From 386653a3db712f270094a90705a2693c4ce27342 Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Tue, 6 Apr 2010 14:43:55 +0000
Subject: [PATCH] Added RepresentativeAtoms
This was previously implemented as ExtractResidueRepresentatives in
the internal repo.
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@1931 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/mol/alg/pymod/views.py | 75 +++++++++++++++++++++++++++++++---
1 file changed, 70 insertions(+), 5 deletions(-)
diff --git a/modules/mol/alg/pymod/views.py b/modules/mol/alg/pymod/views.py
index 2ea396625..7086e7928 100644
--- a/modules/mol/alg/pymod/views.py
+++ b/modules/mol/alg/pymod/views.py
@@ -1,10 +1,7 @@
"""
- Algorithms operating on two views.
+A bunch of algorithms operating on two views.
-All these algorithms return a tuple of views that contain the same number of
-residues. Thes residues at corresponding indices in these two views form pairs.
-
-Author: Marco Biasini
+Authors: Marco Biasini, Pascal Benkert
"""
from ost import io,mol
@@ -53,3 +50,71 @@ def PairResiduesByNum(view_a, view_b,
except StopIteration:
pass
return result_a, result_b
+
+def RepresentativeAtoms(ent, chain=None, alpha_and_beta=False):
+ """
+ Returns a view with one or two representative atom per amino acid residue.
+
+ There are two basic modes, controlled by the alpha_and_beta parameter:
+
+ When the parameter is false, for residues with a sidechain, the C-beta atom is
+ used, for residues without sidechain, the C-alpha atom is used. Note that this
+ is different from using the selection
+
+ (aname=CA and rname=GLY) or (aname=CB and rname!=GLY)
+
+ When the alpha_and_beta parameter is true, both C-alpha and C-beta (if
+ available) are added to the view.
+
+ If chain is not equal to None, only atoms of the chain with that chain name
+ will be added to the view.
+ """
+ if isinstance(ent,mol.EntityHandle):
+ e_view = ent.CreateEmptyView()
+ elif isinstance(ent,mol.EntityView):
+ e_view = ent.GetHandle().CreateEmptyView()
+ if ent.IsValid():
+ # all chains:
+ if chain==None:
+ for res in ent.residues:
+ if res.IsPeptideLinking():
+ atom = res.FindAtom('CB')
+ if atom.IsValid():
+ e_view.AddAtom(atom)
+
+ #also add C-alpha for hybrid-potential:
+ if alpha_and_beta == 1:
+ atom = res.FindAtom('CA')
+ if atom.IsValid():
+ e_view.AddAtom(atom)
+
+ else: # Cbeta does not exist, Calpha?
+ atom = res.FindAtom('CA')
+ if atom.IsValid():
+ e_view.AddAtom(atom)
+
+ # count C_alphas twice for hybrid-potential:
+ if alpha_and_beta == 1:
+ e_view.AddAtom(atom)
+
+ elif chain != "" and ent.FindChain(chain).IsValid():
+ for res in ent.FindChain(chain).GetResidueList():
+ if res.IsPeptideLinking():
+ atom = res.FindAtom('CB')
+ if atom.IsValid():
+ e_view.AddAtom(atom)
+
+ if alpha_and_beta == 1:
+ atom = res.FindAtom('CA')
+ if atom.IsValid():
+ e_view.AddAtom(atom)
+
+ else: # Cbeta does not exist, Calpha?
+ atom = res.FindAtom('CA')
+ if atom.IsValid():
+ e_view.AddAtom(atom)
+
+ # count C_alphas twice for glycine:
+ if alpha_and_beta == 1:
+ e_view.AddAtom(atom)
+ return e_view
--
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