def SuperpositionMatrix ( self, AllowPerturbations = False, AllowFlip = False ):
"""
returns rotation between 0th and 1st HierSetOfPoints
"""
Array1 = self.Content[0]. NonHierarchicalSetOfPoints ( ). Array ( )
if AllowPerturbations:
RMSDs = [ ]; Matrices = [ ];
minRMSD = 1000.0
Centres1 = self. Content[1] # bo to przeciez ten drugi, blargh
# a wiec ten pierwszy powinien byc zrobiony juz tutaj
for Perturbation in Perturbations( len ( self.Content [1] ) ):
Centres1Perturbation = [ Centres1 [i] for i in Perturbation ]
Array2 = Centres1Perturbation. NonHierarchicalSetOfPoints ( ). Array ( )
Matrices. append ( optimal_superposition ( Array1, Array2 ).T )
RMSDs. append ( rmsd (Array1, Array2) )
if AllowFlip:
FlippedSet = [ Helix[::-1] for Helix in Centres1Perturbation ]
Array2 = FlippedSet. NonHierarchicalSetOfPoints ( ). Array ( )
Matrices. append ( optimal_superposition ( Array1, Array2 ).T )
RMSDs. append ( rmsd (Array1, Array2) )
minRMSD = min ( RMSDs );
return Matrices [ RMSDs. index ( minRMSD) ]
else:
Array2 = self.Content[1]. NonHierarchicalSetOfPoints ( ). Array ( )
return optimal_superposition( Array1, Array2 ).T # ok a wiec gdzie jest translacja do zera?
def RotationMatrix ( self ):
"""
returns a rotation from 0th vector to 1st vector
"""
print np.array(self.Content[0]).shape
print np.array(self.Content[1])
return optimal_superposition( np.array( [ [ 0.0, 0.0, 0.0 ], self.Content[0] ] ), np.array( [ [ 0.0, 0.0, 0.0 ], self.Content[1] ] ) ).T
def testSuperPosition(self):
"Tests that rmsd=0 works"
for i in xrange(0, 20):
n = 10
ref_vecs = [vector3d.RandomVec() for i in xrange(0, n)]
ref_crds = make_crds(ref_vecs)
m = vector3d.RandomOriginRotation()
mov_vecs = [m.transform_vec(r) for r in ref_vecs]
mov_crds = make_crds(mov_vecs)
matrix = match.optimal_superposition(ref_crds, mov_crds)
mov_crds[:,:] = numpy.dot(mov_crds, matrix.transpose())
for crd1, crd2 in zip(ref_crds, mov_crds):
for i in xrange(0,3):
self.assertAlmostEqual(crd1[i], crd2[i])
def SuperpositionMatrix ( self, AllowPerturbations = False, AllowFlip = False ):
"""
returns rotation from 0th SetOfPoints on 1st SetOfPoints
"""
print self[0][0]
ciag1 = []
for i in range ( len ( self [0] ) ):
for j in range ( len ( self [0][0] ) ):
Punkt1 = [ float ( Coord ) for Coord in self[0][i][j] ]
ciag1. append ( Punkt1 )
# i powinien chodzic
# ciag 1 jest gotowy
# musze sie doksztalcic z pythona znowu
if AllowPerturbations:
RMSDs = [ ]; Matrices = [ ];
minRMSD = 1000.0;
Centres1 = self.Content[1]
for Perturbation in Perturbations( len ( self.Content[1] ) ):
Centres1Perturbation = [ Centres1 [i] for i in Perturbation ]
ciag2 = []
for i in range ( len (self[0] ) ):
for j in range ( len(self[0][0]) ):
el2 = [ float (c) for c in Centres1Perturbation [i][j] ]
ciag2. append ( el2 );
Matrices. append ( optimal_superposition ( np.array(ciag1), np.array(ciag2) ).T )
RMSDs. append ( rmsd (np.array(ciag1), np.array(ciag2)) )
if AllowFlip:
ciag2 = []
for i in range ( len (self[0] ) ):
for j in range ( len(self[0][0])-1,-1,-1 ):
el2 = [ float (c) for c in Centres1Perturbation [i][j] ]
ciag2. append ( el2 );
Matrices. append ( optimal_superposition ( np.array(ciag1), np.array(ciag2) ).T )
RMSDs. append ( rmsd (np.array(ciag1), np.array(ciag2)) )
minRMSD = min ( RMSDs );
return Matrices [ RMSDs. index ( minRMSD) ]
else:
ciag2 = [ ]
for i in range ( len (self[0] ) ):
for j in range ( len(self[0][0]) ):
el2 = [ float (c) for c in self[1][i][j] ]
ciag2. append ( el2 );
return optimal_superposition( np.array(ciag1), np.array(ciag2) ).T # ok a wiec gdzie jest translacja do zera?
def SuperpositionMatrix ( self, AllowPerturbations = False, AllowFlip = False ):
"""
returns rotation matrix from 0th HierSetOfPoints to 1stHierSetOfPoints
"""
HierarchicalSetOfPointsInstance1, HierarchicalSetOfPointsInstance2 = self. Content
NonHierarchicalSetOfPointsInstance1 = [ ]
for SetOfPointsInstance in self. Content [0]:
NonHierarchicalSetOfPointsInstance1. append ( SetOfPointsInstance )
# pierwszy set jest gotowy
if AllowPerturbations:
RMSDs = [ ]; Matrices = [ ];
minRMSD = 1000.0
for Perturbation in Perturbations( len ( self. Content[1] ) ):
PerturbationInstance = [ self. Content [ 1 ] [i] for i in Perturbation ]
NonHierarchicalSetOfPointsInstance2 = [ ]
for SetOfPointsInstance in PerturbationInstance:
NonHierarchicalSetOfPointsInstance2. append ( SetOfPointsInstance )
Matrices. append ( optimal_superposition ( np.array(ciag1), np.array(ciag2) ).T )
RMSDs. append ( rmsd (np.array(ciag1), np.array(ciag2)) )
if AllowFlip:
ciag2 = []
for i in range ( len (self[0] ) ):
for j in range ( len(self[0][0])-1,-1,-1 ):
el2 = [ float (c) for c in Centres1Perturbation [i][j] ]
ciag2. append ( el2 );
Matrices. append ( optimal_superposition ( np.array(ciag1), np.array(ciag2) ).T )
RMSDs. append ( rmsd (np.array(ciag1), np.array(ciag2)) )
minRMSD = min ( RMSDs );
return Matrices [ RMSDs. index ( minRMSD) ]
else:
ciag2 = [ ]
for i in range ( len (self[0] ) ):
for j in range ( len(self[0][0]) ):
el2 = [ float (c) for c in self[1][i][j] ]
ciag2. append ( el2 );
return optimal_superposition( np.array(ciag1), np.array(ciag2) ).T # ok a wiec gdzie jest translacja do zera?
