From 49db14de1a2e48b29ce576f8d8c41ab8e8be29b0 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Fri, 8 Feb 2019 17:50:53 -0600
Subject: [PATCH] Improved bp detection in pdb model reader
---
mrdna/readers/segmentmodel_from_pdb.py | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/mrdna/readers/segmentmodel_from_pdb.py b/mrdna/readers/segmentmodel_from_pdb.py
index 3cbb683..53b0c31 100644
--- a/mrdna/readers/segmentmodel_from_pdb.py
+++ b/mrdna/readers/segmentmodel_from_pdb.py
@@ -149,16 +149,20 @@ def find_basepairs( u, centers, transforms, selection_text='all' ):
possible_resI = np.where( ids )[0]
possible_resJ = possible_basepairs[ ids ].astype(int)
resI,resJ = [[],[]]
- for i,j,R1,c1,c2 in zip(possible_resI,possible_resJ,
+ for i,j,R1,R2,c1,c2 in zip(possible_resI,possible_resJ,
transforms[possible_resI],
+ transforms[possible_resJ],
centers[possible_resI],
centers[possible_resJ]):
c2_expected = c1 + ref_bp_position.dot(R1)
# fh.write("graphics top cylinder {{{}}} {{{}}} radius 0.2 resolution 30\n".format(printv(c1),printv(c2)))
- if np.linalg.norm(c2_expected-c2) < 2:
- resI.append(i)
- resJ.append(j)
+ if np.linalg.norm(c2_expected-c2) < 3.5:
+ angle= R1.T.dot(np.array((0,0,1))).dot(R2.T.dot(np.array((0,0,1))))
+ if angle < -0.7:
+ resI.append(i)
+ resJ.append(j)
+
resI = np.array(resI, dtype=np.int)
resJ = np.array(resJ, dtype=np.int)
--
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