def compareStructures(coords1, coords2):
for refmol1 in xrange(coords1.nrigid):
for refmol2 in xrange(refmol1, coords1.nrigid):
x1 = coords1.posRigid[refmol1]
x2 = coords2.posRigid[refmol2]
pref1 = coords1.rotRigid[refmol1]
pref2 = coords2.rotRigid[refmol2]
#print "pref",pref1,pref2
M = vec3.invert3x3(rotations.aa2mx(pref1))
M = np.dot(rotations.aa2mx(pref2), M)
# print x1,x2
ptest = pref1
ptrans = rotations.mx2aa(rotations.np.dot(M, rotations.aa2mx(ptest)))
#print "---------------- start try",refmol1,refmol2
match1 = compareTransformed(coords1, coords2, x1, x2, M)
match2 = compareTransformed(coords2, coords1, x2, x1, vec3.invert3x3(M))
if(match1 and match2):
#print "Structures match"
return True
#import dmagmin_ as GMIN
#GMIN.writeCIF("1.cif", coords1.coords)
#GMIN.writeCIF("2.cif", coords2.coords)
#import pickle
#pickle.dump(coords1, open("1.dat", "w"))
#pickle.dump(coords2, open("2.dat", "w"))
#exit()
return False
def compareTransformed(coords1, coords2, x1, x2, M):
# the lattice matrix
ml1 = lattice.lowerTriangular(coords1.lattice)
ml2 = lattice.lowerTriangular(coords2.lattice)
# the inerse lattice matrix
iml2 = vec3.invert3x3(ml2)
for i in xrange(coords1.nrigid):
ptest = coords1.rotRigid[i]
ptrans = rotations.mx2aa(rotations.np.dot(M, rotations.aa2mx(ptest)))
for d in [np.zeros(3),[0.,1.,0.],[0.,1.,0.],[0.,0.,1.]]:
xtest = coords1.posRigid[i] + np.array(d) - x1
xtrans = np.dot(iml2, np.dot(M, np.dot(ml1, xtest)))
match = False
for j in xrange(coords1.nrigid):
dx = coords2.posRigid[j] - xtrans - x2
dx = dx - np.floor(dx)
dx[dx>0.8]-=1.0
dp = rotations.mx2aa(np.dot(vec3.invert3x3(rotations.aa2mx(ptrans)),rotations.aa2mx(coords2.rotRigid[j])))
match = np.linalg.norm(np.dot(ml2, dx)) < tol_shift \
and np.linalg.norm(dp) < tol_rot
if(match):
break
if(not match):
return False
return True