From 73a95017d8b858257e5ac6370226bfcb3ab48062 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 4 Mar 2016 13:54:40 +0100
Subject: [PATCH] Connect all atoms in the constructed sidechains
---
sidechain/pymod/_reconstruct_sidechains.py | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/sidechain/pymod/_reconstruct_sidechains.py b/sidechain/pymod/_reconstruct_sidechains.py
index 2fc82977..7ec0a9f8 100644
--- a/sidechain/pymod/_reconstruct_sidechains.py
+++ b/sidechain/pymod/_reconstruct_sidechains.py
@@ -233,7 +233,10 @@ def Reconstruct(ent, keep_sidechains = False, build_disulfids = True,
cystein_rotamers[i][min_index_k].ApplyOnResidue(prot.residues[cystein_indices[i]].handle,
consider_hydrogens=False)
cystein_rotamers[j][min_index_l].ApplyOnResidue(prot.residues[cystein_indices[j]].handle,
- consider_hydrogens=False)
+ consider_hydrogens=False)
+ sidechain.ConnectSidechain(prot.residues[cystein_indices[i]].handle,sidechain.CYS)
+ sidechain.ConnectSidechain(prot.residues[cystein_indices[j]].handle,sidechain.CYS)
+
#All cysteins participating in a disulfid bond have been applied to the
#structure and added to the frame.
@@ -336,6 +339,7 @@ def Reconstruct(ent, keep_sidechains = False, build_disulfids = True,
for i,rot_group,sol in zip(residues_with_rotamer_group,rotamer_groups,solution):
try:
rot_group[sol].ApplyOnResidue(prot.residues[i].handle,consider_hydrogens=False)
+ sidechain.ConnectSidechain(prot.residues[i].handle,rotamer_ids[i])
except:
print "there is a backbone atom missing... ",prot.residues[i].GetQualifiedName()
--
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