def testMSMSParser():
from Pmv.msmsParser import MSMSParser
msmsParser = MSMSParser()
msmsParser.parse("./gc2.vert", "./gc2.face")
msmsParser.parse("./test_0.vert", "./test_0.face")
from DejaVu import Viewer
vi = Viewer()
from DejaVu.IndexedPolygons import IndexedPolygons
visrf = IndexedPolygons('test', protected=True)
visrf.Set(vertices=msmsParser.vertices,
faces=msmsParser.faces,
vnormals=msmsParser.normals,
tagModified=False)
vi.AddObject(visrf)
GL.glColor4fv(colxf)
GL.glBegin(GL.GL_LINE_STRIP)
for i in range(self.nsegments + 1):
GL.glVertex3fv(self.v[i])
GL.glEnd()
GL.glPopMatrix()
if __name__ == '__main__':
from DejaVu.Arcs3D import Arcs3D, Fan3D
c = Arcs3D('arc3d',
vertices=((0, 0, 0), (5., 0., 0.)),
vnormals=((1.0, 0, 0), (0, 1., 0)),
materials=((1, 0, 0), (0, 0, 1)),
radii=(1.0, 2.0),
angles=(360., 180.))
f = Fan3D('fan3d',
vertices=((0, 0, 0), (5., 0., 0.)),
vnormals=((0, 0, 1), (0, 1., 0)),
materials=((1, 0, 0), (0, 0, 1)),
radii=(1.0, 2.0),
angles=(60., 170.),
vectors=((1, 1, 0), (1, 0, 0)))
from DejaVu import Viewer
vi = Viewer()
vi.AddObject(c)
vi.AddObject(f)
from DejaVu import Viewer
vi = Viewer()
vert = [(0, 1, 0), (1, 0, 1), (1, 1, 0), (2, 0, -1), (2, 1, 0), (3, 0, 1),
(3, 1, 0), (4, 0, -1), (4, 1, 0), (5, 0, 1), (5, 3, 0), (6, -2, 1)]
v1 = Numeric.array(vert)
v2 = v1 + 3.0
v3 = Numeric.concatenate((v1, v2))
colors = [(0, 0, 1), (1, 0, 0), (0, 1, 0), (0, 0, 1), (1, 0, 0), (0, 1, 0),
(0, 0, 1), (1, 0, 0), (0, 1, 0), (0, 0, 1), (1, 0, 0), (0, 1, 0)]
v4 = v2 + 3.0
v5 = Numeric.concatenate((v3, v4))
strip3 = Triangle_strip(vertices=v5,
stripBegin=[0, 12],
materials=[(0, 0, 1), (1, 0, 0), (0, 1, 0),
(0, 0, 1), (1, 0, 0), (0, 1, 0),
(0, 0, 1), (1, 0, 0), (0, 1, 0),
(0, 0, 1), (1, 0, 0), (0, 1, 0)])
#strip.Set(materials = [(1, 0, 0)])
vi.AddObject(strip3)
strip2 = Triangle_strip(vertices=v3,
stripBegin=[0, 12, 24],
materials=colors + colors[0:8])
#strip2.Set(materials = [(0, 1, 0), (0, 0, 1)])
vi.AddObject(strip2)
strip = Triangle_strip(vertices=vert, materials=colors[2:12])
#strip.Set(materials = [(1, 0, 0)])
vi.AddObject(strip)
def restore(self, event=None):
if __debug__:
if hasattr(DejaVu, 'functionName'): DejaVu.functionName()
self.cw.Set(self.savedColor, 'RGB')
if __name__ == '__main__':
import Tkinter
master = Tkinter.Toplevel()
from DejaVu import Viewer
vi = Viewer()
from DejaVu.colorMap import ColorMap
test = MaterialEditor(master, vi)
from DejaVu.Spheres import Spheres
s = Spheres('test',
centers=[[0., 0, 0], [5, 0, 0.], [0, 5, 0]],
quality=30,
matName='tropical',
matInd=0)
vi.AddObject(s)
from DejaVu.materialsDef.tropical import tropical
test.defineMaterial(tropical[0])
test.setObject(s)
## root1 = Tkinter.Tk()
## cc = ColorChooser(root1, title='Color chooser')
def GetSize(self):
return self.volumeSize
if __name__ == '__main__':
# create a DejaVu Viewer
from DejaVu import Viewer
vi = Viewer()
#Create a volumerender geoms
g = UTVolRenGeom('volren')
g.viewer = vi
vi.cameras[0].Activate()
g.InitVolumeRenderer()
g.LoadVolume("vh4.rawiv")
g.grayRamp()
#g.LoadColorMap("/mgl/ms3/python/dev/Volume/SimpleExample/colormap.map")
#g.InitData()
# add a transparent object without a dpylist
vi.AddObject(g)
#Color map editor
## from mglutil.gui.BasicWidgwts.Tk.tablemaker import TableManager
## t = TableManager(master=vi.master,
## ymaxval = 255,
## alphaCallback = g.setVolRenAlpha,
## colorCallback = g.setVolRenColors)
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
g = Geom('organelle_%d' % orga.number)
vi.AddObject(g)
gs = Geom('surface')
for j in range(4):
GL.glVertex3fv(self.ctlpoints[i][j])
GL.glEnd()
GL.glDisable(GL.GL_AUTO_NORMAL)
GL.glDisable(GL.GL_NORMALIZE)
if __name__ == '__main__':
from DejaVu.Nurbs import GLUSurfaceNurbs
from DejaVu import Viewer
vi = Viewer()
nurbsg = GLUSurfaceNurbs('nurbs')
vi.AddObject(nurbsg)
def move():
from random import uniform
for n in range(200):
for i in range(1, 3):
for j in range(1, 3):
nurbsg.ctlpoints[i][j][2] += uniform(-0.3, 0.3)
vi.OneRedraw()
vi.master.update()
import numpy
def move1():
for n in range(1, 11):
v = n * 0.1
'Bases',
vertices=vertices,
faces=faces,
inheritShading=False,
shading=GL.GL_FLAT,
materials=materials,
inheritMaterial=False,
)
return geom_bases
def returnStarOrQuote(atoms, txt):
names = [name.split("@")[0] for name in atoms.name]
try:
idx = names.index(txt + '*')
return atoms[idx]
except:
idx = names.index(txt + "'")
return atoms[idx]
if __name__ == '__main__':
from DejaVu import Viewer
vi = Viewer()
from DejaVu import NucleicBases
b = NucleicBases.Pyrimidine_old('b')
vi.AddObject(b)
while (1):
vi.update()
from DejaVu import Viewer
vi = Viewer()
from DejaVu.IndexedPolygons import IndexedPolygons
tet = IndexedPolygons('surfaceMesh',
vertices=vertices,
faces=faces,
vnormals=vnormals,
inheritFrontPolyMode=False,
frontPolyMode='line',
inheritCulling=0,
culling='none',
inheritShading=0,
shading='flat',
visible=0)
vi.AddObject(tet)
#from DejaVu.Spheres import Spheres
#sectionVsph = Spheres('sectionV', vertices=vertsS, radii=(0.02,))
#vi.AddObject(sectionVsph)
#from DejaVu.Points import Points
#sectionVpts = Points('sectionV', vertices=allvertsS)
#sectionVpts = Points('sectionV', vertices=[vertsS[14], vertsS[159], vertsS[158]])
#vi.AddObject(sectionVpts)
#from DejaVu.IndexedPolylines import IndexedPolylines
#line = IndexedPolylines(
# 'sectionL', vertices=allvertsS, faces=edgesS,
# inheritLinewidth=False, Linewidth=3,
# inheritMaterial=False, materials=( (0,1,0), ))
#vi.AddObject(line)
import profile
# profile.run("smooth, ctrl = ribbon2D( nrib, width, nchords, offset, natoms, cao, [0]*46 );")
profile.run("smooth = ribbon2D( nrib, width, nchords, offset, natoms, cao, [0]*46 );")
from DejaVu import Viewer
vi = Viewer()
from DejaVu.IndexedPolygons import IndexedPolygons
f = []
n = smooth.shape[1]
f = map( lambda x: (x, x+1, x+n+1, x+n), range(smooth.shape[1]-1))
v = Numeric.array(Numeric.reshape(smooth, (-1,4))[:,:3])
p = IndexedPolygons('sheet2D', vertices = v, faces = f, protected=True,)
if self.vf.userpref['Sharp Color Boundaries for MSMS']['value'] == 'blur':
p.Set(inheritSharpColorBoundaries=False, sharpColorBoundaries=False,)
p.replace = False
vi.AddObject(p)
from DejaVu.Spheres import Spheres
ctrl.shape = (-1,4)
p = Spheres('ctrl', centers = ctrl[:, :3], radii = 0.6, protected=True)
p.replace = False
vi.AddObject(p)
from DejaVu.Spheres import Spheres
s = Spheres('sph', vertices = v, quality=5, protected=True)
s.radius = 0.2
vi.AddObject(s)
from MolKit import Read
mol = Read('../1crn.pdb')
allatoms = mol.chains.residues.atoms
