SYMBOL INDEX (596 symbols across 57 files)

FILE: examples/qmlearn.py
  function data (line 7) | def data():
  function preprocessing (line 36) | def preprocessing():
  function representations (line 60) | def representations():
  function kernels (line 87) | def kernels():
  function models (line 126) | def models():
  function pipelines (line 163) | def pipelines():
  function pipelines_2 (line 213) | def pipelines_2():
  function pipelines_3 (line 242) | def pipelines_3():
  function cross_validation (line 271) | def cross_validation():

FILE: examples/test_qmlearn_energy.py
  function parse_qm7_data (line 22) | def parse_qm7_data(num=100):
  function parse_qm9_data (line 41) | def parse_qm9_data(num=100):
  function csv2data (line 58) | def csv2data(csv_filename, num=10):
  function npz2data (line 122) | def npz2data(npy_filename, num=10):
  function pipeline (line 170) | def pipeline():

FILE: examples/test_qmlearn_force.py
  function parse_qm7_data (line 23) | def parse_qm7_data(num=100):
  function parse_qm9_data (line 42) | def parse_qm9_data(num=100):
  function csv2data (line 59) | def csv2data(csv_filename, num=10):
  function npz2data (line 123) | def npz2data(npy_filename, num=10):
  function pipeline (line 171) | def pipeline():

FILE: mkldiscover.py
  function mkl_exists (line 28) | def mkl_exists(verbose=False):

FILE: qml/aglaia/aglaia.py
  class _NN (line 48) | class _NN(BaseEstimator):
    method __init__ (line 54) | def __init__(self, hidden_layer_sizes, l1_reg, l2_reg, batch_size, lea...
    method _set_activation_function (line 143) | def _set_activation_function(self, activation_function):
    method _set_l1_reg (line 172) | def _set_l1_reg(self, l1_reg):
    method _set_l2_reg (line 184) | def _set_l2_reg(self, l2_reg):
    method _set_batch_size (line 196) | def _set_batch_size(self, batch_size):
    method _set_learning_rate (line 214) | def _set_learning_rate(self, learning_rate):
    method _set_iterations (line 226) | def _set_iterations(self, iterations):
    method _set_tf_dtype (line 239) | def _set_tf_dtype(self, tf_dtype):
    method _set_optimiser_param (line 258) | def _set_optimiser_param(self, beta1, beta2, epsilon, rho, initial_acc...
    method _set_optimiser_type (line 307) | def _set_optimiser_type(self, optimiser):
    method _set_optimiser (line 333) | def _set_optimiser(self):
    method _set_scoring_function (line 364) | def _set_scoring_function(self, scoring_function):
    method _set_hidden_layers_sizes (line 379) | def _set_hidden_layers_sizes(self, hidden_layer_sizes):
    method _set_tensorboard (line 401) | def _set_tensorboard(self, tensorboard, store_frequency, tensorboard_s...
    method _init_weight (line 440) | def _init_weight(self, n1, n2, name):
    method _init_bias (line 461) | def _init_bias(self, n, name):
    method _generate_weights (line 477) | def _generate_weights(self, n_out):
    method _l2_loss (line 509) | def _l2_loss(self, weights):
    method _l1_loss (line 526) | def _l1_loss(self, weights):
    method _get_batch_size (line 543) | def _get_batch_size(self):
    method _set_slatm_parameters (line 572) | def _set_slatm_parameters(self, params):
    method _set_acsf_parameters (line 589) | def _set_acsf_parameters(self, params):
    method score (line 606) | def score(self, x, y=None, dy=None, classes=None):
    method _score (line 626) | def _score(self, x, y=None, dy=None, classes=None):
    method generate_compounds (line 651) | def generate_compounds(self, filenames):
    method generate_representation (line 673) | def generate_representation(self, xyz=None, classes=None, method='fort...
    method set_properties (line 703) | def set_properties(self, properties):
    method set_representations (line 719) | def set_representations(self, representations):
    method set_gradients (line 738) | def set_gradients(self, gradients):
    method set_classes (line 756) | def set_classes(self, classes):
    method fit (line 772) | def fit(self, x, y=None, dy=None, classes=None):
    method _check_slatm_values (line 790) | def _check_slatm_values(self):
    method _check_acsf_values (line 816) | def _check_acsf_values(self):
    method _get_msize (line 849) | def _get_msize(self, pad = 0):
    method _get_asize (line 871) | def _get_asize(self, pad = 0):
    method _get_slatm_mbtypes (line 900) | def _get_slatm_mbtypes(self, arr):
    method _get_xyz_from_compounds (line 913) | def _get_xyz_from_compounds(self, indices):
    method _get_properties (line 945) | def _get_properties(self, indices):
    method _get_classes (line 957) | def _get_classes(self, indices):
    method _generate_compounds_from_data (line 985) | def _generate_compounds_from_data(self, xyz, classes):
    method predict (line 1001) | def predict(self, x, classes=None):
  class MRMP (line 1023) | class MRMP(_NN):
    method __init__ (line 1030) | def __init__(self, hidden_layer_sizes = (5,), l1_reg = 0.0, l2_reg = 0...
    method _initialise_representation (line 1051) | def _initialise_representation(self, representation, parameters):
    method _set_representation (line 1081) | def _set_representation(self, representation):
    method _generate_representations_from_data (line 1095) | def _generate_representations_from_data(self, xyz, classes, method):
    method _generate_representations_from_compounds (line 1115) | def _generate_representations_from_compounds(self, method):
    method _fit (line 1176) | def _fit(self, x, y, dy, classes):
    method _model (line 1271) | def _model(self, x, weights, biases):
    method _score_r2 (line 1299) | def _score_r2(self, x, y=None, dy=None, classes=None):
    method _score_mae (line 1323) | def _score_mae(self, x, y=None, dy=None, classes=None):
    method _score_rmse (line 1349) | def _score_rmse(self, x, y=None, dy=None, classes=None):
    method _check_inputs (line 1374) | def _check_inputs(self, x, y, dy, classes):
    method _check_predict_input (line 1430) | def _check_predict_input(self, x, classes):
    method _cost (line 1471) | def _cost(self, y_pred, y, weights):
    method _predict (line 1497) | def _predict(self, x, classes):
    method save_nn (line 1526) | def save_nn(self, save_dir="./saved_model"):
    method load_nn (line 1557) | def load_nn(self, save_dir="saved_model"):
  class ARMP (line 1570) | class ARMP(_NN):
    method __init__ (line 1576) | def __init__(self, hidden_layer_sizes = (5,), l1_reg = 0.0, l2_reg = 0...
    method _initialise_representation (line 1596) | def _initialise_representation(self, representation, parameters):
    method _set_representation (line 1631) | def _set_representation(self, representation):
    method _generate_representations_from_data (line 1639) | def _generate_representations_from_data(self, xyz, classes, method):
    method _generate_acsf_tf (line 1677) | def _generate_acsf_tf(self, xyz, classes):
    method _generate_acsf_fortran (line 1758) | def _generate_acsf_fortran(self, xyz, classes):
    method _generate_representations_from_compounds (line 1821) | def _generate_representations_from_compounds(self, method):
    method _extract_and_pad (line 1854) | def _extract_and_pad(self):
    method _generate_slatm_from_compounds (line 1884) | def _generate_slatm_from_compounds(self):
    method _atomic_model (line 1923) | def _atomic_model(self, x, hidden_layer_sizes, weights, biases):
    method _model (line 1954) | def _model(self, x, zs, element_weights, element_biases):
    method _cost (line 1993) | def _cost(self, y_pred, y, weights_dict):
    method _check_inputs (line 2023) | def _check_inputs(self, x, y, dy, classes):
    method _check_predict_input (line 2084) | def _check_predict_input(self, x, classes):
    method _check_representation_parameters (line 2130) | def _check_representation_parameters(self, parameters):
    method _get_elements_and_pairs (line 2162) | def _get_elements_and_pairs(self, classes):
    method _find_elements (line 2181) | def _find_elements(self, zs):
    method _fit (line 2197) | def _fit(self, x, y, dy, classes):
    method _fit_from_scratch (line 2218) | def _fit_from_scratch(self, x, y, dy, classes):
    method _fit_from_loaded (line 2349) | def _fit_from_loaded(self, x, y, dy, classes):
    method _build_model_from_xyz (line 2428) | def _build_model_from_xyz(self, n_atoms, element_weights, element_bias...
    method _predict (line 2463) | def _predict(self, x, classes):
    method predict_from_xyz (line 2506) | def predict_from_xyz(self, xyz, classes):
    method _score_r2 (line 2542) | def _score_r2(self, x, y=None, dy=None, classes=None):
    method _score_mae (line 2566) | def _score_mae(self, x, y=None, dy=None, classes=None):
    method _score_rmse (line 2595) | def _score_rmse(self, x, y=None, dy=None, classes=None):
    method save_nn (line 2620) | def save_nn(self, save_dir="saved_model"):
    method load_nn (line 2654) | def load_nn(self, save_dir="saved_model"):

FILE: qml/aglaia/graceful_killer.py
  class _GracefulKiller (line 9) | class _GracefulKiller:
    method __init__ (line 12) | def __init__(self):
    method exit_gracefully (line 16) | def exit_gracefully(self,signum, frame):

FILE: qml/aglaia/np_symm_funct.py
  function distance (line 32) | def distance(r1, r2):
  function fc (line 43) | def fc(r_ij, r_c):
  function get_costheta (line 58) | def get_costheta(xyz_i, xyz_j, xyz_k):
  function acsf_rad (line 75) | def acsf_rad(xyzs, Zs, elements, radial_cutoff, radial_rs, eta):
  function acsf_ang (line 125) | def acsf_ang(xyzs, Zs, element_pairs, angular_cutoff, angular_rs, theta_...
  function generate_acsf_np (line 190) | def generate_acsf_np(xyzs, Zs, elements, element_pairs, rcut, acut, nRs2,

FILE: qml/aglaia/symm_funct.py
  function acsf_rad (line 35) | def acsf_rad(xyzs, Zs, radial_cutoff, radial_rs, eta):
  function acsf_ang (line 96) | def acsf_ang(xyzs, Zs, angular_cutoff, angular_rs, theta_s, zeta, eta):
  function sum_rad (line 241) | def sum_rad(pre_sum, Zs, elements_list, radial_rs):
  function sum_ang (line 289) | def sum_ang(pre_sumterm, Zs, element_pairs_list, angular_rs, theta_s):
  function generate_acsf_tf (line 383) | def generate_acsf_tf(xyzs, Zs, elements, element_pairs, rcut, acut,

FILE: qml/aglaia/tensormol_symm_funct.py
  function tf_symmetry_functions_radial_grid (line 32) | def tf_symmetry_functions_radial_grid(xyzs, Zs, radial_cutoff, radial_rs...
  function tf_symmetry_function_angular_grid (line 63) | def tf_symmetry_function_angular_grid(xyzs, Zs, angular_cutoff, angular_...
  function tensormol_acsf (line 129) | def tensormol_acsf(xyzs, Zs, elements, element_pairs, radial_cutoff, ang...

FILE: qml/aglaia/tf_utils.py
  class TensorBoardLogger (line 33) | class TensorBoardLogger(object):
    method __init__ (line 39) | def __init__(self, path):
    method initialise (line 43) | def initialise(self):
    method set_store_frequency (line 52) | def set_store_frequency(self, freq):
    method set_summary_writer (line 55) | def set_summary_writer(self, sess):
    method write_summary (line 58) | def write_summary(self, sess, iteration, feed_dict=None):
    method write_metadata (line 68) | def write_metadata(self, step):
    method write_weight_histogram (line 71) | def write_weight_histogram(self, weights):
    method write_cost_summary (line 77) | def write_cost_summary(self, cost):
  function generate_weights (line 80) | def generate_weights(n_in, n_out, hl):

FILE: qml/arad/arad.py
  function getAngle (line 38) | def getAngle(sp,norms):
  function generate_arad_representation (line 46) | def generate_arad_representation(coordinates, nuclear_charges, size=23, ...
  function get_global_kernels_arad (line 137) | def get_global_kernels_arad(X1, X2, sigmas,
  function get_global_symmetric_kernels_arad (line 184) | def get_global_symmetric_kernels_arad(X1, sigmas,
  function get_local_kernels_arad (line 217) | def get_local_kernels_arad(X1, X2, sigmas,
  function get_local_symmetric_kernels_arad (line 264) | def get_local_symmetric_kernels_arad(X1, sigmas,
  function get_atomic_kernels_arad (line 297) | def get_atomic_kernels_arad(X1, X2, sigmas,
  function get_atomic_symmetric_kernels_arad (line 343) | def get_atomic_symmetric_kernels_arad(X1, sigmas,

FILE: qml/fchl/fchl_electric_field_kernels.py
  function get_atomic_local_electric_field_gradient_kernels (line 132) | def get_atomic_local_electric_field_gradient_kernels(A, B, verbose=False...
  function get_gaussian_process_electric_field_kernels (line 230) | def get_gaussian_process_electric_field_kernels(A, B, verbose=False, fie...
  function get_kernels_ef_field (line 334) | def get_kernels_ef_field(A, B, fields=None, df=0.01, ef_scaling=0.01,\

FILE: qml/fchl/fchl_force_kernels.py
  function get_gaussian_process_kernels (line 43) | def get_gaussian_process_kernels(A, B, verbose=False, dx=0.005, \
  function get_local_gradient_kernels (line 108) | def get_local_gradient_kernels(A, B, verbose=False, dx=0.005,
  function get_local_hessian_kernels (line 173) | def get_local_hessian_kernels(A, B, verbose=False, dx=0.005,
  function get_local_symmetric_hessian_kernels (line 241) | def get_local_symmetric_hessian_kernels(A, verbose=False, dx=0.005,
  function get_force_alphas (line 288) | def get_force_alphas(A, B, F, verbose=False, energy=None, dx=0.005, regu...
  function get_atomic_local_gradient_kernels (line 358) | def get_atomic_local_gradient_kernels(A, B, verbose=False, dx = 0.005,
  function get_atomic_local_gradient_5point_kernels (line 424) | def get_atomic_local_gradient_5point_kernels(A, B, verbose=False, dx = 0...

FILE: qml/fchl/fchl_kernel_functions.py
  function get_gaussian_parameters (line 36) | def get_gaussian_parameters(tags):
  function get_linear_parameters (line 53) | def get_linear_parameters(tags):
  function get_polynomial_parameters (line 68) | def get_polynomial_parameters(tags):
  function get_sigmoid_parameters (line 89) | def get_sigmoid_parameters(tags):
  function get_multiquadratic_parameters (line 108) | def get_multiquadratic_parameters(tags):
  function get_inverse_multiquadratic_parameters (line 126) | def get_inverse_multiquadratic_parameters(tags):
  function get_bessel_parameters (line 144) | def get_bessel_parameters(tags):
  function get_l2_parameters (line 165) | def get_l2_parameters(tags):
  function get_matern_parameters (line 184) | def get_matern_parameters(tags):
  function get_cauchy_parameters (line 213) | def get_cauchy_parameters(tags):
  function get_polynomial2_parameters (line 231) | def get_polynomial2_parameters(tags):
  function get_kernel_parameters (line 249) | def get_kernel_parameters(name, tags):

FILE: qml/fchl/fchl_representations.py
  function generate_representation (line 31) | def generate_representation(coordinates, nuclear_charges,
  function generate_displaced_representations (line 100) | def generate_displaced_representations(coordinates, nuclear_charges,
  function generate_displaced_representations_5point (line 144) | def generate_displaced_representations_5point(coordinates, nuclear_charges,
  function generate_representation_electric_field (line 188) | def generate_representation_electric_field(coordinates, nuclear_charges,

FILE: qml/fchl/fchl_scalar_kernels.py
  function get_local_kernels (line 42) | def get_local_kernels(A, B, verbose=False,\
  function get_local_symmetric_kernels (line 136) | def get_local_symmetric_kernels(A, verbose=False, \
  function get_global_symmetric_kernels (line 212) | def get_global_symmetric_kernels(A, verbose=False, \
  function get_global_kernels (line 288) | def get_global_kernels(A, B, verbose=False, \
  function get_atomic_kernels (line 381) | def get_atomic_kernels(A, B, verbose=False, \
  function get_atomic_symmetric_kernels (line 463) | def get_atomic_symmetric_kernels(A, verbose=False, \
  function get_atomic_local_kernels (line 534) | def get_atomic_local_kernels(A, B, verbose=False, \

FILE: qml/kernels/distance.py
  function manhattan_distance (line 28) | def manhattan_distance(A, B):
  function l2_distance (line 61) | def l2_distance(A, B):
  function p_distance (line 94) | def p_distance(A, B, p = 2):

FILE: qml/kernels/gradient_kernels.py
  function mkl_set_num_threads (line 43) | def mkl_set_num_threads(cores):
  function mkl_get_num_threads (line 57) | def mkl_get_num_threads():
  function get_global_kernel (line 70) | def get_global_kernel(X1, X2, Q1, Q2, SIGMA):
  function get_local_kernels (line 129) | def get_local_kernels(X1, X2, Q1, Q2, SIGMAS):
  function get_local_kernel (line 192) | def get_local_kernel(X1, X2, Q1, Q2, SIGMA):
  function get_local_symmetric_kernels (line 251) | def get_local_symmetric_kernels(X1, Q1, SIGMAS):
  function get_local_symmetric_kernel (line 301) | def get_local_symmetric_kernel(X1, Q1, SIGMA):
  function get_atomic_local_kernel (line 349) | def get_atomic_local_kernel(X1, X2, Q1, Q2, SIGMA):
  function get_atomic_local_gradient_kernel (line 413) | def get_atomic_local_gradient_kernel(X1, X2, dX2, Q1, Q2, SIGMA):
  function get_local_gradient_kernel (line 486) | def get_local_gradient_kernel(X1, X2, dX2, Q1, Q2, SIGMA):
  function get_gdml_kernel (line 558) | def get_gdml_kernel(X1, X2, dX1, dX2, Q1, Q2, SIGMA):
  function get_symmetric_gdml_kernel (line 637) | def get_symmetric_gdml_kernel(X1, dX1, Q1, SIGMA):
  function get_gp_kernel (line 696) | def get_gp_kernel(X1, X2, dX1, dX2, Q1, Q2, SIGMA):
  function get_symmetric_gp_kernel (line 771) | def get_symmetric_gp_kernel(X1, dX1, Q1, SIGMA):

FILE: qml/kernels/kernels.py
  function wasserstein_kernel (line 42) | def wasserstein_kernel(A, B, sigma, p=1, q=1):
  function laplacian_kernel (line 71) | def laplacian_kernel(A, B, sigma):
  function laplacian_kernel_symmetric (line 100) | def laplacian_kernel_symmetric(A, sigma):
  function gaussian_kernel (line 126) | def gaussian_kernel(A, B, sigma):
  function gaussian_kernel_symmetric (line 155) | def gaussian_kernel_symmetric(A, sigma):
  function linear_kernel (line 181) | def linear_kernel(A, B):
  function sargan_kernel (line 209) | def sargan_kernel(A, B, sigma, gammas):
  function matern_kernel (line 245) | def matern_kernel(A, B, sigma, order = 0, metric = "l1"):
  function get_local_kernels_gaussian (line 305) | def get_local_kernels_gaussian(A, B, na, nb, sigmas):
  function get_local_kernels_laplacian (line 346) | def get_local_kernels_laplacian(A, B, na, nb, sigmas):
  function kpca (line 388) | def kpca(K, n=2, centering=True):

FILE: qml/kernels/wrappers.py
  function get_atomic_kernels_laplacian (line 34) | def get_atomic_kernels_laplacian(mols1, mols2, sigmas):
  function get_atomic_kernels_laplacian_symmetric (line 66) | def get_atomic_kernels_laplacian_symmetric(mols, sigmas):
  function arad_local_kernels (line 89) | def arad_local_kernels(mols1, mols2, sigmas,
  function arad_local_symmetric_kernels (line 105) | def arad_local_symmetric_kernels(mols1, sigmas,
  function get_atomic_kernels_laplacian (line 118) | def get_atomic_kernels_laplacian(mols1, mols2, sigmas):
  function get_atomic_kernels_gaussian (line 150) | def get_atomic_kernels_gaussian(mols1, mols2, sigmas):
  function get_atomic_kernels_gaussian_symmetric (line 182) | def get_atomic_kernels_gaussian_symmetric(mols, sigmas):

FILE: qml/math/math.py
  function cho_invert (line 36) | def cho_invert(A):
  function cho_solve (line 62) | def cho_solve(A, y, l2reg=0.0, destructive=False):
  function bkf_invert (line 113) | def bkf_invert(A):
  function bkf_solve (line 140) | def bkf_solve(A, y):
  function svd_solve (line 180) | def svd_solve(A, y, rcond=None):
  function qrlq_solve (line 212) | def qrlq_solve(A, y):
  function condition_number (line 239) | def condition_number(A, method="cholesky"):

FILE: qml/models/kernelridge.py
  class GenericKRR (line 34) | class GenericKRR(MLModel):
    method __init__ (line 36) | def __init__(self, targets, representation="coulomb-matrix",
    method _train (line 46) | def _train(self, data):
    method _predict (line 77) | def _predict(self, data):
    method _restore (line 95) | def _restore(self, path, load_kernel=False):
    method _save (line 103) | def _save(self, path, save_kernel=False):

FILE: qml/models/mlmodel.py
  class MLModel (line 25) | class MLModel(object):
    method __init__ (line 27) | def __init__(self, targets):
    method train (line 30) | def train(self, data):
    method predict (line 33) | def predict(self, data):
    method save (line 36) | def save(self, path):
    method restore (line 39) | def restore(self, path):
    method _train (line 42) | def _train(self, data):
    method _predict (line 45) | def _predict(self, data):
    method _save (line 48) | def _save(self, path):
    method _restore (line 51) | def _restore(self, path):

FILE: qml/qmlearn/data.py
  class Data (line 10) | class Data(object):
    method __init__ (line 17) | def __init__(self, filenames=None, property_type = "energy"):
    method _set_ncompounds (line 49) | def _set_ncompounds(self, n):
    method take (line 54) | def take(self, i, axis=None):
    method __getitem__ (line 63) | def __getitem__(self, i):
    method __len__ (line 67) | def __len__(self):
    method __eq__ (line 73) | def __eq__(self, other):
    method __ne__ (line 94) | def __ne__(self, other):
    method set_energies (line 100) | def set_energies(self, energies):
    method set_forces (line 103) | def set_forces(self, forces):
    method _parse_xyz_files (line 106) | def _parse_xyz_files(self, filenames):

FILE: qml/qmlearn/kernels.py
  class _BaseKernel (line 56) | class _BaseKernel(BaseEstimator):
    method fit (line 61) | def fit(self, X):
    method transform (line 68) | def transform(self, X, y = None):
    method generate (line 74) | def generate(self, **params):
    method _check_data_object (line 77) | def _check_data_object(self, X):
    method _set_representations (line 92) | def _set_representations(self, rep):
    method _set_nuclear_charges (line 95) | def _set_nuclear_charges(self, charge):
    method transform (line 98) | def transform(self, X):
    method _get_elementwise_representations_transform (line 141) | def _get_elementwise_representations_transform(self, representations, ...
    method _get_elementwise_representations_fit (line 173) | def _get_elementwise_representations_fit(self, representations, nuclea...
    method _fit_transform (line 198) | def _fit_transform(self, X):
    method fit_transform (line 236) | def fit_transform(self, X, y=None):
  class GaussianKernel (line 239) | class GaussianKernel(_BaseKernel):
    method __init__ (line 244) | def __init__(self, sigma='auto', alchemy='auto'):
    method _quick_estimate_sigma (line 261) | def _quick_estimate_sigma(self, X, representation_type, sigma_init=100...
    method generate (line 306) | def generate(self, X, Y=None, representation_type='molecular'):
    method _generate_molecular (line 358) | def _generate_molecular(self, X, Y=None):
    method _generate_atomic (line 365) | def _generate_atomic(self, X, Y=None):
  class LaplacianKernel (line 423) | class LaplacianKernel(_BaseKernel):
    method __init__ (line 428) | def __init__(self, sigma='auto', alchemy='auto'):
    method _quick_estimate_sigma (line 444) | def _quick_estimate_sigma(self, X, representation_type, sigma_init=100...
    method generate (line 489) | def generate(self, X, Y=None, representation_type='molecular'):
    method _generate_molecular (line 541) | def _generate_molecular(self, X, Y=None):
    method _generate_atomic (line 548) | def _generate_atomic(self, X, Y=None):
  class FCHLKernel (line 609) | class FCHLKernel(_BaseKernel):
    method __init__ (line 614) | def __init__(self, sigma='auto', alchemy=True, two_body_scaling=np.sqr...
    method _quick_estimate_sigma (line 668) | def _quick_estimate_sigma(self, X, sigma_init=1, count=1):
    method generate (line 707) | def generate(self, X, Y=None):
    method _generate_molecular (line 735) | def _generate_molecular(self, X, Y=None):
    method _generate_atomic (line 759) | def _generate_atomic(self, X, Y=None):
    method fit_transform (line 783) | def fit_transform(self, X, y=None):
  class OQMLForceKernel (line 794) | class OQMLForceKernel(_BaseKernel):
    method __init__ (line 796) | def __init__(self, sigma=10.0, local=True):
    method _quick_estimate_sigma (line 803) | def _quick_estimate_sigma(self, X, sigma_init=1, count=1):
    method generate (line 808) | def generate(self, X, Y=None, representation_type="atomic"):
    method _generate_molecular (line 835) | def _generate_molecular(self, X, Y=None):
    method _generate_atomic (line 840) | def _generate_atomic(self, X, Y=None):
    method fit_transform (line 869) | def fit_transform(self, X, y=None):
  class GPRForceKernel (line 874) | class GPRForceKernel(_BaseKernel):
    method __init__ (line 876) | def __init__(self, sigma=10.0, local=True):
    method _quick_estimate_sigma (line 883) | def _quick_estimate_sigma(self, X, sigma_init=1, count=1):
    method generate (line 888) | def generate(self, X, Y=None, representation_type="atomic"):
    method _generate_molecular (line 915) | def _generate_molecular(self, X, Y=None):
    method _generate_atomic (line 920) | def _generate_atomic(self, X, Y=None):
    method fit_transform (line 943) | def fit_transform(self, X, y=None):
  class GPREnergyKernel (line 948) | class GPREnergyKernel(_BaseKernel):
    method __init__ (line 950) | def __init__(self, sigma=10.0, local=True):
    method _quick_estimate_sigma (line 957) | def _quick_estimate_sigma(self, X, sigma_init=1, count=1):
    method generate (line 962) | def generate(self, X, Y=None, representation_type="atomic"):
    method _generate_molecular (line 991) | def _generate_molecular(self, X, Y=None):
    method _generate_atomic (line 996) | def _generate_atomic(self, X, Y=None):
    method fit_transform (line 1019) | def fit_transform(self, X, y=None):

FILE: qml/qmlearn/models.py
  class _BaseModel (line 48) | class _BaseModel(BaseEstimator):
    method fit (line 55) | def fit(self, X):
    method predict (line 58) | def predict(self, X):
    method score (line 62) | def score(self, X, y=None):
    method _set_scoring (line 103) | def _set_scoring(self, scoring):
  class KernelRidgeRegression (line 109) | class KernelRidgeRegression(_BaseModel):
    method __init__ (line 118) | def __init__(self, l2_reg=1e-10, scoring='neg_mae'):
    method fit (line 124) | def fit(self, X, y=None):
    method predict (line 151) | def predict(self, X):
  class NeuralNetwork (line 183) | class NeuralNetwork(_BaseModel):
    method __init__ (line 213) | def __init__(self, hl1=20, hl2=10, hl3=5, hl4=0, batch_size=200, learn...
    method _set_hl (line 232) | def _set_hl(self, hl1, hl2, hl3, hl4):
    method _set_batch_size (line 244) | def _set_batch_size(self, bs):
    method _set_size (line 251) | def _set_size(self, size):
    method _set_learning_rate (line 258) | def _set_learning_rate(self, lr):
    method _set_iterations (line 265) | def _set_iterations(self, it):
    method _set_reg (line 272) | def _set_reg(self, l1_reg, l2_reg):
    method fit (line 279) | def fit(self, X, y=None, nuclear_charges=None):
    method _remove_constant_features (line 347) | def _remove_constant_features(self, representations):
    method predict (line 371) | def predict(self, X, nuclear_charges=None):
    method _generate_model (line 412) | def _generate_model(self, shape):
    method _atomic_nn (line 516) | def _atomic_nn(self, x, hidden_layer_sizes, weights, biases):
    method _train (line 547) | def _train(self, representations, energies, nuclear_charges):
    method _cost (line 600) | def _cost(self, y_pred, y, weights):
    method _l2_loss (line 640) | def _l2_loss(self, weights):
    method _l1_loss (line 657) | def _l1_loss(self, weights):
    method _predict (line 674) | def _predict(self, representations, nuclear_charges=None):
    method _padding (line 719) | def _padding(self, representation, nuclear_charges):
    method tf_check (line 753) | def tf_check(self):
  class OQMLRegression (line 758) | class OQMLRegression(_BaseModel):
    method __init__ (line 767) | def __init__(self, l2_reg=1e-10, scoring='neg_mae'):
    method fit (line 773) | def fit(self, X, y=None):
    method score (line 800) | def score(self, X, y=None):
    method predict (line 883) | def predict(self, X):
  class GPRRegression (line 915) | class GPRRegression(_BaseModel):
    method __init__ (line 924) | def __init__(self, l2_reg=1e-10, scoring='neg_mae'):
    method fit (line 930) | def fit(self, X, y=None):
    method score (line 970) | def score(self, X, y=None):
    method predict (line 1033) | def predict(self, X):

FILE: qml/qmlearn/preprocessing.py
  class AtomScaler (line 34) | class AtomScaler(BaseEstimator):
    method __init__ (line 39) | def __init__(self, data=None, elements='auto'):
    method _preprocess_input (line 55) | def _preprocess_input(self, X):
    method _check_data (line 111) | def _check_data(self, X):
    method _set_data (line 120) | def _set_data(self, data):
    method _parse_input (line 125) | def _parse_input(self, X, y):
    method fit (line 136) | def fit(self, X, y=None):
    method _fit (line 154) | def _fit(self, X, y=None):
    method fit_transform (line 173) | def fit_transform(self, X, y=None):
    method _transform (line 193) | def _transform(self, data, features, y):
    method _revert_transform (line 209) | def _revert_transform(self, data, features, y):
    method _check_elements (line 224) | def _check_elements(self, nuclear_charges):
    method _featurizer (line 236) | def _featurizer(self, X):
    method transform (line 256) | def transform(self, X, y=None):
    method revert_transform (line 280) | def revert_transform(self, X, y=None):

FILE: qml/qmlearn/representations.py
  class _BaseRepresentation (line 43) | class _BaseRepresentation(BaseEstimator):
    method fit (line 54) | def fit(self, X, y=None):
    method transform (line 61) | def transform(self, X):
    method _extract_data (line 69) | def _extract_data(self, X):
    method _check_data (line 103) | def _check_data(self, X):
    method _set_data (line 108) | def _set_data(self, data):
    method _check_elements (line 114) | def _check_elements(self, nuclear_charges):
    method generate (line 128) | def generate(self, X):
  class _MolecularRepresentation (line 139) | class _MolecularRepresentation(_BaseRepresentation):
  class _AtomicRepresentation (line 146) | class _AtomicRepresentation(_BaseRepresentation):
  class CoulombMatrix (line 154) | class CoulombMatrix(_MolecularRepresentation):
    method __init__ (line 194) | def __init__(self, data=None, size='auto', sorting="row-norm"):
    method fit (line 200) | def fit(self, X, y=None):
    method transform (line 225) | def transform(self, X):
  class AtomicCoulombMatrix (line 269) | class AtomicCoulombMatrix(_AtomicRepresentation):
    method __init__ (line 278) | def __init__(self, data=None, size=23, sorting="distance", central_cut...
    method fit (line 357) | def fit(self, X, y=None):
    method transform (line 376) | def transform(self, X):
  class _SLATM (line 413) | class _SLATM(object):
    method _fit (line 418) | def _fit(self, X, y=None):
    method _transform (line 444) | def _transform(self, X, local):
  class GlobalSLATM (line 479) | class GlobalSLATM(_SLATM, _MolecularRepresentation):
    method __init__ (line 486) | def __init__(self, data=None, sigma2=0.05, sigma3=0.05, dgrid2=0.03,
    method fit (line 529) | def fit(self, X, y=None):
    method transform (line 542) | def transform(self, X):
  class AtomicSLATM (line 555) | class AtomicSLATM(_SLATM, _AtomicRepresentation):
    method __init__ (line 562) | def __init__(self, data=None, sigma2=0.05, sigma3=0.05, dgrid2=0.03,
    method fit (line 605) | def fit(self, X, y=None):
    method transform (line 618) | def transform(self, X):
  class AtomCenteredSymmetryFunctions (line 629) | class AtomCenteredSymmetryFunctions(_AtomicRepresentation):
    method __init__ (line 651) | def __init__(self, data=None, nbasis=3, precision=2, cutoff=5.0, eleme...
    method fit (line 660) | def fit(self, X, y=None):
    method transform (line 678) | def transform(self, X):
  class FCHLRepresentation (line 723) | class FCHLRepresentation(_BaseRepresentation):
    method __init__ (line 730) | def __init__(self, data=None, size='auto', cutoff=10.0):
    method fit (line 746) | def fit(self, X, y=None):
    method transform (line 770) | def transform(self, X):
  class FCHL_ACSF (line 802) | class FCHL_ACSF(_AtomicRepresentation):
    method __init__ (line 817) | def __init__(self, data=None, elements='auto',
    method fit (line 837) | def fit(self, X, y=None):
    method transform (line 855) | def transform(self, X):
  class FCHL_ACSF_Force (line 904) | class FCHL_ACSF_Force(_AtomicRepresentation):
    method __init__ (line 919) | def __init__(self, data=None, elements='auto',
    method fit (line 939) | def fit(self, X, y=None):
    method transform (line 957) | def transform(self, X):

FILE: qml/representations/representations.py
  function vector_to_matrix (line 44) | def vector_to_matrix(v):
  function generate_coulomb_matrix (line 72) | def generate_coulomb_matrix(nuclear_charges, coordinates, size = 23, sor...
  function generate_atomic_coulomb_matrix (line 124) | def generate_atomic_coulomb_matrix(nuclear_charges, coordinates, size = ...
  function generate_eigenvalue_coulomb_matrix (line 238) | def generate_eigenvalue_coulomb_matrix(nuclear_charges, coordinates, siz...
  function generate_bob (line 268) | def generate_bob(nuclear_charges, coordinates, atomtypes, size=23, asize...
  function get_slatm_mbtypes (line 316) | def get_slatm_mbtypes(nuclear_charges, pbc='000'):
  function generate_slatm (line 374) | def generate_slatm(coordinates, nuclear_charges, mbtypes,
  function generate_acsf (line 553) | def generate_acsf(nuclear_charges, coordinates, elements = [1,6,7,8,16],...
  function generate_fchl_acsf (line 630) | def generate_fchl_acsf(nuclear_charges, coordinates, elements = [1,6,7,8...

FILE: qml/representations/slatm.py
  function update_m (line 35) | def update_m(obj, ia, rcut=9.0, pbc=None):
  function get_boa (line 99) | def get_boa(z1, zs_):
  function get_sbop (line 104) | def get_sbop(mbtype, obj, iloc=False, ia=None, normalize=True, sigma=0.0...
  function get_sbot (line 141) | def get_sbot(mbtype, obj, iloc=False, ia=None, normalize=True, sigma=0.0...

FILE: qml/utils/alchemy.py
  function QNum_distance (line 363) | def QNum_distance(a,b, n_width, m_width, l_width, s_width):
  function gen_QNum_distances (line 388) | def gen_QNum_distances(emax=100, n_width = 0.001, m_width = 0.001, l_wid...
  function periodic_distance (line 404) | def periodic_distance(a, b, r_width, c_width):
  function gen_pd (line 423) | def gen_pd(emax=100, r_width=0.001, c_width=0.001):
  function gen_custom (line 441) | def gen_custom(e_vec, emax=100):
  function get_alchemy (line 468) | def get_alchemy(alchemy, emax=100, r_width=0.001, c_width=0.001, element...

FILE: qml/utils/compound.py
  class Compound (line 41) | class Compound(object):
    method __init__ (line 48) | def __init__(self, xyz = None):
    method generate_coulomb_matrix (line 76) | def generate_coulomb_matrix(self, size = 23, sorting = "row-norm", ind...
    method generate_eigenvalue_coulomb_matrix (line 110) | def generate_eigenvalue_coulomb_matrix(self, size = 23):
    method generate_atomic_coulomb_matrix (line 137) | def generate_atomic_coulomb_matrix(self, size = 23, sorting = "row-norm",
    method generate_bob (line 220) | def generate_bob(self, size=23, asize = {"O":3, "C":7, "N":3, "H":16, ...
    method generate_fchl_representation (line 251) | def generate_fchl_representation(self, max_size = 23, cell=None, neigh...
    method generate_slatm (line 261) | def generate_slatm(self, mbtypes,
    method generate_acsf (line 298) | def generate_acsf(self, elements = [1,6,7,8,16], nRs2 = 3, nRs3 = 3, n...
    method read_xyz (line 342) | def read_xyz(self, filename):
    method set_compounds (line 377) | def set_compounds(self, xyz, zs):

FILE: qml/utils/utils.py
  function is_positive (line 26) | def is_positive(x):
  function is_positive_or_zero (line 29) | def is_positive_or_zero(x):
  function is_array_like (line 32) | def is_array_like(x):
  function is_positive_integer (line 35) | def is_positive_integer(x):
  function is_positive_integer_or_zero (line 38) | def is_positive_integer_or_zero(x):
  function is_string (line 41) | def is_string(x):
  function is_dict (line 44) | def is_dict(x):
  function is_numeric (line 47) | def is_numeric(x):
  function is_numeric_array (line 50) | def is_numeric_array(x):
  function is_numeric_1d_array (line 59) | def is_numeric_1d_array(x):
  function is_1d_array (line 63) | def is_1d_array(x):
  function _is_integer (line 67) | def _is_integer(x):
  function is_bool (line 72) | def is_bool(x):
  function is_non_zero_integer (line 75) | def is_non_zero_integer(x):
  function _is_positive_array (line 78) | def _is_positive_array(x):
  function _is_positive_or_zero_array (line 83) | def _is_positive_or_zero_array(x):
  function _is_integer_array (line 88) | def _is_integer_array(x):
  function is_positive_integer_1d_array (line 94) | def is_positive_integer_1d_array(x):
  function is_positive_integer_array (line 97) | def is_positive_integer_array(x):
  function is_positive_integer_or_zero_array (line 100) | def is_positive_integer_or_zero_array(x):
  function check_global_representation (line 105) | def check_global_representation(x):
  function check_local_representation (line 124) | def check_local_representation(x):
  function check_y (line 143) | def check_y(y):
  function check_sizes (line 157) | def check_sizes(x, y=None, dy=None, classes=None):
  function check_dy (line 205) | def check_dy(dy):
  function check_classes (line 231) | def check_classes(classes):
  function get_unique (line 257) | def get_unique(x):
  function get_pairs (line 264) | def get_pairs(x):
  class InputError (line 278) | class InputError(Exception):
  function ceil (line 286) | def ceil(a, b):
  function get_batch_size (line 293) | def get_batch_size(batch_size, n_samples):

FILE: setup.py
  function requirements (line 138) | def requirements():
  function readme (line 144) | def readme():
  function setup_qml (line 149) | def setup_qml():

FILE: test/test_acsf.py
  function test_acsf_1 (line 36) | def test_acsf_1():
  function test_acsf_2 (line 86) | def test_acsf_2():

FILE: test/test_acsf_linear_angles.py
  function get_fchl_acsf_numgrad (line 42) | def get_fchl_acsf_numgrad(mol, dx=1e-5):
  function get_acsf_numgrad (line 81) | def get_acsf_numgrad(mol, dx=1e-5):
  function test_fchl_acsf (line 120) | def test_fchl_acsf():
  function test_acsf (line 147) | def test_acsf():

FILE: test/test_arad.py
  function get_energies (line 43) | def get_energies(filename):
  function test_arad (line 63) | def test_arad():

FILE: test/test_armp.py
  function test_set_representation (line 35) | def test_set_representation():
  function test_set_properties (line 65) | def test_set_properties():
  function test_set_descriptor (line 83) | def test_set_descriptor():
  function test_fit_1 (line 111) | def test_fit_1():
  function test_fit_2 (line 131) | def test_fit_2():
  function test_fit_3 (line 151) | def test_fit_3():
  function test_fit_4 (line 165) | def test_fit_4():
  function test_score_3 (line 187) | def test_score_3():
  function test_predict_3 (line 210) | def test_predict_3():
  function test_predict_fromxyz (line 224) | def test_predict_fromxyz():
  function test_retraining (line 273) | def test_retraining():

FILE: test/test_compound.py
  function compare_lists (line 30) | def compare_lists(a, b):
  function test_compound (line 36) | def test_compound():

FILE: test/test_distance.py
  function test_manhattan (line 30) | def test_manhattan():
  function test_l2 (line 50) | def test_l2():
  function test_p (line 72) | def test_p():

FILE: test/test_energy_krr_atomic_cmat.py
  function get_energies (line 40) | def get_energies(filename):
  function test_krr_gaussian_local_cmat (line 60) | def test_krr_gaussian_local_cmat():
  function test_krr_laplacian_local_cmat (line 141) | def test_krr_laplacian_local_cmat():

FILE: test/test_energy_krr_bob.py
  function get_energies (line 35) | def get_energies(filename):
  function test_krr_bob (line 55) | def test_krr_bob():

FILE: test/test_energy_krr_cmat.py
  function get_energies (line 35) | def get_energies(filename):
  function test_krr_cmat (line 55) | def test_krr_cmat():

FILE: test/test_fchl_acsf.py
  function get_acsf_numgrad (line 39) | def get_acsf_numgrad(mol, dx=1e-5):
  function test_fchl_acsf (line 78) | def test_fchl_acsf():

FILE: test/test_fchl_acsf_energy.py
  function get_energies (line 43) | def get_energies(filename):
  function test_energy (line 63) | def test_energy():

FILE: test/test_fchl_acsf_forces.py
  function get_reps (line 63) | def get_reps(df):
  function test_fchl_acsf_operator (line 102) | def test_fchl_acsf_operator():
  function test_fchl_acsf_gaussian_process (line 168) | def test_fchl_acsf_gaussian_process():

FILE: test/test_fchl_electric_field.py
  function parse_energy (line 60) | def parse_energy(filename):
  function ang2ang (line 85) | def ang2ang(angle):
  function parse_dipole (line 94) | def parse_dipole(filename):
  function parse_csv (line 115) | def parse_csv(filename):
  function test_multiple_operators (line 169) | def test_multiple_operators():
  function test_generate_representation (line 236) | def test_generate_representation():
  function test_gaussian_process (line 280) | def test_gaussian_process():
  function test_gaussian_process_field_dependent (line 334) | def test_gaussian_process_field_dependent():

FILE: test/test_fchl_force.py
  function mae (line 59) | def mae(a, b):
  function csv_to_molecular_reps (line 64) | def csv_to_molecular_reps(csv_filename, force_key="orca_forces", energy_...
  function test_gaussian_process_derivative (line 110) | def test_gaussian_process_derivative():
  function test_gdml_derivative (line 174) | def test_gdml_derivative():
  function test_normal_equation_derivative (line 230) | def test_normal_equation_derivative():
  function test_operator_derivative (line 300) | def test_operator_derivative():
  function test_krr_derivative (line 353) | def test_krr_derivative():

FILE: test/test_fchl_scalar.py
  function get_energies (line 46) | def get_energies(filename):
  function test_krr_fchl_local (line 66) | def test_krr_fchl_local():
  function test_krr_fchl_global (line 151) | def test_krr_fchl_global():
  function test_krr_fchl_atomic (line 226) | def test_krr_fchl_atomic():
  function test_fchl_local_periodic (line 278) | def test_fchl_local_periodic():
  function test_krr_fchl_alchemy (line 433) | def test_krr_fchl_alchemy():
  function test_fchl_linear (line 529) | def test_fchl_linear():
  function test_fchl_polynomial (line 578) | def test_fchl_polynomial():
  function test_fchl_sigmoid (line 634) | def test_fchl_sigmoid():
  function test_fchl_multiquadratic (line 690) | def test_fchl_multiquadratic():
  function test_fchl_inverse_multiquadratic (line 747) | def test_fchl_inverse_multiquadratic():
  function test_fchl_bessel (line 803) | def test_fchl_bessel():
  function test_fchl_l2 (line 868) | def test_fchl_l2():
  function test_fchl_matern (line 924) | def test_fchl_matern():
  function test_fchl_cauchy (line 993) | def test_fchl_cauchy():
  function test_fchl_polynomial2 (line 1050) | def test_fchl_polynomial2():

FILE: test/test_kernel_derivatives.py
  function csv_to_molecular_reps (line 56) | def csv_to_molecular_reps(csv_filename):
  function test_global_kernel (line 112) | def test_global_kernel():
  function test_atomic_local_kernel (line 127) | def test_atomic_local_kernel():
  function test_local_kernel (line 164) | def test_local_kernel():
  function test_atomic_local_kernel (line 206) | def test_atomic_local_kernel():
  function test_atomic_local_gradient (line 244) | def test_atomic_local_gradient():
  function test_local_gradient (line 289) | def test_local_gradient():
  function test_gdml_kernel (line 335) | def test_gdml_kernel():
  function test_symmetric_gdml_kernel (line 396) | def test_symmetric_gdml_kernel():
  function test_gp_kernel (line 418) | def test_gp_kernel():
  function test_local_kernels (line 454) | def test_local_kernels():

FILE: test/test_kernels.py
  function get_energies (line 45) | def get_energies(filename):
  function test_laplacian_kernel (line 65) | def test_laplacian_kernel():
  function test_gaussian_kernel (line 99) | def test_gaussian_kernel():
  function test_linear_kernel (line 133) | def test_linear_kernel():
  function test_matern_kernel (line 162) | def test_matern_kernel():
  function matern (line 170) | def matern(metric, order):
  function test_sargan_kernel (line 210) | def test_sargan_kernel():
  function sargan (line 217) | def sargan(ngamma):
  function array_nan_close (line 252) | def array_nan_close(a, b):
  function test_kpca (line 259) | def test_kpca():
  function test_wasserstein_kernel (line 291) | def test_wasserstein_kernel():

FILE: test/test_math.py
  function test_cho_solve (line 32) | def test_cho_solve():
  function test_cho_invert (line 54) | def test_cho_invert():
  function test_bkf_invert (line 73) | def test_bkf_invert():
  function test_bkf_solve (line 92) | def test_bkf_solve():

FILE: test/test_mrmp.py
  function test_set_representation (line 40) | def test_set_representation():
  function test_set_properties (line 70) | def test_set_properties():
  function test_set_descriptor (line 87) | def test_set_descriptor():
  function test_fit_1 (line 114) | def test_fit_1():
  function test_fit_2 (line 139) | def test_fit_2():
  function test_fit_3 (line 158) | def test_fit_3():
  function test_fit_4 (line 172) | def test_fit_4():
  function test_score (line 188) | def test_score():
  function test_save_local (line 210) | def test_save_local():
  function test_load_external (line 233) | def test_load_external():

FILE: test/test_neural_network.py
  function hidden_layer_sizes (line 37) | def hidden_layer_sizes(C):
  function l1_reg (line 61) | def l1_reg(C):
  function l2_reg (line 80) | def l2_reg(C):
  function batch_size (line 99) | def batch_size(C):
  function learning_rate (line 120) | def learning_rate(C):
  function iterations (line 138) | def iterations(C):
  function tf_dtype (line 157) | def tf_dtype(C):
  function hl1 (line 185) | def hl1(C):
  function hl2 (line 205) | def hl2(C):
  function hl3 (line 225) | def hl3(C):
  function representation (line 245) | def representation(C):
  function scoringfunction (line 266) | def scoringfunction(C):
  function test_input (line 289) | def test_input():
  function test_l2_loss (line 305) | def test_l2_loss():
  function test_l1_loss (line 326) | def test_l1_loss():
  function test_get_batch_size (line 347) | def test_get_batch_size():
  function test_fit1 (line 367) | def test_fit1():

FILE: test/test_representations.py
  function get_asize (line 33) | def get_asize(mols, pad):
  function test_representations (line 45) | def test_representations():
  function coulomb_matrix (line 73) | def coulomb_matrix(mols, size, path):
  function atomic_coulomb_matrix (line 91) | def atomic_coulomb_matrix(mols, size, path):
  function eigenvalue_coulomb_matrix (line 159) | def eigenvalue_coulomb_matrix(mols, size, path):
  function bob (line 169) | def bob(mols, size, asize, path):
  function print_mol (line 178) | def print_mol(mol):

FILE: test/test_slatm.py
  function test_slatm_global_representation (line 31) | def test_slatm_global_representation():
  function test_slatm_local_representation (line 64) | def test_slatm_local_representation():

FILE: test/test_symm_funct.py
  function pad (line 36) | def pad(size, coordinates, nuclear_charges):
  function test_acsf (line 53) | def test_acsf():
  function fort_acsf (line 83) | def fort_acsf(mols, path, elements):
  function tf_acsf (line 106) | def tf_acsf(mols, path, elements):
  function fort_acsf_gradients (line 141) | def fort_acsf_gradients(mols, path, elements):