def createGeometries(self, obj):
from DejaVu.Geom import Geom
geomC = obj.geomContainer
c = Geom('path', shape=(0,0), protected=True)
c.replace = 'force'
geomC.addGeom(c, parent=geomC.masterGeom)
for a in obj.allAtoms:
a.colors['path']=(1.,1.,1.)
a.opacities['path']=1.0
for chain in obj.chains:
if not hasattr(chain, 'sheet2D') or chain.sheet2D is None:
continue
# HACK TO DEBUG SECONDARYSTRUCTURE
if not chain.sheet2D.has_key('ssSheet2D') or \
chain.sheet2D['ssSheet2D'] is None:
continue
# Create a geometry per sheet2D
name = 'path'+ chain.id
g = Spheres( name, quality = 10, radii = 0.15, protected=True)
g.replace = 'force'
geomC.addGeom( g, parent=c)
self.managedGeometries.append(g)
# FIXME to update this geom we would have to implement
# self.updateGeom specifically for this command
geomC.atoms[name] = ResidueSet()
g.chain = chain
geomC.atomPropToVertices[name] = self.atomPropToVertices
geomC.geomPickToAtoms[name] = self.pickedVerticesToAtoms
geomC.geomPickToBonds[name] = None
def createGeometries(self, obj):
from DejaVu.Geom import Geom
geomC = obj.geomContainer
c = Geom('path', shape=(0, 0), protected=True)
c.replace = 'force'
geomC.addGeom(c, parent=geomC.masterGeom)
for a in obj.allAtoms:
a.colors['path'] = (1., 1., 1.)
a.opacities['path'] = 1.0
for chain in obj.chains:
if not hasattr(chain, 'sheet2D') or chain.sheet2D is None:
continue
# HACK TO DEBUG SECONDARYSTRUCTURE
if not chain.sheet2D.has_key('ssSheet2D') or \
chain.sheet2D['ssSheet2D'] is None:
continue
# Create a geometry per sheet2D
name = 'path' + chain.id
g = Spheres(name, quality=10, radii=0.15, protected=True)
g.replace = 'force'
geomC.addGeom(g, parent=c)
self.managedGeometries.append(g)
# FIXME to update this geom we would have to implement
# self.updateGeom specifically for this command
geomC.atoms[name] = ResidueSet()
g.chain = chain
geomC.atomPropToVertices[name] = self.atomPropToVertices
geomC.geomPickToAtoms[name] = self.pickedVerticesToAtoms
geomC.geomPickToBonds[name] = None
def Add(self, check=1, redo=1, **kw):
"""Add glfLabels
"""
#print "Add glfLabels"
if __debug__:
if check:
apply(checkKeywords, (self.name, self.keywords), kw)
v = kw.get('vertices')
if v:
self.redoDspLst = 1
labels = kw.get('labels')
if labels:
#labels is apparently a tuple
self.labels = self.labels + labels
self.redoDspLst = 1
Geom.Add(self,
check=0,
redo=0,
vertices=kw.get('vertices'),
materials=kw.get('materials'))
if self.viewer and redo:
if self.redoDspLst:
self.viewer.objectsNeedingRedo[self] = None
def initGeom(self):
self.cylinders = self.geom = Cylinders('hbondCylinders',
quality=40,
culling=GL.GL_NONE,
radii=(0.2),
materials=((0, 1, 0), ),
pickable=0,
inheritMaterial=0)
#DejaVu.Cylinders overwrites kw cull so have to reset it here
self.cylinders.culling = GL.GL_NONE
geoms = [self.cylinders]
miscGeom = self.vf.GUI.miscGeom
hbond_geoms = check_hbond_geoms(self.vf.GUI)
self.masterGeom = Geom('StrutsAsCylindersGeoms',
shape=(0, 0),
pickable=0,
protected=True)
self.vf.GUI.VIEWER.AddObject(self.masterGeom, parent=hbond_geoms)
for item in geoms:
self.vf.GUI.VIEWER.AddObject(item, parent=self.masterGeom)
self.hasGeom = 0
self.radii = 0.2
self.length = 1.0
self.oldlength = 1.0
self.verts = []
self.faces = []
def getState(self, full=False):
"""return a dictionary describing this object's state
This dictionary can be passed to the Set method to restore the object's state
"""
state = Geom.getState(self, full).copy()
state.update(self.getSubClassState())
return state
def initGeom(self):
from DejaVu.IndexedPolylines import IndexedPolylines
#from DejaVu.Labels import Labels
self.quality = 4
self.spheres = self.geom = Spheres('strutsSpheres',
materials=((0, 1, 0), ),
shape=(0, 3),
radii=0.1,
quality=4,
pickable=0,
inheritMaterial=0,
protected=True)
geoms = [self.spheres]
self.masterGeom = Geom('strutsAsSpheresGeoms',
shape=(0, 0),
pickable=0,
protected=True)
self.masterGeom.isScalable = 0
if self.vf.hasGui:
miscGeom = self.vf.GUI.miscGeom
hbond_geoms = check_hbond_geoms(self.vf.GUI)
self.vf.GUI.VIEWER.AddObject(self.masterGeom, parent=hbond_geoms)
for item in geoms:
self.vf.GUI.VIEWER.AddObject(item, parent=self.masterGeom)
self.hasGeom = 0
self.spacing = .40
self.radii = 0.1
self.verts = []
def check_measure_geoms(VFGUI):
measure_geoms_list = VFGUI.VIEWER.findGeomsByName('measure_geoms')
if measure_geoms_list == []:
measure_geoms = Geom("measure_geoms", shape=(0, 0), protected=True)
VFGUI.VIEWER.AddObject(measure_geoms, parent=VFGUI.miscGeom)
measure_geoms_list = [measure_geoms]
return measure_geoms_list[0]
def check_hbond_geoms(VFGUI):
hbond_geoms_list = VFGUI.VIEWER.findGeomsByName('struts_geoms')
if hbond_geoms_list == []:
hbond_geoms = Geom("struts_geoms", shape=(0, 0), protected=True)
VFGUI.VIEWER.AddObject(hbond_geoms, parent=VFGUI.miscGeom)
hbond_geoms_list = [hbond_geoms]
return hbond_geoms_list[0]
def getState(self, full=False):
if __debug__:
if hasattr(DejaVu, 'functionName'): DejaVu.functionName()
state = Geom.getState(self, full)
if full:
state['faces'] = self.getFaces()
state['fnormals'] = self.getFNormals()
return state
def getState(self, full=False):
state = Geom.getState(self, full)
# add knots, ctrlPts, displayMode to state
## state['quality'] = self.quality
## if full:
## rad = self.vertexSet.radii.array
## if len(rad):
## state['radii'] = rad
return state
def getState(self, full=False):
state = Geom.getState(self, full)
# add knots, ctrlPts, displayMode to state
## state['quality'] = self.quality
## if full:
## rad = self.vertexSet.radii.array
## if len(rad):
## state['radii'] = rad
return state
def getState(self, full=False):
if __debug__:
if hasattr(DejaVu, 'functionName'): DejaVu.functionName()
state = Geom.getState(self, full)
state['quality'] = self.quality
if full:
rad = self.vertexSet.radii.array
if len(rad):
state['radii'] = rad
return state
def getState(self, full=False):
if __debug__:
if hasattr(DejaVu, 'functionName'): DejaVu.functionName()
state = Geom.getState(self, full)
state['quality'] = self.quality
if full:
rad = self.vertexSet.radii.array
if len(rad):
state['radii'] = rad
return state
def onAddCmdToViewer(self):
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands',
'setICOM',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('measureDistance'):
self.vf.loadCommand('measureCommands',
'measureDistance',
'Pmv',
topCommand=0)
self.masterGeom = Geom('measureDistGeom', shape=(0, 0), pickable=0)
self.masterGeom.isScalable = 0
if self.vf.hasGui:
measure_geoms = check_measure_geoms(self.vf.GUI)
self.vf.GUI.VIEWER.AddObject(self.masterGeom, parent=measure_geoms)
self.lines = IndexedPolylines('distLine',
materials=((1, 1, 0), ),
inheritMaterial=0,
lineWidth=3.,
stippleLines=1,
pickable=0)
self.labels = GlfLabels(name='distLabel',
shape=(0, 3),
font='arial1.glf',
fontStyle='solid3d',
fontScales=(.5, .5, .3),
inheritMaterial=0,
materials=((1, 1, 0), ))
self.spheres = Spheres(name='distSpheres',
shape=(0, 3),
inheritMaterial=0,
radii=0.2,
quality=15,
materials=((1., 1., 0.), ))
if self.vf.hasGui:
for item in [self.lines, self.labels, self.spheres]:
self.vf.GUI.VIEWER.AddObject(item, parent=self.masterGeom)
def DisplayFunction(self):
""" Either executes the present display list or creates a display
list to display the triangle strip. """
# if in select mode, switches to IndexedPolygons
if self.viewer.currentCamera.renderMode == GL.GL_SELECT:
temp = self.primitiveType
if self.frontPolyMode == GL.GL_FILL:
self.primitiveType = GL.GL_POLYGON
elif self.frontPolyMode == GL.GL_LINE:
self.primitiveType = GL.GL_LINE_LOOP
elif self.frontPolyMode == GL.GL_POINT:
self.primitiveType = GL.GL_POINTS
self.faceSet = self.IndexedFaceSet
IndexedPolygons.DisplayFunction(self)
self.faceSet = self.StripFaceSet
self.primitiveType = temp
return
if self.dpyList:
Geom.DisplayFunction(self)
def onAddCmdToViewer(self):
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands',
'setICOM',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('addBonds'):
self.vf.loadCommand('bondsCommands',
'addBonds',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('removeBondsGC'):
self.vf.loadCommand('bondsCommands',
'removeBondsGC',
'Pmv',
topCommand=0)
self.masterGeom = Geom('addBondsGeom',
shape=(0, 0),
pickable=0,
protected=True)
self.masterGeom.isScalable = 0
self.spheres = Spheres(name='addBondsSpheres',
shape=(0, 3),
inheritMaterial=0,
radii=0.2,
quality=15,
materials=((1., 1., 0.), ),
protected=True)
if not self.vf.commands.has_key('labelByExpression'):
self.vf.loadCommand('labelCommands', [
'labelByExpression',
],
'Pmv',
topCommand=0)
if self.vf.hasGui:
miscGeom = self.vf.GUI.miscGeom
self.vf.GUI.VIEWER.AddObject(self.masterGeom, parent=miscGeom)
self.vf.GUI.VIEWER.AddObject(self.spheres, parent=self.masterGeom)
def createGeometries(self, name):
from DejaVu.Geom import Geom
t = Geom(name, shape=(0, 0), protected=True)
self.vf.vectfield[name] = t
t.replace = True
self.vf.GUI.VIEWER.AddObject(t, redo=0)
from Blender import Window, Scene, Draw
bb=[[0, -400.0, -400.0], [400.0, 400.0, 400.0]]
sc = bl.getCurrentScene()
#display fill box
fbb = bl.box('fillpBB',cornerPoints=bb) #maybe /10.
bl.addObjectToScene(sc,fbb)
#fbb = Box('fillpBB', cornerPoints=bb, visible=1)
#vi.AddObject(fbb)
# create master for extra cellular compartment
#
bg = bl.newEmpty('extra cellular')
orgaToMasterGeom = {}
g = Geom('extra cellular', visible=0)
orgaToMasterGeom[0] = g
orgaToMasterGeom[h1] = g
bl.addObjectToScene(sc,bg)
# display organelle mesh
for orga in h1.organelles:
# create master for organelle
bg = bl.newEmpty('organelle_%d'%orga.number)
g = Geom('organelle_%d'%orga.number)
bl.addObjectToScene(sc,bg)
gs = Geom('surface')
bgs = bl.newEmpty('surface')
bl.addObjectToScene(sc,bgs, parent=bg)
gc = Geom('cytoplasm')
bgc = bl.newEmpty('cytoplasm')
def createGeometries(self, name):
from DejaVu.Geom import Geom
t = Geom(name,shape=(0,0), protected=True)
self.vf.vectfield[name]=t
t.replace = True
self.vf.GUI.VIEWER.AddObject(t, redo=0)
def onAddCmdToViewer(self):
if not hasattr(self.vf, 'GUI'):
return
self.undoNow = 0
self.save = None
from DejaVu.bitPatterns import pat3
from DejaVu.IndexedPolygons import IndexedPolygons
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands',
'setICOM',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('measureTorsion'):
self.vf.loadCommand('measureCommands',
'measureTorsion',
'Pmv',
topCommand=0)
self.masterGeom = Geom('setTorsionGeom',
shape=(0, 0),
pickable=0,
protected=True)
self.masterGeom.isScalable = 0
self.vf.GUI.VIEWER.AddObject(self.masterGeom,
parent=self.vf.GUI.miscGeom)
self.lines = IndexedPolygons(
'settorsionLine',
materials=((0, 1, 1), ),
inheritMaterial=0,
stipplePolygons=1,
protected=True,
)
if self.vf.userpref['Sharp Color Boundaries for MSMS'][
'value'] == 'blur':
self.lines.Set(
inheritSharpColorBoundaries=False,
sharpColorBoundaries=False,
)
self.lines.polygonstipple.Set(pattern=pat3) #, tagModified=False)
#self.lines.RenderMode(GL.GL_FILL, face=GL.GL_BACK)
self.lines.Set(backPolyMode=GL.GL_FILL)
self.labels = GlfLabels(name='settorsionLabel',
shape=(0, 3),
inheritMaterial=0,
materials=((0, 1, 1), ))
self.spheres = Spheres(name='settorsionSpheres',
shape=(0, 3),
radii=0.2,
quality=15,
inheritMaterial=0,
materials=((0., 1., 1.), ),
protected=True)
for item in [self.lines, self.labels, self.spheres]:
self.vf.GUI.VIEWER.AddObject(item, parent=self.masterGeom)
self.snakeLength = 1
self.oldValue = None
self.torsionType = Tkinter.StringVar()
self.torsionType.set('1')
self.newAngList = Tkinter.StringVar()
self.TAHdata = None
self.molecule = None
#self.bondString = Tkinter.StringVar()
self.callbackDict = {}
self.callbackDict['measureDistanceGC'] = 'update'
self.callbackDict['measureAngleGC'] = 'update'
self.callbackDict['measureTorsionGC'] = 'update'
def onAddCmdToViewer(self):
from DejaVu.bitPatterns import pat3
from DejaVu.IndexedPolygons import IndexedPolygons
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands',
'setICOM',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('measureAngle'):
self.vf.loadCommand('measureCommands',
'measureAngle',
'Pmv',
topCommand=0)
self.masterGeom = Geom('measureTorsionGeom',
shape=(0, 0),
pickable=0,
protected=True)
self.masterGeom.isScalable = 0
if self.vf.hasGui:
measure_geoms = check_measure_geoms(self.vf.GUI)
self.vf.GUI.VIEWER.AddObject(self.masterGeom, parent=measure_geoms)
self.lines = IndexedPolygons('torsionLine',
materials=((0, 1, 1), ),
culling=GL.GL_NONE,
inheritStipplePolygons=0,
inheritMaterial=0,
stipplePolygons=1,
backPolyMode=GL.GL_FILL,
frontPolyMode=GL.GL_FILL,
protected=True,
pickable=0)
if self.vf.userpref['Sharp Color Boundaries for MSMS'][
'value'] == 'blur':
self.lines.Set(
inheritSharpColorBoundaries=False,
sharpColorBoundaries=False,
)
self.lines.polygonstipple.Set(pattern=pat3)
#self.lines.polygonstipple.Set(pattern=pat3, tagModified=False)
#self.lines.RenderMode(GL.GL_FILL)
#self.lines.RenderMode(GL.GL_FILL, face=GL.GL_BACK)
self.labels = GlfLabels(name='torsionLabel',
shape=(0, 3),
font='arial1.glf',
fontStyle='solid3d',
fontScales=(.5, .5, .3),
inheritMaterial=0,
materials=((0, 1, 1), ))
self.spheres = Spheres(name='torsionSpheres',
shape=(0, 3),
inheritMaterial=0,
radii=0.2,
quality=15,
materials=((0., 1., 1.), ),
protected=True)
if self.vf.hasGui:
for item in [self.lines, self.labels, self.spheres]:
self.vf.GUI.VIEWER.AddObject(item, parent=self.masterGeom)
doc = """Number of labeled torsions displayed.
Valid values are integers>0"""
self.vf.userpref.add('Measured Torsions',
4,
callbackFunc=[self.setLength_cb],
category="Molecules",
validateFunc=lambda x: x > 0,
doc=doc)
#used after startICOM is invoked
doc = """Continuous update of torsions if 'transformRoot only' is
turned off and viewer's current object is not Root."""
choices = ['yes', 'no']
self.vf.userpref.add('Continuous Update Torsion',
'yes',
choices,
callbackFunc=[self.continuousUpdate_cb],
category="Molecules",
doc=doc)
self.snakeLength = 4
def onAddCmdToViewer(self):
from DejaVu.Points import CrossSet
self.startCross = CrossSet('StartCross',
materials=((1., 1., 0), ),
inheritMaterial=0,
protected=True,
offset=1.0,
lineWidth=5,
visible=0,
pickable=0,
listed=0)
self.endCross = CrossSet('EndCross',
materials=((0, 1, 1), ),
inheritMaterial=0,
protected=True,
offset=1.0,
lineWidth=5,
visible=0,
pickable=0,
listed=0)
from DejaVu.IndexedPolygons import IndexedPolygons
from DejaVu.Box import Box
from DejaVu.Spheres import Spheres
from DejaVu import viewerConst
from DejaVu.bitPatterns import patternList
from opengltk.OpenGL import GL
face = ((0, 3, 2, 1), (3, 7, 6, 2), (7, 4, 5, 6), (0, 1, 5, 4),
(1, 2, 6, 5), (0, 4, 7, 3))
coords = ((1, 1, -1), (-1, 1, -1), (-1, -1, -1), (1, -1, -1),
(1, 1, 1), (-1, 1, 1), (-1, -1, 1), (1, -1, 1))
#new style RGB->
materials = (
(0, 0, 1),
(0, 1, 0),
(0, 0, 1),
(0, 1, 0),
(1, 0, 0),
(1, 0, 0),
)
box = IndexedPolygons('Box',
materials=materials,
vertices=coords,
faces=face,
inheritMaterial=0,
visible=0,
protected=True,
listed=0)
box.Set(frontPolyMode=GL.GL_LINE)
box.Set(backPolyMode=GL.GL_LINE)
box.Set(culling=GL.GL_NONE)
box.inheritShading = 0
box.shading = GL.GL_FLAT
box.Set(matBind=viewerConst.PER_PART)
box.polygonstipple.Set(pattern=patternList[0])
box.Set(stipplePolygons=1)
box.transparent = 0
self.box = box
self.spheres = Spheres('Spheres',
visible=0,
inheritMaterial=0,
radii=(0.3, ),
protected=True,
listed=0)
self.halo = Spheres('Halo',
visible=0,
inheritMaterial=0,
radii=(0.5, ),
protected=True,
listed=0)
from DejaVu.Geom import Geom
AutoLigand_geoms = Geom("AutoLigand_geoms", shape=(0, 0), listed=0)
self.vf.GUI.VIEWER.AddObject(AutoLigand_geoms,
parent=self.vf.GUI.miscGeom)
self.vf.GUI.VIEWER.AddObject(self.startCross, parent=AutoLigand_geoms)
self.vf.GUI.VIEWER.AddObject(self.endCross, parent=AutoLigand_geoms)
self.vf.GUI.VIEWER.AddObject(self.box, parent=AutoLigand_geoms)
self.vf.GUI.VIEWER.AddObject(self.spheres, parent=AutoLigand_geoms)
self.vf.GUI.VIEWER.AddObject(self.halo, parent=AutoLigand_geoms)
self.grids = {}
self.vf.showCitation.citations["AutoLigand"] = """
from Pmv.hostappInterface import pdb_blender
vi = pdb_blender
Box = pdb_blender.box
Geom = pdb_blender.newEmpty
IndexedPolygons = pdb_blender.polygons
sc = pdb_blender.getCurrentScene()
Points = None
#display fill box
#fbb = Box('fillpBB',cornerPoints=bb,visible=1) #maybe /10.
#vi.AddObject(fbb)
# create master for cytoplasm compartment
#
orgaToMasterGeom = {}
g = Geom('cytoplasm', visible=0)
orgaToMasterGeom[0] = g
orgaToMasterGeom[h1] = g
vi.AddObject(g)
# create masters for ingredients
r = h1.exteriorRecipe
if r:
for ingr in r.ingredients:
gi = Geom('%s %s' % (ingr.pdb, ingr.name))
vi.AddObject(gi, parent=g)
orgaToMasterGeom[ingr] = gi
# display organelle mesh
for orga in h1.organelles:
# create master for organelle
