From 557477bee3d4f542f37355b53f68c9b4281bdacc Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 16 Oct 2020 15:39:44 +0200
Subject: [PATCH] Add CB atom in sidechain reconstruction if necessary
---
modelling/pymod/_reconstruct_sidechains.py | 23 ++++++++++++++++++++++
1 file changed, 23 insertions(+)
diff --git a/modelling/pymod/_reconstruct_sidechains.py b/modelling/pymod/_reconstruct_sidechains.py
index 73563312..47228fb0 100644
--- a/modelling/pymod/_reconstruct_sidechains.py
+++ b/modelling/pymod/_reconstruct_sidechains.py
@@ -396,6 +396,26 @@ def _GetDisulfidBridges(frame_residues, keep_sidechains, cystein_indices,
return disulfid_indices, disulfid_rotamers
+def _AddCB(prot):
+ '''Checks if every residue has a CB atom. Constructs them if necessary.'''
+ edi = prot.handle.EditXCS(mol.BUFFERED_EDIT)
+ for r in prot.residues:
+ olc = r.one_letter_code
+ if olc not in ['G', 'g']:
+ cb = r.handle.FindAtom('CB')
+ if not cb.IsValid():
+ n = r.handle.FindAtom('N')
+ ca = r.handle.FindAtom('CA')
+ c = r.handle.FindAtom('C')
+ if n.IsValid() and ca.IsValid() and c.IsValid():
+ cb_pos = core.ConstructCBetaPos(n.GetPos(), ca.GetPos(),
+ c.GetPos())
+ cb = edi.InsertAtom(r.handle, "CB", cb_pos, "C");
+ # prot is a view on the underlying handle, so we also have
+ # to add it to the view
+ r.AddAtom(cb)
+
+
###############################################################################
def ReconstructSidechains(ent, keep_sidechains=False, build_disulfids=True,
@@ -484,6 +504,9 @@ def ReconstructSidechains(ent, keep_sidechains=False, build_disulfids=True,
# take out ligand chain and any non-peptides
prot = ent.Select("peptide=true and cname!='_'")
+
+ # make sure that we have all CB atoms
+ _AddCB(prot)
# parse residues (all lists of length len(prot.residues))
rotamer_ids = _GetRotamerIDs(prot.residues)
--
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