diff --git a/examples/dokk/datafiles/2CF8_lig.sdf b/examples/dokk/datafiles/thrombin/ligand.sdf
similarity index 100%
rename from examples/dokk/datafiles/2CF8_lig.sdf
rename to examples/dokk/datafiles/thrombin/ligand.sdf
diff --git a/examples/dokk/datafiles/2CF8_prot.pdb b/examples/dokk/datafiles/thrombin/protein.pdb
similarity index 100%
rename from examples/dokk/datafiles/2CF8_prot.pdb
rename to examples/dokk/datafiles/thrombin/protein.pdb
diff --git a/examples/dokk/datafiles/2CF8_surf.face b/examples/dokk/datafiles/thrombin/surface.face
similarity index 100%
rename from examples/dokk/datafiles/2CF8_surf.face
rename to examples/dokk/datafiles/thrombin/surface.face
diff --git a/examples/dokk/datafiles/2CF8_surf.vert b/examples/dokk/datafiles/thrombin/surface.vert
similarity index 100%
rename from examples/dokk/datafiles/2CF8_surf.vert
rename to examples/dokk/datafiles/thrombin/surface.vert
diff --git a/examples/dokk/dokk.py b/examples/dokk/dokk.py
index fcdb8e2298ee991df37edff46fc4c9d44fb3cefd..60abd7d89d1484676507072b3e4f46013cd4a426 100644
--- a/examples/dokk/dokk.py
+++ b/examples/dokk/dokk.py
@@ -1,27 +1,12 @@
import glwin
-from ost import gfx
-from ost import io
+from ost import io, geom, gfx
-prot=io.LoadPDB('datafiles/2CF8_prot.pdb')
-prot_go=gfx.Entity('prot', prot)
-scene.Add(prot_go)
-
-surf=io.LoadSurface('datafiles/2CF8_surf','msms')
-surf.Attach(prot,5)
-surf_go=gfx.Surface('surf',surf)
-scene.Add(surf_go)
-
-lig=io.LoadSDF('datafiles/2CF8_lig.sdf')
-lig_go=gfx.Entity('lig', lig)
-lig_go.SetRenderMode(gfx.CUSTOM)
-lig_go.SetColor(gfx.GREEN,'ele=C')
-scene.Add(lig_go)
+from level import Level
dokk_win=glwin.DokkGLWin()
-scene.CenterOn(lig_go)
-if '--fullscreen' in sys.argv:
- dokk_win.Show(fullscreen=True)
-else:
- dokk_win.Show(fullscreen=False)
+level=Level('thrombin')
+dokk_win.SetLevel(level)
+dokk_win.Show(fullscreen=('--fullscreen' in sys.argv))
+
diff --git a/examples/dokk/glwin.py b/examples/dokk/glwin.py
index bb49f5d6859965b1bdc1c324904303694a3367c7..78017b1cd8bd8d5a7c620f1efa5b6d771b588229 100644
--- a/examples/dokk/glwin.py
+++ b/examples/dokk/glwin.py
@@ -10,15 +10,17 @@ class DokkGLCanvas(QGLWidget):
def __init__(self, format, parent=None):
QGLWidget.__init__(self, format, parent)
- self.last_pos_=QPoint()
+ self.last_pos_=QPoint()
self.setAutoFillBackground(False)
- self.setAttribute(Qt.WA_KeyCompression,True)
-
+ #self.setAttribute(Qt.WA_KeyCompression,True)
+ self.resize(800, 800)
def initializeGL(self):
gfx.Scene().InitGL()
def paintGL(self):
gfx.Scene().RenderGL()
+ def SetLevel(self, level):
+ self.level_=level
def paintEvent(self, event):
gfx.Scene().RenderGL()
painter=QPainter(self)
@@ -30,7 +32,7 @@ class DokkGLCanvas(QGLWidget):
painter.drawRect(QRect(QPoint(0, 0), QSize(self.width(), 25)))
painter.setPen(QPen(QColor(255,255,255), Qt.SolidLine))
painter.setFont(QFont("Verdana"))
- painter.drawText(QPoint(10, 20), "Test Message")
+ painter.drawText(QPoint(10, 20), "You are %.1f away from the solution" % self.level_.GetRMSD())
def resizeGL(self, w, h):
gfx.Scene().Resize(w, h)
@@ -40,16 +42,33 @@ class DokkGLCanvas(QGLWidget):
def mouseMoveEvent(self, event):
delta=QPoint(event.x(), event.y())-self.last_point_
self.last_point_=QPoint(event.x(), event.y())
- if delta.y()!=0:
- gfx.Scene().Apply(gfx.InputEvent(gfx.INPUT_DEVICE_MOUSE,
- gfx.INPUT_COMMAND_ROTX, delta.y()*0.5),
- False)
- if delta.x()!=0:
- gfx.Scene().Apply(gfx.InputEvent(gfx.INPUT_DEVICE_MOUSE,
- gfx.INPUT_COMMAND_ROTY, delta.x()*0.5),
- False)
- self.update()
-
+ if event.button() & Qt.LeftButton:
+ tf=gfx.Scene().GetTransform()
+ if event.modifiers() & Qt.ShiftModifier:
+ if event.modifiers() & Qt.AltModifier:
+ self.level_.Shift(tf.GetRot().GetRow(2)*delta.y()*0.1)
+ else:
+ self.level_.Shift((tf.GetRot().GetRow(0)*delta.x()
+ -tf.GetRot().GetRow(1)*delta.y())*0.1)
+ else:
+ if delta.y()!=0:
+ self.level_.RotateAxis(tf.GetRot().GetRow(0), delta.y()*0.005)
+ if delta.x()!=0:
+ self.level_.RotateAxis(tf.GetRot().GetRow(1), delta.x()*0.005)
+ self.level_.UpdateScores()
+ self.update()
+ elif event.button() & Qt.RightButton:
+ if delta.y()!=0:
+ gfx.Scene().Apply(gfx.InputEvent(gfx.INPUT_DEVICE_MOUSE,
+ gfx.INPUT_COMMAND_ROTX, delta.y()*0.5),
+ False)
+ if delta.x()!=0:
+ gfx.Scene().Apply(gfx.InputEvent(gfx.INPUT_DEVICE_MOUSE,
+ gfx.INPUT_COMMAND_ROTY, delta.x()*0.5),
+ False)
+ self.update()
+ def mouseDoubleClickEvent(self, event):
+ self.level_.SetPivot(event.x(), self.height()-event.y())
def wheelEvent(self, event):
self.OnTransform(gfx.INPUT_COMMAND_TRANSZ,0,gfx.TRANSFORM_VIEW,
0.1*(-event.delta()))
@@ -86,7 +105,8 @@ class DokkGLWin(gfx.GLWinBase):
self.canvas_=DokkGLCanvas(self._CreateFormat())
def DoRefresh(self):
self.refresh_=True
-
+ def SetLevel(self, level):
+ self.canvas_.SetLevel(level)
def Show(self, fullscreen):
if fullscreen:
self.canvas_.showFullScreen()
diff --git a/examples/dokk/level.py b/examples/dokk/level.py
new file mode 100644
index 0000000000000000000000000000000000000000..850abdaea4b36356605da802d43bf83aff5255aa
--- /dev/null
+++ b/examples/dokk/level.py
@@ -0,0 +1,44 @@
+import os
+from ost import io, gfx, qa, geom
+from ligand import Ligand
+from surface import Surface
+from protein import Protein
+
+class Level:
+ def __init__(self, name):
+ self.name_=name
+ self.Load()
+ def Load(self):
+ print 'Loading %s' % self.name_
+ level_dir=os.path.join('datafiles', self.name_)
+ ligand_ent=io.LoadSDF(os.path.join(level_dir, 'ligand.sdf'))
+ self.ligand=Ligand(ligand_ent)
+ protein_ent=io.LoadPDB(os.path.join(level_dir, 'protein.pdb'))
+ self.protein=Protein(protein_ent)
+ surface=io.LoadSurface(os.path.join(level_dir, 'surface'), 'msms')
+ self.surface=Surface(surface)
+ self.surface.handle.Attach(self.protein.handle, 5.0)
+ gfx.Scene().SetCenter(self.ligand.GetCenter())
+ print 'Done Loading'
+ self.UpdateScores()
+ def RotateAxis(self, axis, angle):
+ self.ligand.RotateAxis(axis, angle)
+ def SetPivot(self, x, y):
+ v1=gfx.Scene().UnProject(geom.Vec3(x, y, 0.0));
+ v2=gfx.Scene().UnProject(geom.Vec3(x, y, 1.0));
+ atom=self.ligand.go.PickAtom(geom.Line3(v1, v2), 0.1)
+ if atom.IsValid():
+ self.ligand.SetPivot(atom)
+
+ def Shift(self, vec):
+ self.ligand.Shift(vec)
+ def UpdateScores(self):
+ prot_within=self.protein.handle.FindWithin(self.ligand.GetCenter(),
+ self.ligand.radius)
+ lig_view=self.ligand.handle.CreateFullView()
+ for a in prot_within:
+ score=qa.ClashScore(a, lig_view)
+ a.SetGenericFloatProperty('clash', score)
+ self.surface.go.ReapplyColorOps()
+ def GetRMSD(self):
+ return self.ligand.RMSDToSolution()
\ No newline at end of file
diff --git a/examples/dokk/ligand.py b/examples/dokk/ligand.py
new file mode 100644
index 0000000000000000000000000000000000000000..5cda3e484153b6e0a8e6407f6a9cc3d118fdb6be
--- /dev/null
+++ b/examples/dokk/ligand.py
@@ -0,0 +1,46 @@
+from ost import gfx, geom
+from ost.mol import alg
+from ost import mol
+class Ligand:
+ def __init__(self, ligand):
+ self.handle=ligand
+ self.the_solution_=ligand.Copy().CreateFullView()
+ self.go=gfx.Entity("Ligand", gfx.CUSTOM, self.handle)
+ self.go.SetColor(gfx.GREEN, 'ele=C')
+ gfx.Scene().Add(self.go)
+ gfx.Scene().SetCenter(self.go.center)
+ bbox=self.go.GetBoundingBox()
+ self.radius=geom.Length(bbox.GetMax()-bbox.GetMin())+3.0
+ self.pivot_=mol.AtomHandle()
+ def SetPivot(self, pivot):
+ self.pivot_=pivot
+ def GetCenter(self):
+ return self.handle.GetGeometricCenter()
+ def RotateAxis(self, axis, angle):
+ edi=self.handle.RequestXCSEditor()
+ rot=geom.Mat4(geom.AxisRotation(axis, angle))
+ trans=geom.Mat4()
+
+ center=self.handle.GetGeometricCenter()
+ if self.pivot_.IsValid():
+ center=self.pivot_.GetPos()
+ trans.PasteTranslation(-center)
+ trans2=geom.Mat4()
+ trans2.PasteTranslation(center)
+ full_tf=trans2*rot*trans
+ edi.ApplyTransform(full_tf)
+ self.go.UpdatePositions()
+ def Shift(self, vec):
+ trans=geom.Mat4()
+ trans.PasteTranslation(vec)
+ edi=self.handle.RequestXCSEditor()
+ edi.ApplyTransform(trans)
+ self.go.UpdatePositions()
+
+ def UpdateScores(self):
+ for a in self.b.view.atoms:
+ score=qa.ClashScore(a.handle, self.a.view)
+ a.SetGenericFloatProperty('clash', score)
+ def RMSDToSolution(self):
+ return alg.CalculateRMSD(self.handle.CreateFullView(),
+ self.the_solution_)
\ No newline at end of file
diff --git a/examples/dokk/protein.py b/examples/dokk/protein.py
new file mode 100644
index 0000000000000000000000000000000000000000..ad4025c528b1300925c537713f62a0d8071583b4
--- /dev/null
+++ b/examples/dokk/protein.py
@@ -0,0 +1,8 @@
+from ost import gfx
+class Protein:
+ def __init__(self, prot):
+ self.handle=prot
+ for a in self.handle.atoms:
+ a.SetGenericFloatProperty('clash', 0.0)
+ self.prot_go_=gfx.Entity("Prot", self.handle)
+ gfx.Scene().Add(self.prot_go_)
\ No newline at end of file
diff --git a/examples/dokk/surface.py b/examples/dokk/surface.py
new file mode 100644
index 0000000000000000000000000000000000000000..8b5a58a73352ebdb449dcb762e153248ec3fd069
--- /dev/null
+++ b/examples/dokk/surface.py
@@ -0,0 +1,13 @@
+from ost import gfx
+from ost import mol
+class Surface:
+ def __init__(self, surf):
+ self.handle=surf
+ self.go=gfx.Surface("Surf", self.handle)
+
+ gfx.Scene().Add(self.go)
+ grad=gfx.Gradient()
+ grad.SetColorAt(0.0, gfx.Color(1.0, 1.0, 1.0))
+ grad.SetColorAt(0.7, gfx.Color(1.0, 1.0, 0.0))
+ grad.SetColorAt(1.0, gfx.Color(1.0, 0.0, 0.0))
+ self.go.ColorBy('clash', grad, 0.0, 10.0, mol.Prop.Level.ATOM)
\ No newline at end of file
diff --git a/modules/geom/pymod/export_composite3.cc b/modules/geom/pymod/export_composite3.cc
index 1d646b5289ab91269f5770315b1c8a2dd6b5e461..8468578df28234c4b1d2ad11eafa6b57a4cde915 100644
--- a/modules/geom/pymod/export_composite3.cc
+++ b/modules/geom/pymod/export_composite3.cc
@@ -133,6 +133,9 @@ scope PlaneScope =
return_value_policy<copy_const_reference>())
.def("GetHalfExtents", &Cuboid::GetHalfExtents)
;
-
+ class_<AlignedCuboid>("AlignedCuboid", init<geom::Vec3, geom::Vec3>())
+ .def("GetMin", &AlignedCuboid::GetMin, return_value_policy<copy_const_reference>())
+ .def("GetMax", &AlignedCuboid::GetMax, return_value_policy<copy_const_reference>())
+ ;
}
diff --git a/modules/geom/pymod/export_mat3.cc b/modules/geom/pymod/export_mat3.cc
index 9efe5a8dd8a43b0635561e0df71e75975616be62..ee66e38d6439c54dab43058f9e2d73d1cca3a56b 100644
--- a/modules/geom/pymod/export_mat3.cc
+++ b/modules/geom/pymod/export_mat3.cc
@@ -74,5 +74,7 @@ void export_Mat3()
.def("__getitem__",Mat3_getslice)
.def("__setitem__",Mat3_setitem)
.def("__setitem__",Mat3_setslice)
+ .def("GetCol", &Mat3::GetCol)
+ .def("GetRow", &Mat3::GetRow)
;
}
diff --git a/modules/gfx/pymod/export_entity.cc b/modules/gfx/pymod/export_entity.cc
index b4a5fad25682847980fced80ac384cf4adbaab0b..1807c2e2b9b4d65294a650259ed37d2966cd433a 100644
--- a/modules/gfx/pymod/export_entity.cc
+++ b/modules/gfx/pymod/export_entity.cc
@@ -260,7 +260,8 @@ void export_Entity()
.def("RadiusBy", radius_by_03)
.def("RadiusBy", radius_by_04)
.def("ResetRadiusBy", &Entity::ResetRadiusBy)
-
+ .def("PickAtom", &Entity::PickAtom)
+ .def("PickBond", &Entity::PickBond)
.def("ColorByElement",&Entity::ColorByElement)
.def("CleanColorOps", &Entity::CleanColorOps)
.def("ReapplyColorOps", &Entity::ReapplyColorOps)
diff --git a/modules/gfx/pymod/export_scene.cc b/modules/gfx/pymod/export_scene.cc
index ec1dd53ebce61d984a036799b3680b73404e2e23..5bd9c75e04a880b0603cc9eb07411d401399bd99 100644
--- a/modules/gfx/pymod/export_scene.cc
+++ b/modules/gfx/pymod/export_scene.cc
@@ -87,6 +87,7 @@ void export_Scene()
.def("GetCenter",&Scene::GetCenter)
.def("CenterOn",center_on1)
.def("CenterOn",center_on2)
+ .def("UnProject", &Scene::UnProject, arg("ignore_vp")=false)
.def("InitGL", &Scene::InitGL)
.def("RenderGL", &Scene::RenderGL)
.def("Resize", &Scene::Resize)
diff --git a/modules/mol/base/pymod/export_entity.cc b/modules/mol/base/pymod/export_entity.cc
index e8c0caffc92305df01d112fdab8ededaad337764..67d273b09a1db687a7b651f1ce89ff85c2e2479f 100644
--- a/modules/mol/base/pymod/export_entity.cc
+++ b/modules/mol/base/pymod/export_entity.cc
@@ -102,7 +102,12 @@ void export_Entity()
.add_property("residues", &EntityHandle::GetResidueList)
.add_property("atoms", &EntityHandle::GetAtomList)
.add_property("chains", &EntityHandle::GetChainList)
- .add_property("bonds", &EntityHandle::GetBondList)
+ .add_property("bonds", &EntityHandle::GetBondList)
+ .def("GetTransformationMatrix", &EntityHandle::GetTransformationMatrix,
+ return_value_policy<copy_const_reference>())
+ .add_property("transform",
+ make_function(&EntityHandle::GetTransformationMatrix,
+ return_value_policy<copy_const_reference>()))
.def("RequestICSEditor", &EntityHandle::RequestICSEditor,
X_ics_editor_overloads(args("mode")))
.def("RequestXCSEditor", &EntityHandle::RequestXCSEditor,