def fit_by_ndx(ref, model, ndx1, ndx2):
crd1 = map(lambda i: ref.atoms[i-1].x, ndx1)
crd2 = map(lambda i: model.atoms[i-1].x, ndx2)
assert( len(crd1) == len(crd2) )
m = map(lambda x: 1., crd1) # dummy array
v = _p.center_vec( crd1 )
v2 = _p.center_vec( crd2 )
R = _p.calc_fit_R(crd1, crd2, m)
model.translate( [-v2[0], -v2[1], -v2[2] ] )
apply_fit_R( model.atoms, R)
model.translate( v )
def fit_atoms( fit_atoms1, fit_atoms2, rot_atoms2 ):
cs1 = map(lambda a: a.x, fit_atoms1)
cs2 = map(lambda a: a.x, fit_atoms2)
assert len(cs1) == len(cs2)
m = map(lambda x: 1., cs1) # dummy array
v = _p.center_vec( cs1 )
v2 = _p.center_vec( cs2 )
R = _p.calc_fit_R(cs1, cs2, m)
for atom in rot_atoms2:
atom.x[0]-=v2[0]
atom.x[1]-=v2[1]
atom.x[2]-=v2[2]
apply_fit_R( rot_atoms2, R)
for atom in rot_atoms2:
atom.x[0]+=v[0]
atom.x[1]+=v[1]
atom.x[2]+=v[2]
def fit(model1, model2, atom_names = []):
if atom_names:
subset1 = model1.fetch_atoms( atom_names )
subset2 = model2.fetch_atoms( atom_names )
cs1 = map(lambda a: a.x, subset1)
cs2 = map(lambda a: a.x, subset2)
else:
cs1 = model1.coords()
cs2 = model2.coords()
assert( len(cs1) == len(cs2) )
m = map(lambda x: 1., cs1) # dummy array
v = _p.center_vec( cs1 )
v2 = _p.center_vec( cs2 )
R = _p.calc_fit_R(cs1, cs2, m)
model2.translate( [-v2[0], -v2[1], -v2[2] ] )
apply_fit_R( model2.atoms, R)
model2.translate( v )
def fit_atoms( fit_atoms1, fit_atoms2, rot_atoms2 ):
cs1 = map(lambda a: a.x, fit_atoms1)
cs2 = map(lambda a: a.x, fit_atoms2)
assert len(cs1) == len(cs2)
m = map(lambda x: 1., cs1) # dummy array
v = _p.center_vec( cs1 )
v2 = _p.center_vec( cs2 )
R = _p.calc_fit_R(cs1, cs2, m)
for atom in rot_atoms2:
atom.x[0]-=v2[0]
atom.x[1]-=v2[1]
atom.x[2]-=v2[2]
apply_fit_R( rot_atoms2, R)
for atom in rot_atoms2:
atom.x[0]+=v[0]
atom.x[1]+=v[1]
atom.x[2]+=v[2]
def fit(model1, model2, atom_names = []):
if atom_names:
subset1 = model1.fetch_atoms( atom_names )
subset2 = model2.fetch_atoms( atom_names )
cs1 = map(lambda a: a.x, subset1)
cs2 = map(lambda a: a.x, subset2)
else:
cs1 = model1.coords()
cs2 = model2.coords()
assert( len(cs1) == len(cs2) )
m = map(lambda x: 1., cs1) # dummy array
v = _p.center_vec( cs1 )
v2 = _p.center_vec( cs2 )
R = _p.calc_fit_R(cs1, cs2, m)
model2.translate( [-v2[0], -v2[1], -v2[2] ] )
apply_fit_R( model2.atoms, R)
model2.translate( v )
def calc_fit_R(cs1, cs2, m):
R = _p.calc_fit_R(cs1, cs2, m)
return (R)