Merge branch 'release-1.4' of https://dng.biozentrum.unibas.ch/git/ost into release-1.4

examples/code_fragments/harmony/harmony

 #!/bin/sh
-gosty harmony.py Harmony $@
\ No newline at end of file
+dng -s harmony.py

examples/code_fragments/harmony/harmony.py

@@ -4,7 +4,7 @@ from ost import io, geom, gfx, mol
 class World:
   def __init__(self):
     self.atom_string=mol.CreateEntity()
-    edi=self.atom_string.RequestXCSEditor(mol.EditMode.BUFFERED_EDIT)
+    edi=self.atom_string.EditXCS(mol.EditMode.BUFFERED_EDIT)
     chain=edi.InsertChain("A")
     r=edi.AppendResidue(chain, "STRING")
     prev_atom=mol.AtomHandle()
@@ -51,7 +51,7 @@ class World:
         force=((1.0/length)**12-(1.0/length)**6)*diff
         self.forces[i]+=force
         self.forces[j]-=force
-    edi=self.atom_string.RequestXCSEditor(mol.EditMode.BUFFERED_EDIT)
+    edi=self.atom_string.EditXCS(mol.EditMode.BUFFERED_EDIT)
     for force, atom in zip(self.forces, self.atom_string.atoms):
       edi.SetAtomPos(atom, atom.pos+force*0.004)
     self.go.Rebuild()

examples/code_fragments/misc/roll_helix.py

@@ -14,16 +14,7 @@ for r in c.GetResidueList():
   
 edi.UpdateXCS()
 
-for r in c.GetResidueList():
-  phi=r.GetPhiTorsion()
-  psi=r.GetPsiTorsion()
-  if phi.IsValid(): 
-    print 'PHI %3.0f' % math.degrees(phi.GetAngle())
-  if psi.IsValid(): 
-    print 'PSI %3.0f'  % math.degrees(psi.GetAngle())
-
 g=gfx.Entity('helix', e.Select('aname=CA,N,O,C,CB'))
-#g=gfx.Entity('helix', e)
 scene.Add(g)
 scene.SetCenter(g.GetCenter())
 

modules/doc/intro.rst

@@ -11,11 +11,6 @@ please refer to :doc:`install`.
 What will be covered in this tutorial?
 --------------------------------------------------------------------------------
 
-This tutorial is aimed at users that would like to get their hands dirty and 
-execute commands in Python and write scripts rather clicking their way through a 
-shiny user interface. The user interface of OpenStructure is in a very early 
-state anyway that you probably won't go far by clicking your way through...
-
 The tutorial is divided into several parts. The first part of the tutorial is a 
 walk-through of the basic functionality you will be using in your everyday work, followed by an introduction to the :mod:`~ost.mol`, :mod:`~ost.img` and :mod:`~ost.seq` modules.
 

modules/gfx/pymod/export_scene.cc

@@ -143,7 +143,7 @@ void export_Scene()
     .def("CenterOn",center_on2)
     .def("UnProject",  &Scene::UnProject, arg("ignore_vp")=false)
     .def("Project",  &Scene::Project, arg("ignore_vp")=false)
-    .def("InitGL", &Scene::InitGL)
+    .def("InitGL", &Scene::InitGL, arg("full")=true)
     .def("RenderGL", &Scene::RenderGL)
     .def("Resize", &Scene::Resize)
     .def("HasNode", &Scene::HasNode)