def _fitter_worker(self, tasks, coords, subset_coords, masses, subset_masses, rmsdmat, pbar_counter):
'''
Fitter RMSD Matrix calculator. See encore.confdistmatrix.RMSDMatrixGenerator._fitter_worker for details.
'''
if subset_coords == None:
for i,j in trm_indeces(tasks[0],tasks[1]):
coords[i] -= average(coords[i], axis=0, weights=masses)
coords[j] -= average(coords[j], axis=0, weights=masses)
weights = asarray(masses)/mean(masses)
rmsdmat[(i+1)*i/2+j] = - rmsd(coords[i],coords[j],weights=weights)
pbar_counter.value += 1
else:
for i,j in trm_indeces(tasks[0],tasks[1]):
#masses = asarray(masses)/mean(masses)
summasses = sum(masses)
com_i = average(subset_coords[i], axis=0, weights=subset_masses)
translated_i = coords[i] - com_i
subset1_coords = subset_coords[i] - com_i
com_j = average(subset_coords[j], axis=0, weights=subset_masses)
translated_j = coords[j] - com_j
subset2_coords = subset_coords[j] - com_j
rotamat = rotation_matrix(subset1_coords, subset2_coords, subset_masses)[0]
rotated_i = transpose(dot(rotamat, transpose(translated_i)))
rmsdmat[(i+1)*i/2+j] = MinusRMSD(rotated_i.astype(float64), translated_j.astype(float64), coords[j].shape[0], masses, summasses)
pbar_counter.value += 1
def _fitter_worker(self, tasks, coords, subset_coords, masses,
subset_masses, rmsdmat, pbar_counter):
'''
Fitter RMSD Matrix calculator. See encore.confdistmatrix.RMSDMatrixGenerator._fitter_worker for details.
'''
if subset_coords == None:
for i, j in trm_indeces(tasks[0], tasks[1]):
coords[i] -= average(coords[i], axis=0, weights=masses)
coords[j] -= average(coords[j], axis=0, weights=masses)
weights = asarray(masses) / mean(masses)
rmsdmat[(i + 1) * i / 2 +
j] = -rmsd(coords[i], coords[j], weights=weights)
pbar_counter.value += 1
else:
for i, j in trm_indeces(tasks[0], tasks[1]):
#masses = asarray(masses)/mean(masses)
summasses = sum(masses)
com_i = average(subset_coords[i],
axis=0,
weights=subset_masses)
translated_i = coords[i] - com_i
subset1_coords = subset_coords[i] - com_i
com_j = average(subset_coords[j],
axis=0,
weights=subset_masses)
translated_j = coords[j] - com_j
subset2_coords = subset_coords[j] - com_j
rotamat = rotation_matrix(subset1_coords, subset2_coords,
subset_masses)[0]
rotated_i = transpose(dot(rotamat, transpose(translated_i)))
rmsdmat[(i + 1) * i / 2 + j] = MinusRMSD(
rotated_i.astype(float64), translated_j.astype(float64),
coords[j].shape[0], masses, summasses)
pbar_counter.value += 1
def _fitter_worker(
self, tasks, coords, subset_coords, masses, subset_masses, rmsdmat,
pbar_counter
): # Prototype fitter worker: pairwase align and calculate metric. To be ovverridden in heir classes
'''Fitter worker prototype; to be overriden in derived classes
'''
if subset_coords == None:
for i, j in trm_indeces(tasks[0], tasks[1]):
coords[i] -= average(coords[i], axis=0, weights=masses)
coords[j] -= average(coords[j], axis=0, weights=masses)
pbar_counter.value += 1
pass
else:
for i, j in trm_indeces(tasks[0], tasks[1]):
com_i = average(coords[i], axis=0, weights=masses)
translated_i = coords[i] - com_i
subset1_coords = subset_coords[i] - com_i
com_j = average(coords[j], axis=0, weights=masses)
translated_j = coords[j] - com_j
subset2_coords = subset_coords[j] - com_j
rotamat = rotation_matrix(subset1_coords, subset2_coords,
subset_masses)[0]
rotated_i = transpose(dot(rotamat, transpose(translated_i)))
pbar_counter.value += 1
pass
def _fitter_worker(self, tasks, coords, subset_coords, masses,
subset_masses, rmsdmat, pbar_counter):
'''
Fitter RMSD Matrix calculator: performs least-square fitting between each pair of structures before calculating the RMSD.
**Arguments:**
`tasks` : iterator of int of length 2
Given a triangular matrix written in a row-major order, this worker will calculate RMSD values from element tasks[0] to tasks[1]. Since the matrix is triangular. the trm_indeces function automatically calculates the corrisponding i,j matrix indeces. (see the see encore.utils.TriangularMatrix for details).
`coords` : numpy.array
Array of the ensemble coordinates
`subset_coords` : numpy.array or None
Array of the coordinates used for fitting
`masses` : numpy.array or None
Array of atomic masses, having the same order as the coordinates array. If None, coords will be used instead.
`subset_masses` : numpy.array
Array of atomic masses, having the same order as the subset_coords array
`rmsdmat` : encore.utils.TriangularMatrix
Memory-shared triangular matrix object
`pbar_counter` : multiprocessing.RawValue
Thread-safe shared value. This counter is updated at every cycle and used to evaluate the progress of each worker.
'''
if subset_coords == None:
for i, j in trm_indeces(tasks[0], tasks[1]):
coords[i] -= average(coords[i], axis=0, weights=masses)
coords[j] -= average(coords[j], axis=0, weights=masses)
weights = asarray(masses) / mean(masses)
rmsdmat[(i + 1) * i / 2 + j] = rmsd(coords[i],
coords[j],
weights=weights)
pbar_counter.value += 1
else:
for i, j in trm_indeces(tasks[0], tasks[1]):
summasses = sum(masses)
subset_weights = asarray(subset_masses) / mean(subset_masses)
com_i = average(subset_coords[i],
axis=0,
weights=subset_masses)
translated_i = coords[i] - com_i
subset1_coords = subset_coords[i] - com_i
com_j = average(subset_coords[j],
axis=0,
weights=subset_masses)
translated_j = coords[j] - com_j
subset2_coords = subset_coords[j] - com_j
rotamat = rotation_matrix(subset1_coords, subset2_coords,
subset_weights)[0]
rotated_i = transpose(dot(rotamat, transpose(translated_i)))
rmsdmat[(i + 1) * i / 2 + j] = PureRMSD(
rotated_i.astype(float64), translated_j.astype(float64),
coords[j].shape[0], masses, summasses)
pbar_counter.value += 1
def _fitter_worker(self, tasks, coords, subset_coords, masses, subset_masses, rmsdmat, pbar_counter):
'''
Fitter RMSD Matrix calculator: performs least-square fitting between each pair of structures before calculating the RMSD.
**Arguments:**
`tasks` : iterator of int of length 2
Given a triangular matrix written in a row-major order, this worker will calculate RMSD values from element tasks[0] to tasks[1]. Since the matrix is triangular. the trm_indeces function automatically calculates the corrisponding i,j matrix indeces. (see the see encore.utils.TriangularMatrix for details).
`coords` : numpy.array
Array of the ensemble coordinates
`subset_coords` : numpy.array or None
Array of the coordinates used for fitting
`masses` : numpy.array or None
Array of atomic masses, having the same order as the coordinates array. If None, coords will be used instead.
`subset_masses` : numpy.array
Array of atomic masses, having the same order as the subset_coords array
`rmsdmat` : encore.utils.TriangularMatrix
Memory-shared triangular matrix object
`pbar_counter` : multiprocessing.RawValue
Thread-safe shared value. This counter is updated at every cycle and used to evaluate the progress of each worker.
'''
if subset_coords == None:
for i,j in trm_indeces(tasks[0],tasks[1]):
coords[i] -= average(coords[i], axis=0, weights=masses)
coords[j] -= average(coords[j], axis=0, weights=masses)
weights = asarray(masses)/mean(masses)
rmsdmat[(i+1)*i/2+j] = rmsd(coords[i],coords[j],weights=weights)
pbar_counter.value += 1
else:
for i,j in trm_indeces(tasks[0],tasks[1]):
summasses = sum(masses)
subset_weights = asarray(subset_masses)/mean(subset_masses)
com_i = average(subset_coords[i], axis=0, weights=subset_masses)
translated_i = coords[i] - com_i
subset1_coords = subset_coords[i] - com_i
com_j = average(subset_coords[j], axis=0, weights=subset_masses)
translated_j = coords[j] - com_j
subset2_coords = subset_coords[j] - com_j
rotamat = rotation_matrix(subset1_coords, subset2_coords, subset_weights)[0]
rotated_i = transpose(dot(rotamat, transpose(translated_i)))
rmsdmat[(i+1)*i/2+j] = PureRMSD(rotated_i.astype(float64), translated_j.astype(float64), coords[j].shape[0], masses, summasses)
pbar_counter.value += 1
def _simple_worker(self, tasks, coords, masses, rmsdmat, pbar_counter):
'''
Simple RMSD Matrix calculator.
**Arguments:**
`tasks` : iterator of int of length 2
Given a triangular matrix, this worker will calculate RMSD values from element tasks[0] to tasks[1]. Since the matrix is triangular, the trm_indeces matrix automatically calculates the corrisponding i,j matrix indices. The matrix is written as an array in a row-major order (see the TriangularMatrix class for details).
`coords` : numpy.array
Array of the ensemble coordinates
`masses` : numpy.array
Array of atomic masses, having the same order as the coordinates array
`rmsdmat` : encore.utils.TriangularMatrix
Memory-shared triangular matrix object
`pbar_counter` : multiprocessing.RawValue
Thread-safe shared value. This counter is updated at every cycle and used to evaluate the progress of each worker.
'''
for i,j in trm_indeces(tasks[0],tasks[1]):
#masses = asarray(masses)/mean(masses)
summasses = sum(masses)
rmsdmat[(i+1)*i/2+j] = PureRMSD(coords[i].astype(float64), coords[j].astype(float64), coords[j].shape[0], masses, summasses)
pbar_counter.value += 1
def _simple_worker(self, tasks, coords, masses, rmsdmat, pbar_counter):
'''
Simple RMSD Matrix calculator.
**Arguments:**
`tasks` : iterator of int of length 2
Given a triangular matrix, this worker will calculate RMSD values from element tasks[0] to tasks[1]. Since the matrix is triangular, the trm_indeces matrix automatically calculates the corrisponding i,j matrix indices. The matrix is written as an array in a row-major order (see the TriangularMatrix class for details).
`coords` : numpy.array
Array of the ensemble coordinates
`masses` : numpy.array
Array of atomic masses, having the same order as the coordinates array
`rmsdmat` : encore.utils.TriangularMatrix
Memory-shared triangular matrix object
`pbar_counter` : multiprocessing.RawValue
Thread-safe shared value. This counter is updated at every cycle and used to evaluate the progress of each worker.
'''
for i, j in trm_indeces(tasks[0], tasks[1]):
#masses = asarray(masses)/mean(masses)
summasses = sum(masses)
rmsdmat[(i + 1) * i / 2 + j] = PureRMSD(coords[i].astype(float64),
coords[j].astype(float64),
coords[j].shape[0], masses,
summasses)
pbar_counter.value += 1
def _simple_worker(self, tasks, coords, masses, rmsdmat, pbar_counter):
'''
Simple RMSD Matrix calculator. See encore.confdistmatrix.RMSDMatrixGenerator._simple_worker for details.
'''
for i,j in trm_indeces(tasks[0],tasks[1]):
#masses = asarray(masses)/mean(masses)
summasses = sum(masses)
rmsdmat[(i+1)*i/2+j] = MinusRMSD(coords[i].astype(float64), coords[j].astype(float64), coords[j].shape[0], masses, summasses)
pbar_counter.value += 1
def _simple_worker(self, tasks, coords, masses, rmsdmat, pbar_counter):
'''
Simple RMSD Matrix calculator. See encore.confdistmatrix.RMSDMatrixGenerator._simple_worker for details.
'''
for i, j in trm_indeces(tasks[0], tasks[1]):
#masses = asarray(masses)/mean(masses)
summasses = sum(masses)
rmsdmat[(i + 1) * i / 2 + j] = MinusRMSD(coords[i].astype(float64),
coords[j].astype(float64),
coords[j].shape[0],
masses, summasses)
pbar_counter.value += 1
def _fitter_worker(self, tasks, coords, subset_coords, masses, subset_masses, rmsdmat, pbar_counter): # Prototype fitter worker: pairwase align and calculate metric. To be ovverridden in heir classes
'''Fitter worker prototype; to be overriden in derived classes
'''
if subset_coords == None:
for i,j in trm_indeces(tasks[0],tasks[1]):
coords[i] -= average(coords[i], axis=0, weights=masses)
coords[j] -= average(coords[j], axis=0, weights=masses)
pbar_counter.value += 1
pass
else:
for i,j in trm_indeces(tasks[0],tasks[1]):
com_i = average(coords[i], axis=0, weights=masses)
translated_i = coords[i] - com_i
subset1_coords = subset_coords[i] - com_i
com_j = average(coords[j], axis=0, weights=masses)
translated_j = coords[j] - com_j
subset2_coords = subset_coords[j] - com_j
rotamat = rotation_matrix(subset1_coords, subset2_coords, subset_masses)[0]
rotated_i = transpose(dot(rotamat, transpose(translated_i)))
pbar_counter.value += 1
pass
def _simple_worker(self, tasks, coords, masses, rmsdmat, pbar_counter):
'''Simple worker prototype; to be overriden in derived classes
'''
for i,j in trm_indeces(tasks[0],tasks[1]):
pass
def _simple_worker(self, tasks, coords, masses, rmsdmat, pbar_counter):
'''Simple worker prototype; to be overriden in derived classes
'''
for i, j in trm_indeces(tasks[0], tasks[1]):
pass
