def oneVsFollowing(self, conformation_number):
"""
Calculates the RMSD between a reference conformation and all other conformations with an id greater than it.
If fitting symmetry groups are used, input coordinates won't be modified (as it works with coordinate copies).
@param conformation_number: The id of the reference structure.
@return: A numpy array of RMSD values.
@author: vgil
@date: 26/11/2012
"""
np_coords_fit, np_coords_calc = self.__coords_reshaping()
if self.fit_symmetry_groups == []:
rmsds = pyRMSD.calculators.oneVsFollowing(
availableCalculators()[self.calculator_type], np_coords_fit,
self.number_of_fitting_atoms, np_coords_calc,
self.number_of_calculation_atoms, conformation_number,
self.number_of_conformations, self.calc_symmetry_groups,
self.__number_of_threads, self.__threads_per_block,
self.__blocks_per_grid)
else:
# If we have fitting symmetry groups, we have to try with all possible combinations.
# Calculation symmetry groups are applied at C level, changing the way RMSD is calculated.
symm_rmsds = []
for permutation in symm_permutations(self.fit_symmetry_groups):
# Copy the coordinates and convert to matrix form for ease of indexing
coords_copy = numpy.array(np_coords_fit,
copy=True,
dtype=numpy.float64)
coords_copy.shape = (self.number_of_conformations,
self.number_of_fitting_atoms, 3)
# Apply the changes to reference
for symm_group in permutation:
# Do it only if the symm. group is not permuted. Otherwise we would always permute!
if not symm_group in self.fit_symmetry_groups:
for symm_pair in symm_group:
swap_atoms(coords_copy[conformation_number],
symm_pair[0], symm_pair[1])
# Flatten again to feed the C calculator
coords_copy.shape = (self.number_of_conformations *
self.number_of_fitting_atoms * 3)
# And calculate the RMSD of this permutation
symm_rmsds.append(
pyRMSD.calculators.oneVsFollowing(
availableCalculators()[self.calculator_type],
coords_copy, self.number_of_fitting_atoms,
np_coords_calc, self.number_of_calculation_atoms,
conformation_number, self.number_of_conformations,
self.calc_symmetry_groups, self.__number_of_threads,
self.__threads_per_block, self.__blocks_per_grid))
# Pick the minimum rmsd of all possibilities.
rmsds = min_rmsd_of_rmsds_list(numpy.array(symm_rmsds))
return rmsds
def test_symm_group_permutations(self):
groups = [
[ [1,2] ],
[ [3,4],[5,6] ]
]
expected_permutations = [
[ [[1,2]], [[3,4], [5,6]]],
[ [[1,2]], [[4,3], [6,5]]],
[ [[2,1]], [[3,4], [5,6]]],
[ [[2,1]], [[4,3], [6,5]]]
]
for i, perm in enumerate(symm_permutations(groups)):
self.assertSequenceEqual(expected_permutations[i], perm)
def oneVsFollowing(self, conformation_number):
"""
Calculates the RMSD between a reference conformation and all other conformations with an id greater than it.
If fitting symmetry groups are used, input coordinates won't be modified (as it works with coordinate copies).
@param conformation_number: The id of the reference structure.
@return: A numpy array of RMSD values.
@author: vgil
@date: 26/11/2012
"""
np_coords_fit, np_coords_calc = self.__coords_reshaping()
if self.fit_symmetry_groups == []:
rmsds = pyRMSD.calculators.oneVsFollowing(
availableCalculators()[self.calculator_type],
np_coords_fit,
self.number_of_fitting_atoms,
np_coords_calc,
self.number_of_calculation_atoms,
conformation_number,
self.number_of_conformations,
self.calc_symmetry_groups,
self.__number_of_threads,
self.__threads_per_block,
self.__blocks_per_grid,
)
else:
# If we have fitting symmetry groups, we have to try with all possible combinations.
# Calculation symmetry groups are applied at C level, changing the way RMSD is calculated.
symm_rmsds = []
for permutation in symm_permutations(self.fit_symmetry_groups):
# Copy the coordinates and convert to matrix form for ease of indexing
coords_copy = numpy.array(np_coords_fit, copy=True, dtype=numpy.float64)
coords_copy.shape = (self.number_of_conformations, self.number_of_fitting_atoms, 3)
# Apply the changes to reference
for symm_group in permutation:
# Do it only if the symm. group is not permuted. Otherwise we would always permute!
if not symm_group in self.fit_symmetry_groups:
for symm_pair in symm_group:
swap_atoms(coords_copy[conformation_number], symm_pair[0], symm_pair[1])
# Flatten again to feed the C calculator
coords_copy.shape = self.number_of_conformations * self.number_of_fitting_atoms * 3
# And calculate the RMSD of this permutation
symm_rmsds.append(
pyRMSD.calculators.oneVsFollowing(
availableCalculators()[self.calculator_type],
coords_copy,
self.number_of_fitting_atoms,
np_coords_calc,
self.number_of_calculation_atoms,
conformation_number,
self.number_of_conformations,
self.calc_symmetry_groups,
self.__number_of_threads,
self.__threads_per_block,
self.__blocks_per_grid,
)
)
# Pick the minimum rmsd of all possibilities.
rmsds = min_rmsd_of_rmsds_list(numpy.array(symm_rmsds))
return rmsds