From 4270b88a220156921f30a915dfad34b2c860ea37 Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Wed, 4 May 2011 11:49:07 +0200
Subject: [PATCH] use 'ligand' property in the conservation example
---
examples/demos/conservation.py | 13 ++++++-------
examples/demos/data/sh2.pdb | 1 +
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/examples/demos/conservation.py b/examples/demos/conservation.py
index e4a254448..0e079ea68 100644
--- a/examples/demos/conservation.py
+++ b/examples/demos/conservation.py
@@ -1,10 +1,9 @@
-from ost.seq import alg
scene.RemoveAll()
#-------------------------------------------------------------------------------
# Loading structure and alignment
#-------------------------------------------------------------------------------
m=io.LoadPDB('data/sh2.pdb')
-mp=m.Select('ishetatm=false')
+mp=m.Select('ligand=false')
aln=io.LoadAlignment('data/sh2.aln')
aln.AttachView(0, mp)
aln.SetSequenceOffset(0, 1)
@@ -13,7 +12,7 @@ aln.SetSequenceOffset(0, 1)
# First we set all properties to zero, then let alg.Conservation assign the
# conservation scores to the residues
#-------------------------------------------------------------------------------
-alg.Conservation(aln)
+seq.alg.Conservation(aln)
#-------------------------------------------------------------------------------
# Setup Graphical Objects for Rendering
@@ -25,7 +24,7 @@ scene.Add(gs)
scene.Add(g)
scene.CenterOn(g)
-s.Attach(mp.Select('ishetatm=false'), 8.0)
+s.Attach(mp.Select('ligand=false'), 8.0)
gr=gfx.Gradient()
gr.SetColorAt(0.0, gfx.Color(0.1, 0.1, 0.8))
@@ -34,10 +33,10 @@ gr.SetColorAt(1.0, gfx.Color(0.8, 0.1, 0.1))
gs.ColorBy('cons', gr, 0.8, 1.0,
mol.Prop.Level.RESIDUE)
g.SetRenderMode(gfx.HSC,
- m.Select('ishetatm=false'))
+ m.Select('ligand=false'))
g.SetRenderMode(gfx.CUSTOM,
- m.Select('ishetatm=true'))
-g.SetColor(gfx.YELLOW, 'ishetatm=true')
+ m.Select('ligand=true'))
+g.SetColor(gfx.YELLOW, 'ligand=true')
#-------------------------------------------------------------------------------
# Create alignment viewer and show it on the screen
diff --git a/examples/demos/data/sh2.pdb b/examples/demos/data/sh2.pdb
index e254cf039..e4ef85faa 100644
--- a/examples/demos/data/sh2.pdb
+++ b/examples/demos/data/sh2.pdb
@@ -1,3 +1,4 @@
+HET AYI A 1 37
HELIX 1 1 PRO A 66 LYS A 76 1 11
HELIX 2 2 SER A 127 HIS A 135 1 9
SHEET 1 A 4 PHE A 83 GLU A 87 0
--
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