diff --git a/examples/code_fragments/harmony/harmony b/examples/code_fragments/harmony/harmony index f55eec9e481880eec721632ef05d67346d628c30..c315b3f085f5fd3e0ad977c5618d8fffec8fd2cc 100755 --- a/examples/code_fragments/harmony/harmony +++ b/examples/code_fragments/harmony/harmony @@ -1,2 +1,2 @@ #!/bin/sh -gosty harmony.py Harmony $@ \ No newline at end of file +dng -s harmony.py diff --git a/examples/code_fragments/harmony/harmony.py b/examples/code_fragments/harmony/harmony.py index 0e1ddc0d4db0b6d24afbf2e759d3a58b481d3e56..d9f98316d49d295e71f5d8f488b8b7052df5e392 100644 --- a/examples/code_fragments/harmony/harmony.py +++ b/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() diff --git a/examples/code_fragments/misc/roll_helix.py b/examples/code_fragments/misc/roll_helix.py index 9ec477644f75533a7d9648a8a85171d08d7102d6..0dec6c1160c7ce0de7ac237211ba941a931392ae 100644 --- a/examples/code_fragments/misc/roll_helix.py +++ b/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()) diff --git a/modules/doc/intro.rst b/modules/doc/intro.rst index 9da3856631e82265e0dc301a0cea9eb71801d191..3bd89cb82595c4b4a39678ea00657531d5109dd7 100644 --- a/modules/doc/intro.rst +++ b/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. diff --git a/modules/gfx/pymod/export_scene.cc b/modules/gfx/pymod/export_scene.cc index ba8274d371d4981ab04d63f3ae278df4464fa940..0c4ff6b870f7f7097f944f5fccca51346856ac25 100644 --- a/modules/gfx/pymod/export_scene.cc +++ b/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)