- orientation = np.array([np.array(o).T.dot(_yrot) for o in zip(perp_dir,-base_dir,-normal_dir)]).T
+ orientation = np.array([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"]
@@ -148,6 +148,8 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
nt_prop["orientation"]=orientation
nt_prop["r"]=list(r)
except:
+ if virt2nuc is not None:
+ logger.info("warning: virt2nuc not read. guessing structure...")
## Reverse direction so indices run 5'-to-3'
top_data = [a[::-1] for a in top_data]
conf_data = conf_data[::-1,:]
--
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