def GetOrientTransmat(self, biounit=False, target=False):
cen = np.zeros((3,1))
cenlist = self.Centroid(biounit, target)
cen[0:3] = [[cenlist[0]],[cenlist[1]],[cenlist[2]]]
tmat = translation_matrix(-self.Centroid(biounit, target))
max = 0
farthestxyz = None
for atom in self.IterAtoms(biounit, target):
dist = np.sum((atom.xyz[0:3] - cen)**2)
if dist > max:
farthestxyz = atom.xyz[0:3] - cen
max = dist
firstrotax = np.cross(farthestxyz.transpose().tolist()[0], np.array([1,0,0]))
firstrotang = np.arccos(np.dot(farthestxyz.transpose().tolist()[0], np.array([1,0,0]))/(np.sqrt(np.dot(farthestxyz.transpose().tolist()[0], farthestxyz.transpose().tolist()[0]))))
firstrotmat = rotation_matrix(firstrotang, firstrotax, self.Centroid(biounit, target))
max = 0
firsttransmat = tmat.dot(firstrotmat)
for atom in self.IterAtoms(biounit, target):
dist = sum(firsttransmat.dot(atom.xyz)[1:3]**2)
if dist > max:
secfarthestyz = firsttransmat.dot(atom.xyz)[0:3]
max = dist
secfarthestyz[0] = 0
secondrotax = np.array([1,0,0])
secondrotang = np.arccos(np.dot(secfarthestyz.transpose().tolist()[0], np.array([0,1,0]))/np.sqrt(np.dot(secfarthestyz.transpose().tolist()[0],secfarthestyz.transpose().tolist()[0])))
secondrotmat = rotation_matrix(secondrotang, secondrotax, self.Centroid(biounit, target))
return secondrotmat.dot(firsttransmat)
def RotateSplit(self, angle, direction, point=None, biounit=False, ca=True):
if point==None:
point=[0,0,0]
tmat = translation_matrix(point)
newcentroid = np.array(point) + self.Centroid(biounit, ca)
rotmat = rotation_matrix(angle, direction, newcentroid.tolist())
for atom in self.IterAtoms(biounit):
atom.xyz = rotmat.dot(tmat.dot(atom.xyz))
def PairObjectiveSplit(self, other, angvecpnt, biounit=False, ca=True):
tmat = translation_matrix(angvecpnt[4:7])
newcentroid = np.array(angvecpnt[4:7]) + self.Centroid(biounit, ca)
rotmat = rotation_matrix(angvecpnt[0], angvecpnt[1:4], newcentroid.tolist())
sqdists = []
for atom in (atom for atom in self.IterAtoms(biounit, ca) if atom.pair!=None):
sqdist = np.sum((atom.pair.xyz - rotmat.dot(tmat.dot(atom.xyz)))**2)
if sqdist < 10000000:
sqdists.append(sqdist)
if len(sqdists) > 0:
return np.sqrt(np.mean(sqdists))
else:
return 99.0
def UnbiasedObjective(self, other, angvecpnt, biounit=False, ca=True):
mins = []
tmat = translation_matrix(angvecpnt[4:7])
newcentroid = np.array(angvecpnt[4:7]) + self.Centroid(biounit, ca)
rotmat = rotation_matrix(angvecpnt[0], angvecpnt[1:4], newcentroid.tolist())
if self.counter % 5==0:
oatoms = [oatom for oatom in other.IterAtoms(biounit,ca)]
for satom in self.IterAtoms(biounit,ca):
oatoms.sort(key=lambda atom: np.sum((atom.xyz - rotmat.dot(tmat.dot(satom.xyz)))**2))
satom.nearby = oatoms[:10]
self.counter += 1
for satom in self.IterAtoms(biounit, ca):
mins.append(np.min([np.sum((oatom.xyz - rotmat.dot(tmat.dot(satom.xyz)))**2) for oatom in satom.nearby]))
return np.sqrt(np.mean(mins))
def OverlaySegMat(seg0, seg1):
'''returns 4x4 transformation matrix that will overlay seg0 on seg1. each seg is a line segment represented by a list of two points'''
vec0 = np.array(seg0[1]) - np.array(seg0[0])
vec1 = np.array(seg1[1]) - np.array(seg1[0])
axis = np.cross(vec0, vec1)
if np.allclose([0,0,0],axis):
axis = (0,0,1)
if np.allclose(vec0,vec1):
ang = 0
elif np.allclose(vec0,-vec1):
ang = math.pi
else:
ang = np.arccos(np.dot(vec0, vec1)/(np.sqrt(np.dot(vec0, vec0))*np.sqrt(np.dot(vec1, vec1))))
# if np.isnan(ang):
# ang = math.pi
trans = np.array(seg1[0]) - np.array(seg0[0])
return translation_matrix(trans).dot(rotation_matrix(ang, axis, point=seg0[0]))
def TranslateMat(pnt0, pnt1):
'''returns 4x4 transformation matrix that translates from pnt0 to pnt1'''
vec = np.array(pnt1) - np.array(pnt0)
return translation_matrix(vec)
def Center(self, biounit=False, target=False):
tmat = translation_matrix(-self.Centroid(biounit, target))
self.Transform(tmat, biounit, target)
def RotateBiounit(self, trans, rot):
mat = rotation_matrix(rot[2], (0,0,1), self.Centroid(biounit, ca)).dot(rotation_matrix(rot[1], (0,1,0), self.Centroid(biounit, ca))).dot(rotation_matrix(rot[0], (1,0,0), self.Centroid(biounit, ca))).dot(translation_matrix(trans[0:3]))
for atom in self.IterAtoms(biounit=True):
atom.xyz = mat.dot(atom.xyz)
def Objective(self, other, transrot, biounit=False, ca=True):
now = time.time()
mins = []
mat = rotation_matrix(transrot[5], (0,0,1), self.Centroid(biounit, ca)).dot(rotation_matrix(transrot[4], (0,1,0), self.Centroid(biounit, ca))).dot(rotation_matrix(transrot[3], (1,0,0), self.Centroid(biounit, ca))).dot(translation_matrix(transrot[0:3]))
if self.counter % 10==0:
oatoms = [oatom for oatom in other.IterAtoms(biounit,ca)]
for satom in self.IterAtoms(biounit,ca):
oatoms.sort(key=lambda atom: np.sum((atom.xyz - mat.dot(satom.xyz))**2))
satom.nearby = oatoms[:100]
# satom_gen = self.IterAtoms(biounit,ca)
# for i in range(20):
# satom_gen.next()
# test_satom = satom_gen.next()
# print test_satom.resseq
# for oatom in test_satom.nearby:
# print oatom.resseq
self.counter += 1
for satom in self.IterAtoms(biounit, ca):
mins.append(np.min([np.sum((oatom.xyz - mat.dot(satom.xyz))**2) for oatom in satom.nearby]))
print 'one objective took %f' % (time.time() - now)
print transrot
return np.sqrt(np.mean(mins))