diff --git a/examples/dokk/config.py b/examples/dokk/config.py
new file mode 100644
index 0000000000000000000000000000000000000000..0323a34613db55427c16022f672ce468c61f49f8
--- /dev/null
+++ b/examples/dokk/config.py
@@ -0,0 +1,20 @@
+import ConfigParser
+import string
+
+class Config:
+ def __init__(self, path):
+ config = ConfigParser.ConfigParser()
+ config.read(path)
+
+ self.values = dict()
+ for section in config.sections():
+ section_dict = dict()
+ for option in config.options(section):
+ section_dict[str(option).upper()]=config.get(section, option)
+ self.values[str(section).lower()]=section_dict
+
+ def __getattr__(self, item):
+ item = str(item).lower()
+ if self.values.has_key(item):
+ return self.values[item]
+ raise AttributeError(item)
diff --git a/examples/dokk/dokk.py b/examples/dokk/dokk.py
index 60abd7d89d1484676507072b3e4f46013cd4a426..03603f942ee2193f96d963fb2c7086fbab5331ea 100644
--- a/examples/dokk/dokk.py
+++ b/examples/dokk/dokk.py
@@ -8,5 +8,6 @@ dokk_win=glwin.DokkGLWin()
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 6124806ee4838d6fc1f1f26a05c335431cddefc3..29c9df1c0b8f7096163a2711e451a9b5a991ce63 100644
--- a/examples/dokk/glwin.py
+++ b/examples/dokk/glwin.py
@@ -57,7 +57,6 @@ class DokkGLCanvas(QGLWidget):
self.last_point_=QPoint(event.x(), event.y())
def mouseMoveEvent(self, event):
- print "MOUSE MOVE"
delta=QPoint(event.x(), event.y())-self.last_point_
self.last_point_=QPoint(event.x(), event.y())
if event.buttons() & Qt.LeftButton:
diff --git a/examples/dokk/level.py b/examples/dokk/level.py
index 1c9c51557c96f668548009593f1529bfe57748ea..d3c4f2bf2a991ca76ce5d730f5a798f1a9d71ad6 100644
--- a/examples/dokk/level.py
+++ b/examples/dokk/level.py
@@ -4,24 +4,27 @@ from ligand import Ligand
from surface import Surface
from protein import Protein
from score_updater import ScoreUpdater
+from config import Config
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_)
+ self.config = Config(os.path.join(level_dir, 'level.ini'))
+ print 'Loading %s' % self.config.Level["NAME"]
ligand_ent=io.LoadSDF(os.path.join(level_dir, 'ligand.sdf'))
- self.ligand=Ligand(ligand_ent)
+ self.ligand=Ligand(ligand_ent,self.config)
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())
+ gfx.Scene().SetCenter(self.surface.go.GetCenter())
print 'Done Loading'
self.su = ScoreUpdater(self)
+ self.transform_ = gfx.Scene().GetTransform()
def RotateAxis(self, axis, angle):
self.ligand.RotateAxis(axis, angle)
@@ -40,3 +43,17 @@ class Level:
def GetRMSD(self):
return self.ligand.RMSDToSolution()
+
+ def Reset(self):
+ self.ligand.Reset()
+ gfx.Scene().SetTransform(self.transform_)
+ gfx.Scene().SetCenter(self.surface.go.GetCenter())
+ gfx.Scene().RequestRedraw()
+ self.su.UpdateScores()
+
+ def Solve(self):
+ self.ligand.Solve()
+ gfx.Scene().SetTransform(self.transform_)
+ gfx.Scene().SetCenter(self.surface.go.GetCenter())
+ gfx.Scene().RequestRedraw()
+ self.su.UpdateScores()
\ No newline at end of file
diff --git a/examples/dokk/ligand.py b/examples/dokk/ligand.py
index 960ab06ad9a54ed9fadaf20862603213504b91b8..c37bb8859fe68fd832a7e2069868e93dbdcc1959 100644
--- a/examples/dokk/ligand.py
+++ b/examples/dokk/ligand.py
@@ -2,7 +2,7 @@ from ost import gfx, geom
from ost.mol import alg
from ost import mol
class Ligand:
- def __init__(self, ligand):
+ def __init__(self, ligand, config=None):
self.handle=ligand
self.the_solution_=ligand.Copy().CreateFullView()
self.go=gfx.Entity("Ligand", gfx.CUSTOM, self.handle)
@@ -12,7 +12,16 @@ class Ligand:
bbox=self.go.GetBoundingBox()
self.radius=geom.Length(bbox.GetMax()-bbox.GetMin())+3.0
self.pivot_=mol.AtomHandle()
-
+ self.start_tf_=geom.Mat4()
+ self.config = config
+ self.box_max = geom.Vec3(float(self.config.Box["XMAX"]),
+ float(self.config.Box["YMAX"]),
+ float(self.config.Box["ZMAX"]))
+ self.box_min = geom.Vec3(float(self.config.Box["XMIN"]),
+ float(self.config.Box["YMIN"]),
+ float(self.config.Box["ZMIN"]))
+ self.Reset()
+
def SetPivot(self, pivot):
self.pivot_=pivot
@@ -34,11 +43,12 @@ class Ligand:
self.go.UpdatePositions()
def Shift(self, vec):
- trans=geom.Mat4()
- trans.PasteTranslation(vec)
- edi=self.handle.RequestXCSEditor()
- edi.ApplyTransform(trans)
- self.go.UpdatePositions()
+ if self.__IsInside(self.GetCenter()+vec):
+ trans=geom.Mat4()
+ trans.PasteTranslation(vec)
+ edi=self.handle.RequestXCSEditor()
+ edi.ApplyTransform(trans)
+ self.go.UpdatePositions()
def SetTF(self, tf):
edi=self.handle.RequestXCSEditor()
@@ -49,7 +59,11 @@ class Ligand:
center=self.pivot_.GetPos()
trans.PasteTranslation(-center)
trans2=geom.Mat4()
- trans2.PasteTranslation(center+tf.GetTrans())
+ trans2_vec = center+((tf.GetTrans())*gfx.Scene().GetTransform().GetRot())
+ if self.__IsInside(trans2_vec):
+ trans2.PasteTranslation(trans2_vec)
+ else:
+ trans2.PasteTranslation(center)
full_tf = trans2*rot*trans
edi.ApplyTransform(full_tf)
self.go.UpdatePositions()
@@ -62,3 +76,29 @@ class Ligand:
def RMSDToSolution(self):
return alg.CalculateRMSD(self.handle.CreateFullView(),
self.the_solution_)
+
+ def Solve(self):
+ edi=self.handle.RequestXCSEditor()
+ edi.SetTransform(self.start_tf_)
+ self.go.UpdatePositions()
+
+ def Reset(self):
+ if self.config is not None:
+ edi=self.handle.RequestXCSEditor()
+ shift_vec = geom.Vec3(float(self.config.start["POSX"]),
+ float(self.config.start["POSY"]),
+ float(self.config.start["POSZ"]))
+ transf = mol.Transform()
+ transf.SetTrans(shift_vec)
+ edi.SetTransform(transf.GetMatrix())
+ self.RotateAxis(geom.Vec3(1,0,0), float(self.config.start["ROTX"]))
+ self.RotateAxis(geom.Vec3(0,1,0), float(self.config.start["ROTY"]))
+ self.RotateAxis(geom.Vec3(0,0,1), float(self.config.start["ROTZ"]))
+ self.go.UpdatePositions()
+
+ def __IsInside(self, vec):
+ if vec[0]< self.box_max[0] and vec[0]> self.box_min[0] and \
+ vec[1]< self.box_max[1] and vec[1]> self.box_min[1] and \
+ vec[2]< self.box_max[2] and vec[2]> self.box_min[2] :
+ return True
+ return False
\ No newline at end of file
diff --git a/examples/dokk/score_updater.py b/examples/dokk/score_updater.py
index d33bcfcafb3d185cfe8dd09389ac7f8966c8553a..b968d35b980f2cc68c1c1513d4b14a09c94bd46a 100644
--- a/examples/dokk/score_updater.py
+++ b/examples/dokk/score_updater.py
@@ -6,27 +6,8 @@ class ScoreUpdater(QtCore.QObject):
def __init__(self, level, parent=None):
QtCore.QObject.__init__(self, parent)
self.level = level
- self.ut = UpdateThread(level)
- self.ut.start()
- def UpdateScores(self):
- self.ut.UpdateScores()
-
-
-class UpdateThread(QtCore.QProcess):
- def __init__(self,level,parent=None):
- QtCore.QProcess.__init__(self,parent)
- self.level = level
-
- def run ( self ):
- i=0
- while(True):
- i+=1
- print "UPDATE",i
- self.UpdateScores()
- self.sleep(2)
-
def UpdateScores(self):
ligand = self.level.ligand
prot_within=self.level.protein.handle.FindWithin(ligand.GetCenter(),
@@ -35,4 +16,4 @@ class UpdateThread(QtCore.QProcess):
for a in prot_within:
score=qa.ClashScore(a, lig_view)
a.SetGenericFloatProperty('clash', score)
- self.level.surface.go.ReapplyColorOps()
\ No newline at end of file
+ self.level.surface.go.ReapplyColorOps()
diff --git a/examples/dokk/spnav_input.py b/examples/dokk/spnav_input.py
index f7c742e8f68d06cbc770c968e8f8f0658bfe0eb8..b62c889eadda74f5d95fc65444e58015232425b5 100644
--- a/examples/dokk/spnav_input.py
+++ b/examples/dokk/spnav_input.py
@@ -2,9 +2,12 @@ from PyQt4 import QtCore, QtGui
from ost import mol, geom, gfx, gui
+DEFAULT_REFRESHRATE = 30
+
class SpnavInputDevice(QtCore.QObject):
def __init__(self, gfx_win, parent=None):
QtCore.QObject.__init__(self, parent)
+ self.refresh_rate_ = DEFAULT_REFRESHRATE
self.spnav = gui.SpnavInput.GetQThread()
self.spnav.start()
self.gfx_win = gfx_win
@@ -15,29 +18,49 @@ class SpnavInputDevice(QtCore.QObject):
self.trans = True
self.rot = True
+ self.score_scip = 0
def SetLevel(self, level):
self.level=level
+ try:
+ self.refresh_rate_ = int(level.config.Score["FRAMESKIP"])
+ except:
+ pass
- def InputChanged(self, tx,ty,tz,rx,ry,rz):
- ligand = self.level.ligand
- transf = mol.Transform()
- if(self.trans):
- transf.ApplyXAxisTranslation(tx/480.0)
- transf.ApplyYAxisTranslation(ty/480.0)
- transf.ApplyZAxisTranslation(-tz/480.0)
- if(self.rot):
- transf.ApplyXAxisRotation(rx/480.0)
- transf.ApplyYAxisRotation(ry/480.0)
- transf.ApplyZAxisRotation(rz/480.0)
- ligand.SetTF(transf)
- gfx.Scene().RequestRedraw()
- self.gfx_win.update()
+ def InputChanged(self, tx,ty,tz,rx,ry,rz):
+ if self.level is not None:
+ ligand = self.level.ligand
+ transf = mol.Transform()
+ if(self.trans):
+ scene_rot = geom.Mat4(gfx.Scene().GetTransform().GetRot())
+ center = gfx.Scene().GetCenter()
+ delta = geom.Vec3 (tx/480.0, ty/480.0, -tz/480.0)
+ transf.SetTrans(delta)
+ if(self.rot):
+ transf.ApplyXAxisRotation(rx/480.0)
+ transf.ApplyYAxisRotation(ry/480.0)
+ transf.ApplyZAxisRotation(rz/480.0)
+ ligand.SetTF(transf)
+ if self.score_scip >= self.refresh_rate_:
+ self.level.UpdateScores()
+ self.score_scip = 0
+ self.score_scip += 1
+ gfx.Scene().RequestRedraw()
+ self.gfx_win.update()
def ToggleInputMode(self, button):
+ print button
if button == 0:
self.trans = not self.trans
print "Translation Enabled:",self.trans
elif button == 1:
self.rot = not self.rot
print "Rotation Enabled:",self.rot
-
+ elif button == 6:
+ QtGui.QApplication.exit()
+ elif button == 10:
+ self.level.Reset()
+ self.gfx_win.update()
+ elif button == 11:
+ self.level.Solve()
+ self.gfx_win.update()
+
diff --git a/examples/dokk/surface.py b/examples/dokk/surface.py
index 8b5a58a73352ebdb449dcb762e153248ec3fd069..7fdcf1ff4786de81f2c41922bb3147aa7590333e 100644
--- a/examples/dokk/surface.py
+++ b/examples/dokk/surface.py
@@ -10,4 +10,4 @@ class Surface:
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
+ self.go.ColorBy('clash', grad, 0.0, 10.0, mol.Prop.Level.ATOM)