diff --git a/examples/demos/bbox.py b/examples/demos/bbox.py
index 1e4215f456887ce75341d2a2ac6ff8074dc6a054..fa85b9a26676e876beb53f44494b44db108ff19a 100644
--- a/examples/demos/bbox.py
+++ b/examples/demos/bbox.py
@@ -1,17 +1,26 @@
-sdh=io.LoadPDB('sdh.pdb')
+# This code example shows how to calculate and display an oriented bounding box
+# that contains all the atoms of an entity.
+
+# remove all objects from scene, just in case
+scene.RemoveAll()
+
+# Load sdh molecule
+sdh=io.LoadPDB('data/sdh.pdb')
+# Select backbone atoms of residues 99-128, which form a helix.
helix=sdh.Select('rnum=99:128 and cname=A and aname=CA,C,N,O')
+# create a graphical representation of the helix and render it with simple
+# lines.
go=gfx.Entity('helix', gfx.SIMPLE, helix)
+# add it to the scene
scene.Add(go)
+# calculate the bounding box for the helix
bbox=mol.BoundingBoxFromEntity(helix)
-def RenderBBox(bbox):
- bb=gfx.Cuboid('xxx', bbox)
- bb.SetFillColor(gfx.Color(0.5, 0.8, 0.5, 0.2))
- scene.Add(bb)
+# create a graphical representation of the bounding box and add it to the scene
+bb=gfx.Cuboid('xxx', bbox)
+bb.SetFillColor(gfx.Color(0.5, 0.8, 0.5, 0.2))
+scene.Add(bb)
-print 'Center:',(helix.GetGeometricStart()+helix.GetGeometricEnd())*.5
-
-RenderBBox(bbox)
+# center the camera on the graphical object
scene.center=go.center
-print 'Demo2: Translucent bounding box around an OpenStructure entity'
diff --git a/examples/demos/charmm_trj_blur.py b/examples/demos/charmm_trj_blur.py
index eedba6bb32e05392775aca4ada5a6459316ba500..8edfdc0c2768007b83698acf22cd8f2caa012da7 100644
--- a/examples/demos/charmm_trj_blur.py
+++ b/examples/demos/charmm_trj_blur.py
@@ -1,33 +1,45 @@
# trajectory generated by Raimund Dutzler
from PyQt4 import QtCore
+scene.RemoveAll()
+
class Anim(QtCore.QTimer):
- def __init__(self,cg,go):
- QtCore.QTimer.__init__(self)
- self.cg_=cg
- self.go_=go
- self.frame_=0
- QtCore.QObject.connect(self, QtCore.SIGNAL("timeout()"), self.OnTimer)
-
- def OnTimer(self):
- self.step()
+ """
+ Timer used to animate the trajectory on screen. Each time the OnTimer
+ method gets called we advance the trajectory by one step and render
+ the scene on the screen.
+ """
+ def __init__(self,cg,go):
+ QtCore.QTimer.__init__(self)
+ self.cg_=cg
+ self.go_=go
+ self.frame_=0
+ QtCore.QObject.connect(self, QtCore.SIGNAL("timeout()"), self.OnTimer)
+
+ def OnTimer(self):
+ self.frame_=(self.frame_+1)%self.cg_.GetFrameCount()
+ self.go_.BlurSnapshot()
+ self.cg_.CopyFrame(self.frame_)
+ self.go_.UpdatePositions()
- def step(self):
- self.frame_=(self.frame_+1)%self.cg_.GetFrameCount()
- go.BlurSnapshot()
- self.cg_.CopyFrame(self.frame_)
- go.UpdatePositions()
-cg = io.LoadCHARMMTraj("sample.pdb","sample.dcd")
+# load CHARMM trajectory from sample.pdb and sample.dcd
+cg = io.LoadCHARMMTraj("data/sample.pdb","data/sample.dcd")
+# create graphical representation of the entity
eh=cg.GetEntity()
+# we don't want to display the hydrogen atoms, so select everything that is
+# not a hydrogen and pass that view to the gfx.Entity() constructor.
ev=eh.Select("not ele=H")
go=gfx.Entity("mol",gfx.SIMPLE, ev)
+# enable the blur effect
go.SetBlur(True)
+# add it to the scene for rendering
scene.Add(go)
scene.SetCenter(go.GetCenter())
scene.AutoAutoslab(True)
+# create an animation timer and start it
anim=Anim(cg,go)
print 'Demo 6: Import of a CHARMM trajectory. Type anim.stop() to halt animation, anim.start(100) to start it again with stepsize 100!Starting animation now....'
anim.start(50)
diff --git a/examples/demos/conservation.py b/examples/demos/conservation.py
index 8399ef05bf7560dd9a0b6e079fb7712008a15ad9..8ecce056648e082f70cd4f16f6ea5b7cd0ab3077 100644
--- a/examples/demos/conservation.py
+++ b/examples/demos/conservation.py
@@ -1,22 +1,27 @@
from ost.seq import alg
+scene.RemoveAll()
#-------------------------------------------------------------------------------
# Loading structure and alignment
#-------------------------------------------------------------------------------
-m=io.LoadPDB('sh2.pdb')
+m=io.LoadPDB('data/sh2.pdb')
mp=m.Select('ishetatm=false')
-aln=io.LoadAlignment('sh2.aln')
+aln=io.LoadAlignment('data/sh2.aln')
aln.AttachView(0, mp)
+
#-------------------------------------------------------------------------------
# Calculate conservation of alignment
+# First we set all properties to zero, then let alg.Conservation assign the
+# conservation scores to the residues
#-------------------------------------------------------------------------------
for r in m.residues:
r.SetFloatProp('cons', 0)
alg.Conservation(aln)
+
#-------------------------------------------------------------------------------
# Setup Graphical Objects for Rendering
#-------------------------------------------------------------------------------
g=gfx.Entity('SH2', m)
-s=io.LoadSurface('sh2.vert')
+s=io.LoadSurface('data/sh2.vert')
gs=gfx.Surface('SH2-surf', s)
scene.Add(gs)
scene.Add(g)
@@ -36,9 +41,11 @@ g.SetRenderMode(gfx.CUSTOM,
m.Select('ishetatm=true'))
g.SetColor(gfx.YELLOW, 'ishetatm=true')
-
+#-------------------------------------------------------------------------------
+# Create alignment viewer and show it on the screen
+#-------------------------------------------------------------------------------
seq_viewer=gui.SequenceViewer()
seq_viewer.AddAlignment(aln)
seq_viewer.Show()
-print 'Colouring the active site according to the level of conservation found inthe sequences shown in the sequence viewer. Highly conserved regions are shown in blue, variable regions in red.'
+
diff --git a/examples/demos/gfx_mapslab.py b/examples/demos/gfx_mapslab.py
index 3174677a8d0c3d55b7bdb003ec774c3f91cad170..de59b2e5d1df8ee8386ae75921543139bddefde6 100644
--- a/examples/demos/gfx_mapslab.py
+++ b/examples/demos/gfx_mapslab.py
@@ -1,5 +1,9 @@
import math,random
from ost import img
+
+# remove all objects from scene, just in case
+scene.RemoveAll()
+
vmax=-10000.0
vmin=+10000.0
mh=img.CreateMap(img.Size(32,32,32))
@@ -45,6 +49,7 @@ go1.SetLineWidth(1.5)
scene.Add(go1)
scene.SetCenter(go1.GetCenter())
+
go2 = gfx.MapSlab("slab",mh,geom.Plane(go1.GetCenter(),geom.Vec3(0.0,0.0,1.0)))
scene.Add(go2)
go2.ColorBy(gfx.YELLOW,gfx.GREEN,0.2,0.8)
diff --git a/examples/demos/load_and_display.py b/examples/demos/load_and_display.py
index 382197ea7822ee2506125236722f7a0569bbb423..be2783a00f0a7c6c048580ccd0200f95d4c0d919 100644
--- a/examples/demos/load_and_display.py
+++ b/examples/demos/load_and_display.py
@@ -1,5 +1,7 @@
+# remove all objects from scene, just in case
+scene.RemoveAll()
# Load chain A of SDH
-ent=io.LoadPDB('sdh.pdb', restrict_chains='A')
+ent=io.LoadPDB('data/sdh.pdb', restrict_chains='A')
# create graphics object
go=gfx.Entity('SDH', ent)
diff --git a/examples/demos/rendermodes.py b/examples/demos/rendermodes.py
index b45cd500cfde0531f35754b90486ba413fb3c233..a7d08937dbf14f950349f6f68b50222a51c5649e 100644
--- a/examples/demos/rendermodes.py
+++ b/examples/demos/rendermodes.py
@@ -1,5 +1,12 @@
-# load pdb file
-eh=io.LoadEntity("sdh.pdb")
+# This script shows how to switch between different render modes
+# programmatically and change render options.
+
+
+# remove all objects from scene, just in case
+scene.RemoveAll()
+
+# load pdb structure
+eh=io.LoadPDB("data/sdh.pdb")
sdh_go=gfx.Entity("SDH2", eh.Select("cname=A"))
@@ -9,7 +16,7 @@ scene.CenterOn(sdh_go)
def Tube():
sdh_go.SetRenderMode(gfx.TUBE)
- sdh_go.GetOptions(gfx.TUBE).SetTubeRadius(0.8)
+ sdh_go.tube_options.SetTubeRadius(0.8)
# apply color gradient for the atomic bfactors
sdh_go.ColorBy("abfac",gfx.BLUE,gfx.RED)
# and apply radius gradient as well
@@ -32,15 +39,15 @@ def Cartoon():
sdh_go.SetColor(gfx.Color(1,0,0),"rtype=E")
sdh_go.SetDetailColor(gfx.Color(1.0,0.8,0.2),"rtype=E")
# these are the default params for the rendering
- #sdh_go.GetOptions(gfx.HSC).SetArcDetail(4) # circular profile detail
- #sdh_go.GetOptions(gfx.HSC).SetSphereDetail(4) # sphere detail
- #sdh_go.GetOptions(gfx.HSC).SetSplineDetail(8) # segments between backbone atoms
- #sdh_go.GetOptions(gfx.HSC).SetTubeRadius(0.4) # coil radius
- #sdh_go.GetOptions(gfx.HSC).SetTubeRatio(1.0) # coil axial ratio
- #sdh_go.GetOptions(gfx.HSC).SetHelixWidth(1.1) # helical width
- #sdh_go.GetOptions(gfx.HSC).SetHelixThickness(0.2) # helical thickness
- #sdh_go.GetOptions(gfx.HSC).SetStrandWidth(1.2) # strand width
- #sdh_go.GetOptions(gfx.HSC).SetStrandThickness(0.2) # strand thickness
+ #sdh_go.cartoon_options.SetArcDetail(4) # circular profile detail
+ #sdh_go.cartoon_options.SetSphereDetail(4) # sphere detail
+ #sdh_go.cartoon_options.SetSplineDetail(8) # segments between backbone atoms
+ #sdh_go.cartoon_options.SetTubeRadius(0.4) # coil radius
+ #sdh_go.cartoon_options.SetTubeRatio(1.0) # coil axial ratio
+ #sdh_go.cartoon_options.SetHelixWidth(1.1) # helical width
+ #sdh_go.cartoon_options.SetHelixThickness(0.2) # helical thickness
+ #sdh_go.cartoon_options.SetStrandWidth(1.2) # strand width
+ #sdh_go.cartoon_options.SetStrandThickness(0.2) # strand thickness
Cartoon()
-print 'Demo 5: Type Spheres(), Tube(), Trace(), or Cartoon()\n to switch render modes'
+
diff --git a/examples/demos/the_hammer.py b/examples/demos/the_hammer.py
index 7db8abab34478c27382e5c6c96fc7dc780ad5d9b..f6c77ebca38b663fd03b5e922604ccb3a3ef73e8 100644
--- a/examples/demos/the_hammer.py
+++ b/examples/demos/the_hammer.py
@@ -1,6 +1,10 @@
from PyQt4 import QtCore
import math
from ost import qa
+
+# remove all objects from scene, just in case
+scene.RemoveAll()
+
class Anim(QtCore.QTimer):
def __init__(self, a, b):
QtCore.QTimer.__init__(self)