From d9b4d567001dc5ad6788c15874e960df12917192 Mon Sep 17 00:00:00 2001
From: pinyili2 <pinyili2@illinois.edu>
Date: Mon, 5 Aug 2024 21:53:07 -0500
Subject: [PATCH] a
---
mrdna/readers/segmentmodel_from_cadnano.py | 25 +---------------------
1 file changed, 1 insertion(+), 24 deletions(-)
diff --git a/mrdna/readers/segmentmodel_from_cadnano.py b/mrdna/readers/segmentmodel_from_cadnano.py
index c003ea7..3576388 100644
--- a/mrdna/readers/segmentmodel_from_cadnano.py
+++ b/mrdna/readers/segmentmodel_from_cadnano.py
@@ -60,29 +60,6 @@ def get_lattice(part):
print("WARNING: unable to determine cadnano part lattice type")
return lattice_type
-def get_helix_angle(cadnanopart,helix_id, indices):
- """ Get "start_orientation" for helix """
- # import ipdb
- # ipdb.set_trace()
- """ FROM CADNANO2.5
- + angle is CCW
- - angle is CW
- Right handed DNA rotates clockwise from 5' to 3'
- we use the convention the 5' end starts at 0 degrees
- and it's pair is minor_groove_angle degrees away
- direction, hence the minus signs. eulerZ
- """
-
- hp, bpr, tpr, eulerZ, mgroove = cadnanopart.vh_properties.loc[helix_id,
- ['helical_pitch',
- 'bases_per_repeat',
- 'turns_per_repeat',
- 'eulerZ',
- 'minor_groove_angle']]
- twist_per_base = tpr*360./bpr
- # angle = eulerZ - twist_per_base*indices + 0.5*mgroove + 180
- angle = eulerZ + twist_per_base*indices - 0.5*mgroove
- return angle
def mrdna_model_from_cadnano(json_data,**model_parameters):
part,vslist=decode_cadnano_part(json_data)
@@ -97,6 +74,6 @@ def mrdna_model_from_cadnano(json_data,**model_parameters):
except:
origins = {hid:part.getVirtualHelixOrigin(hid)[:2] for hid in part.getidNums()}
cad_bps=part.getIndices(0)
-
+
model = model_from_basepair_stack_3prime( r, bp, stack, three_prime, seq, orientation, **model_parameters )
--
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