def getClosestBHtree(coords, mpos):
from bhtree import bhtreelib
tree = bhtreelib.BHtree(coords, None, 10)
index = []
for i in range(len(mpos)):
pos = mpos[i]
result = numpy.zeros(len(coords)).astype('i')
nb = tree.closePoints((pos[0], pos[1], pos[2]), 77.0, result)
index.append(result[:nb])
#index = [result[:tree.closePoints((pos[0],pos[1],pos[2]), 77.0, result )] for pos in mpos]
return index
def collide_bhtree(residues, matrix, mesh):
#object tree
from bhtree import bhtreelib
v = helper.ApplyMatrix(mesh.getVertices(), matrix.reshape(4, 4))
print len(v), v[0], len(coordinates)
tree = bhtreelib.BHtree(tuple(v), None, 10)
#lipids positon
c = []
at = []
res = []
for r in residues:
for a in r:
c.append(a.get_coord())
at.append(a)
res.append(r)
closest = tree.closestPointsArray(numpy.array(c).tolist(), 30, 0)
indices = numpy.nonzero(numpy.greater(closest, 0))
indices_close = numpy.take(closest, indices)
# collide = False
return indices_close[0], at, res
def displayClustersBonds(self, clusters, factor=0.7, ev=1.0):
colors = [getattr(upy_colors, name) for name in upy_colors.cnames]
centers = []
radiiG = []
radiiM = []
radii = []
if clusters is None:
return
for i, cluster in enumerate(clusters):
centers.append(cluster.centroid.coords)
radg = cluster.radiusOfGyration()
radm = cluster.encapsualtingRadius()
self.radg = radg #added by Graham 4/4/11
self.radm = radm #added by Graham 4/4/11
#rad = radg/0.7
rad = radg + factor * (radm - radg)
radiiG.append(radg)
radiiM.append(radm)
radii.append(rad)
ptCoords = [x.coords for x in cluster.points]
# Create a bhtree for the ptCoords using a granility of 10
bht = bhtreelib.BHtree(centers, radiiM, 10)
# find all pairs of atoms for which the distance is less than 1.1
# times the sum of the radii
print("cutoff ", ev)
pairs = bht.closePointsPairsInTree(ev)
bhtreelib.freeBHtree(bht)
# pairs is list of tuple of atom indices.
nbc = len(clusters)
bonds = {}
for i, pair in enumerate(pairs):
# 1- Get the atoms corresponding of the indices of the pair
cl1 = clusters[int(pair[0])]
cl2 = clusters[int(pair[1])]
head = cl1.centroid.coords
tail = cl2.centroid.coords
rad = cl1.radiusOfGyration() + factor * (
cl1.encapsualtingRadius() - cl1.radiusOfGyration()
) #or diameter ?
pinstance = self.helper.getObject("BC")
if pinstance is None:
pinstance = self.helper.Cylinder("BC",
radius=1.,
length=1.,
res=10,
pos=[0., 0., 0.],
parent=None)[0]
cyl = self.helper.getObject("clbond" + str(i))
if cyl is None:
cyl = self.helper.oneCylinder("clbond" + str(i),
head,
tail,
radius=rad,
instance=pinstance,
material=None,
parent=self.CenterSpheres,
color=colors[nbc])
else:
self.helper.updateOneCylinder("clbond" + str(i),
head,
tail,
radius=rad,
color=colors[nbc])
self.clusterCenterCyl["clbond" + str(i)] = [head, tail, rad]
if len(self.clusterCenterCyl) > len(pairs):
for j in range(len(pairs), len(self.clusterCenterCyl)):
# for cy in self.clusterCenterCyl[len(pair):]:
# o=self.clusterCenterCyl[]
self.helper.deleteObject("clbond" + str(j))
def set_surfPtsBht(self, verts):
from bhtree import bhtreelib
self.surfPtsBht = None
if verts:
self.surfPtsBht = bhtreelib.BHtree(verts, None, 10)
# node = pud.addSingleSphereRB(r,name=str(i))
# node.setPos(pos[0],pos[1],pos[2])
# return node
#nodes =[addSphere(rads[i],grdPos[i],i) for i in range(NPT) ]
#node = pud.addMultiSphereRB(rads,grdPos)
#print ("time sphere ",time()-t)
#t=time()
#add the mesh
vertices, faces, fn = tetrahedron(10.0)
meshnode = pud.addMeshRB(vertices, faces)
#print ("time mesh",time()-t)
#computeCollisionTest
#t=time()
srfPts = vertices
from panda3d.core import Mat4, Vec3, Point3
bht = bhtreelib.BHtree(tuple(vertices), None, 10)
returnNullIfFail = 0
closest = bht.closestPointsArray(tuple(grdPos), diag, returnNullIfFail)
hit = []
for i in range(NPT):
start = Point3(grdPos[i][0], grdPos[i][1], grdPos[i][2])
end = Point3(srfPts[closest[i]][0] * diag, srfPts[closest[i]][1] * diag,
srfPts[closest[i]][2] * diag)
res = pud.world.rayTestAll(start, end)
if res.hasHits():
print res.getNumHits()
hit.append(res)
#meshcontacts = pud.world.contactTest(meshnode.node())
#N=meshcontacts.getNumContacts()
#for ct in meshcontacts.getContacts():
# m=ct.getManifoldPoint ()
def set_surfPtsBht(self, verts):
from bhtree import bhtreelib
self.surfPtsBht = None
if verts != None and len(verts):
self.surfPtsBht = bhtreelib.BHtree(verts, None, 10)
self.nbSurfacePoints = len(verts)