def __sub__(self, other):
"""
Return rmsd between two fragments.
Example:
>>> rmsd=fragment1-fragment2
@return: rmsd between fragments
@rtype: float
"""
sup = SVDSuperimposer()
sup.set(self.coords_ca, other.coords_ca)
sup.run()
return sup.get_rms()
def __sub__(self, other):
"""
Return rmsd between two fragments.
Example:
>>> rmsd=fragment1-fragment2
@return: rmsd between fragments
@rtype: float
"""
sup=SVDSuperimposer()
sup.set(self.coords_ca, other.coords_ca)
sup.run()
return sup.get_rms()
def set_atoms(self, fixed, moving):
"""
Put (translate/rotate) the atoms in fixed on the atoms in
moving, in such a way that the RMSD is minimized.
@param fixed: list of (fixed) atoms
@param moving: list of (moving) atoms
@type fixed,moving: [L{Atom}, L{Atom},...]
"""
if not (len(fixed) == len(moving)):
raise PDBException("Fixed and moving atom lists differ in size")
l = len(fixed)
fixed_coord = numpy.zeros((l, 3))
moving_coord = numpy.zeros((l, 3))
for i in range(0, len(fixed)):
fixed_coord[i] = fixed[i].get_coord()
moving_coord[i] = moving[i].get_coord()
sup = SVDSuperimposer()
sup.set(fixed_coord, moving_coord)
sup.run()
self.rms = sup.get_rms()
self.rotran = sup.get_rotran()
def set_atoms(self, fixed, moving):
"""
Put (translate/rotate) the atoms in fixed on the atoms in
moving, in such a way that the RMSD is minimized.
@param fixed: list of (fixed) atoms
@param moving: list of (moving) atoms
@type fixed,moving: [L{Atom}, L{Atom},...]
"""
if not (len(fixed)==len(moving)):
raise PDBException("Fixed and moving atom lists differ in size")
l=len(fixed)
fixed_coord=numpy.zeros((l, 3))
moving_coord=numpy.zeros((l, 3))
for i in range(0, len(fixed)):
fixed_coord[i]=fixed[i].get_coord()
moving_coord[i]=moving[i].get_coord()
sup=SVDSuperimposer()
sup.set(fixed_coord, moving_coord)
sup.run()
self.rms=sup.get_rms()
self.rotran=sup.get_rotran()