Exemple #1
0
                            name='0ABL kinase0', nbJitter=20,
                            meshFile=wrkDir+'/recipes/cyto/1ABL_centered',
                            packingMode='close')
rCyto1.addIngredient( kinase0 )


# create HistoVol
h1 = HistoVol()

# create and add oganelles
from DejaVu.IndexedPolygons import IndexedPolygonsFromFile
geomS = IndexedPolygonsFromFile(wrkDir+'/organelles/vesicle_r20nm', 'vesicle')
faces = geomS.getFaces()
vertices = geomS.getVertices()
vnormals = geomS.getVNormals()
o1 = Organelle(vertices, faces, vnormals)
h1.addOrganelle(o1)

# set recipe
o1.setSurfaceRecipe(rSurf1)
o1.setInnerRecipe(rCyto1)


h1.setMinMaxProteinSize()
print('Surf', rSurf1.getMinMaxProteinSize())
print('Cyto', rCyto1.getMinMaxProteinSize())
print('o1', o1.getMinMaxProteinSize())
print('smallest', h1.smallestProteinSize)
print('largest', h1.largestProteinSize)
print('Bounding box', h1.boundingBox)
#                           meshFile='recipes/cyto/1TWV_centered',
#                           color=cornflowerblue, packingPriority=1)
#rCyto.addIngredient( ingr1TWV )

# vesicle
from DejaVu.IndexedPolygons import IndexedPolygonsFromFile

# create HistoVol
h1 = HistoVol()

# create and add oganelles
geomS = IndexedPolygonsFromFile(wrkDir+'/organelles/vesicle_r20nm', 'vesicle')
faces = geomS.getFaces()
vertices = geomS.getVertices()
vnormals = geomS.getVNormals()
o1 = Organelle(vertices, faces, vnormals)
h1.addOrganelle(o1)

# set recipes
h1.setExteriorRecipe(rCyto)

o1.setSurfaceRecipe(rSurf1)
#o1.setInnerRecipe(rMatrix1)

h1.setMinMaxProteinSize()
print 'Cyto', rCyto.getMinMaxProteinSize()
print 'Surf', rSurf1.getMinMaxProteinSize()
print 'Matrix', rMatrix1.getMinMaxProteinSize()
print 'o1', o1.getMinMaxProteinSize()
print 'smallest', h1.smallestProteinSize
print 'largest', h1.largestProteinSize
Exemple #3
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h1 = HistoVol()
# set recipes
h1.setExteriorRecipe(rCyto)
#o1.setSurfaceRecipe(rSurf1)
#o1.setInnerRecipe(rMatrix1)

from Pmv.hostappInterface.cinema4d_dev import helperC4D as helper
#display the organel, the box, and prepare the hierachy...
doc = helper.getCurrentScene()
sel = doc.GetSelection()

c4dorganlle = sel[0]
helper.triangulate(c4dorganlle)
faces,vertices,vnormals = helper.DecomposeMesh(c4dorganlle,edit=True,copy=True,tri=True)

o1 = Organelle(vertices, faces, vnormals)
h1.addOrganelle(o1)
o1.setSurfaceRecipe(rSurf1)
#o1.setInnerRecipe(rCyto)

#define the viewer type dejavu,c4d,blender
ViewerType='c4d'
afviewer = AFViewer(ViewerType=ViewerType)
#make some option here 
afviewer.doPoints = False
afviewer.doSpheres = False

afviewer.quality = 1 #lowest quality for sphere and cylinder

h1.setMinMaxProteinSize()
print 'Cyto', rCyto.getMinMaxProteinSize()
## print 'time to fill', time()-t1
## h1.printFillInfo()
## execfile('displayFill.py')
from Pmv.hostappInterface.cinema4d import helperC4D as helper
#display the organel, the box, and prepare the hierachy...
doc = helper.getCurrentScene()
sel = doc.get_selection()

c4dorganlle = sel[0]
helper.triangulate(c4dorganlle)

faces = c4dorganlle.get_polygons()
c4dvertices = c4dorganlle.get_points()
vertices = map(helper.vc4d,c4dvertices)
vnormals = helper.GetFaces(c4dorganlle)
o1 = Organelle(vertices, faces, vnormals)
h1.addOrganelle(o1)
o1.setSurfaceRecipe(rSurf1)

# add padding
bb = h1.boundingBox
pad = 100.
x,y,z = bb[0]
bb[0] = [x-pad, y-pad, z-pad]
x,y,z = bb[1]
bb[1] = [x+pad, y+pad, z+pad]
print 'Bounding box with padding', h1.boundingBox


h1.setMinMaxProteinSize()
print 'Cyto', rCyto.getMinMaxProteinSize()
Exemple #5
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#                           color=cornflowerblue, packingPriority=1)
#rCyto.addIngredient( ingr1TWV )

# vesicle
from DejaVu.IndexedPolygons import IndexedPolygonsFromFile

# create HistoVol
h1 = HistoVol()

# create and add oganelles
geomS = IndexedPolygonsFromFile(wrkDir + '/organelles/vesicle_r20nm',
                                'vesicle')
faces = geomS.getFaces()
vertices = geomS.getVertices()
vnormals = geomS.getVNormals()
o1 = Organelle(vertices, faces, vnormals)
h1.addOrganelle(o1)

# set recipes
h1.setExteriorRecipe(rCyto)

o1.setSurfaceRecipe(rSurf1)
#o1.setInnerRecipe(rMatrix1)

h1.setMinMaxProteinSize()
print 'Cyto', rCyto.getMinMaxProteinSize()
print 'Surf', rSurf1.getMinMaxProteinSize()
print 'Matrix', rMatrix1.getMinMaxProteinSize()
print 'o1', o1.getMinMaxProteinSize()
print 'smallest', h1.smallestProteinSize
print 'largest', h1.largestProteinSize