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)
#get the current slider value
o = self.helper.getObject("newCube")
#get the cube
if o is not None:
#if the cube exists change the scale value
self.helper.scaleObj(o, scale)
#this is a script, we need some special code for the Tk and the Qt case.
#the most important part are the instanciation of our dialog class,
#and the two functio setup and display
#setup initialise the widget and the layout
#display wil actually show the dialog.
if uiadaptor.host == "tk":
from DejaVu import Viewer
vi = Viewer()
#require a master
#import Tkinter #Tkinter if python2.x tkinter for python3.x
#root = Tkinter.Tk()
mygui = Cubi(title="CubeUI", master=vi)
mygui.setup(vi=vi)
#mygui.display()
elif uiadaptor.host == "qt":
from PyQt4 import QtGui
app = QtGui.QApplication(sys.argv)
mygui = Cubi(title="CubeUI")
mygui.setup()
#ex.show()
else:
mygui = Cubi(title="CubeUI")
mygui.setup()
GL.GL_BACK, propConst[k],
backMat[k][sB[stripNum] + i])
# draw vertex
#GL.glVertex3dv(v)
gllib.glVertex3fv(v)
i = i + 1
GL.glEnd()
GL.glPopName()
return 1
if __name__ == '__main__':
import pdb, numpy.oldnumeric as Numeric
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),
# create a Viewer
from DejaVu import Viewer
if ViewerType == 'dejavu':
vi = Viewer()
from DejaVu.Box import Box
from DejaVu.Spheres import Spheres
from DejaVu.Cylinders import Cylinders
from DejaVu.Geom import Geom
from DejaVu.IndexedPolygons import IndexedPolygons
from DejaVu.Points import Points
from DejaVu.glfLabels import GlfLabels
from DejaVu.Polylines import Polylines
elif ViewerType == 'c4d':
import c4d
#from Pmv.hostappInterface import pdb_c4d
import Pmv.hostappInterface.cinema4d.helperC4D as pdb_c4d
vi = pdb_c4d
Box = pdb_c4d.box
Geom = pdb_c4d.newEmpty
IndexedPolygons = pdb_c4d.polygons
Points = pdb_c4d.PointCloudObject
sc = pdb_c4d.getCurrentScene()
dejavumat = vi.createDejaVuColorMat()
helper = pdb_c4d
elif ViewerType == 'blender':
import Blender
from Pmv.hostappInterface import pdb_blender
vi = pdb_blender
Box = pdb_blender.box
Geom = pdb_blender.newEmpty
IndexedPolygons = pdb_blender.polygons
GL.glColor3f(1.0, 1.0, 0.0)
GL.glBegin(GL.GL_POINTS)
for i in range(4):
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
'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()
faces = []
for residue in residues:
faces.extend(residue._base_faces)
geom_bases = IndexedPolygons('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()
# create a Viewer
from DejaVu import Viewer
if ViewerType == 'dejavu':
vi = Viewer()
from DejaVu.Box import Box
from DejaVu.Spheres import Spheres
from DejaVu.Cylinders import Cylinders
from DejaVu.Geom import Geom
from DejaVu.IndexedPolygons import IndexedPolygons
from DejaVu.Points import Points
from DejaVu.glfLabels import GlfLabels
from DejaVu.Polylines import Polylines
elif ViewerType == 'c4d':
import c4d
#from Pmv.hostappInterface import pdb_c4d
import Pmv.hostappInterface.cinema4d.helperC4D as pdb_c4d
vi = pdb_c4d
Box = pdb_c4d.box
Geom = pdb_c4d.newEmpty
IndexedPolygons = pdb_c4d.polygons
Points = pdb_c4d.PointCloudObject
sc=pdb_c4d.getCurrentScene()
dejavumat = vi.createDejaVuColorMat()
helper = pdb_c4d
elif ViewerType == 'blender':
import Blender
from Pmv.hostappInterface import pdb_blender
vi = pdb_blender
Box = pdb_blender.box
Geom = pdb_blender.newEmpty
IndexedPolygons = pdb_blender.polygons
if __name__ == '__main__':
from DejaVu.IndexedPolygons import IndexedPolygonsFromFile
geomS = IndexedPolygonsFromFile('cv', 'mesh')
faces = geomS.getFaces()
vertices = geomS.getVertices()
vnormals = geomS.getVNormals()
planePoint = (3., 0., 0.)
planeNormal = (1., 0., 0.)
vertsC, facesC = cap(vertices, faces, planePoint, planeNormal)
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)
( 15.445000, 7.667000, 15.246000 ), (16.093000, 5.705000, 14.039000),
( 13.512000, 5.395000, 12.878000 ), (13.733000, 6.929000, 11.026000)))
nchords=10
nrib=2
nres=46
natoms=2*nres
offset=1.2
width=1.5
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