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__compute_feature__() (in module deeprank.features.AtomicFeature)
(in module deeprank.features.BSA)
(in module deeprank.features.FullPSSM)
(in module deeprank.features.PSSM_IC)
(in module deeprank.features.ResidueDensity)
__compute_target__() (in module deeprank.targets.binary_class)
(in module deeprank.targets.capri_class)
(in module deeprank.targets.dockQ)
(in module deeprank.targets.rmsd_fnat)
_add_aug_pdb() (deeprank.generate.DataGenerator.DataGenerator method)
_add_pdb() (deeprank.generate.DataGenerator.DataGenerator method)
_clip_feature() (deeprank.learn.DataSet.DataSet method)
_compile_cuda_kernel() (deeprank.generate.DataGenerator.DataGenerator static method)
_compute_features() (deeprank.generate.DataGenerator.DataGenerator static method)
_compute_hitrate() (deeprank.learn.NeuralNet.NeuralNet method)
_compute_targets() (deeprank.generate.DataGenerator.DataGenerator static method)
_densgrid() (deeprank.learn.DataSet.DataSet static method)
_divide_dataset() (deeprank.learn.NeuralNet.NeuralNet method)
_epoch() (deeprank.learn.NeuralNet.NeuralNet method)
_export_data() (deeprank.generate.NormalizeData.NormalizeData method)
_export_epoch_hdf5() (deeprank.learn.NeuralNet.NeuralNet method)
_export_losses() (deeprank.learn.NeuralNet.NeuralNet method)
_export_metrics() (deeprank.learn.NeuralNet.NeuralNet method)
_extend_contact_to_residue() (deeprank.features.AtomicFeature.AtomicFeature method)
_extract_data() (deeprank.generate.NormalizeData.NormalizeData method)
_extract_shape() (deeprank.generate.NormalizeData.NormalizeData method)
_featgrid() (deeprank.learn.DataSet.DataSet static method)
_filter_cplx() (deeprank.generate.DataGenerator.DataGenerator method)
_get_aligned_rotation_axis_angle() (deeprank.generate.DataGenerator.DataGenerator static method)
_get_aligned_sqldb() (deeprank.generate.DataGenerator.DataGenerator method)
_get_altResName() (deeprank.features.AtomicFeature.AtomicFeature static method)
_get_binclass_prediction() (deeprank.learn.NeuralNet.NeuralNet static method)
_get_charge() (deeprank.features.AtomicFeature.AtomicFeature method)
_get_classmetrics() (deeprank.learn.NeuralNet.NeuralNet method)
_get_cuda_function() (deeprank.generate.DataGenerator.DataGenerator static method)
_get_database_name() (deeprank.learn.DataSet.DataSet static method)
_get_grid_center() (deeprank.generate.DataGenerator.DataGenerator method)
_get_relevance() (deeprank.learn.NeuralNet.NeuralNet method)
_get_single_index() (deeprank.tools.sparse.FLANgrid method)
_get_single_index_array() (deeprank.tools.sparse.FLANgrid method)
_get_target_ordering() (deeprank.learn.DataSet.DataSet method)
_get_variables() (deeprank.learn.NeuralNet.NeuralNet method)
_get_vdw() (deeprank.features.AtomicFeature.AtomicFeature method)
_init_conv_layer_random() (deeprank.learn.modelGenerator.NetworkGenerator method)
_init_fc_layer_random() (deeprank.learn.modelGenerator.NetworkGenerator method)
_load() (deeprank.generate.NormalizeData.NormalizeData method)
_mad_based_outliers() (deeprank.learn.DataSet.DataSet static method)
_normalize_feature() (deeprank.learn.DataSet.DataSet method)
_normalize_target() (deeprank.learn.DataSet.DataSet method)
_plot_boxplot_class() (deeprank.learn.NeuralNet.NeuralNet method)
_plot_scatter_reg() (deeprank.learn.NeuralNet.NeuralNet method)
_prefactor_vdw() (deeprank.features.AtomicFeature.AtomicFeature static method)
_printif() (in module deeprank.generate.DataGenerator)
(in module deeprank.tools.sparse)
_process_data() (deeprank.generate.NormalizeData.NormalizeData method)
_read_norm() (deeprank.learn.DataSet.DataSet method)
_rotate_feature() (deeprank.generate.DataGenerator.DataGenerator static method)
_select_pdb() (deeprank.learn.DataSet.DataSet method)
_test_cuda() (deeprank.generate.DataGenerator.DataGenerator method)
_train() (deeprank.learn.NeuralNet.NeuralNet method)
_tunable_kernel() (deeprank.generate.DataGenerator.DataGenerator static method)
_tune_cuda_kernel() (deeprank.generate.DataGenerator.DataGenerator method)
_write_conv_output() (deeprank.learn.modelGenerator.NetworkGenerator static method)
_write_definition() (deeprank.learn.modelGenerator.NetworkGenerator method)
_write_forward() (deeprank.learn.modelGenerator.NetworkGenerator method)
_write_forward_feature() (deeprank.learn.modelGenerator.NetworkGenerator method)
_write_import() (deeprank.learn.modelGenerator.NetworkGenerator static method)
_write_init() (deeprank.learn.modelGenerator.NetworkGenerator method)
A
add() (deeprank.generate.NormalizeData.NormParam method)
add_all_atomic_densities() (deeprank.generate.GridTools.GridTools method)
add_all_features() (deeprank.generate.GridTools.GridTools method)
add_feature() (deeprank.generate.DataGenerator.DataGenerator method)
add_target() (deeprank.generate.DataGenerator.DataGenerator method)
add_unique_target() (deeprank.generate.DataGenerator.DataGenerator method)
assign_parameters() (deeprank.features.AtomicFeature.AtomicFeature method)
AtomicFeature (class in deeprank.features.AtomicFeature)
aug_data() (deeprank.generate.DataGenerator.DataGenerator method)
B
backtransform_target() (deeprank.learn.DataSet.DataSet method)
BSA (class in deeprank.features.BSA)
C
check_hdf5_files() (deeprank.learn.DataSet.DataSet static method)
compute_coulomb_interchain_only() (deeprank.features.AtomicFeature.AtomicFeature method)
compute_norm() (deeprank.learn.DataSet.DataSet method)
compute_vdw_interchain_only() (deeprank.features.AtomicFeature.AtomicFeature method)
conv (class in deeprank.learn.modelGenerator)
convert2d() (deeprank.learn.DataSet.DataSet static method)
convertSeconds2Days() (deeprank.learn.NeuralNet.NeuralNet static method)
create_database() (deeprank.generate.DataGenerator.DataGenerator method)
create_index_molecules() (deeprank.learn.DataSet.DataSet method)
create_new_data() (deeprank.generate.GridTools.GridTools method)
D
DataGenerator (class in deeprank.generate.DataGenerator)
DataSet (class in deeprank.learn.DataSet)
deeprank.features.AtomicFeature (module)
deeprank.features.BSA (module)
deeprank.features.FeatureClass (module)
deeprank.features.FullPSSM (module)
deeprank.features.PSSM_IC (module)
deeprank.features.ResidueDensity (module)
deeprank.generate (module)
deeprank.generate.DataGenerator (module)
deeprank.generate.GridTools (module)
deeprank.generate.NormalizeData (module)
deeprank.learn (module)
deeprank.learn.DataSet (module)
deeprank.learn.modelGenerator (module)
deeprank.learn.NeuralNet (module)
deeprank.targets (module)
deeprank.tools (module)
deeprank.tools.sasa (module)
deeprank.tools.sparse (module)
define_grid_points() (deeprank.generate.GridTools.GridTools method)
densgrid() (deeprank.generate.GridTools.GridTools method)
dropout (class in deeprank.learn.modelGenerator)
E
evaluate_charges() (deeprank.features.AtomicFeature.AtomicFeature method)
evaluate_pair_interaction() (deeprank.features.AtomicFeature.AtomicFeature method)
export_data_hdf5() (deeprank.features.FeatureClass.FeatureClass method)
export_dataxyz_hdf5() (deeprank.features.FeatureClass.FeatureClass method)
export_grid_points() (deeprank.generate.GridTools.GridTools method)
extract_features() (deeprank.features.ResidueDensity.ResidueDensity method)
F
fc (class in deeprank.learn.modelGenerator)
featgrid() (deeprank.generate.GridTools.GridTools method)
FeatureClass (class in deeprank.features.FeatureClass)
filter() (deeprank.learn.DataSet.DataSet method)
FLANgrid (class in deeprank.tools.sparse)
from_dense() (deeprank.tools.sparse.FLANgrid method)
FullPSSM (class in deeprank.features.FullPSSM)
G
get() (deeprank.features.ResidueDensity.ResidueDensity method)
(deeprank.generate.NormalizeData.NormalizeData method)
get_center() (deeprank.tools.sasa.SASA method)
get_contact_atoms() (deeprank.features.AtomicFeature.AtomicFeature method)
get_contact_center() (deeprank.generate.GridTools.GridTools method)
get_contact_residue_sasa() (deeprank.features.BSA.BSA method)
get_feature_value() (deeprank.features.FullPSSM.FullPSSM method)
get_grid() (deeprank.learn.DataSet.DataSet method)
get_grid_shape() (deeprank.learn.DataSet.DataSet method)
get_input_shape() (deeprank.learn.DataSet.DataSet method)
get_mapped_feature_name() (deeprank.learn.DataSet.DataSet method)
get_new_random_model() (deeprank.learn.modelGenerator.NetworkGenerator method)
get_norm() (deeprank.learn.DataSet.DataSet method)
get_pairing_feature() (deeprank.learn.DataSet.DataSet method)
get_raw_feature_name() (deeprank.learn.DataSet.DataSet method)
get_ref_mol_name() (deeprank.features.FullPSSM.FullPSSM static method)
get_residue_carbon_beta() (deeprank.tools.sasa.SASA method)
get_residue_center() (deeprank.features.FeatureClass.FeatureClass static method)
(deeprank.tools.sasa.SASA method)
get_structure() (deeprank.features.BSA.BSA method)
GridTools (class in deeprank.generate.GridTools)
H
hdf5_grid_data() (deeprank.generate.GridTools.GridTools method)
L
load_data_params() (deeprank.learn.NeuralNet.NeuralNet method)
load_model_params() (deeprank.learn.NeuralNet.NeuralNet method)
load_nn_params() (deeprank.learn.NeuralNet.NeuralNet method)
load_one_molecule() (deeprank.learn.DataSet.DataSet method)
load_optimizer_params() (deeprank.learn.NeuralNet.NeuralNet method)
logif() (in module deeprank.generate.GridTools)
M
make_feature_pair() (deeprank.learn.DataSet.DataSet static method)
map_atomic_densities() (deeprank.generate.GridTools.GridTools method)
(deeprank.learn.DataSet.DataSet method)
map_feature() (deeprank.learn.DataSet.DataSet method)
map_features() (deeprank.generate.DataGenerator.DataGenerator method)
(deeprank.generate.GridTools.GridTools method)
map_one_molecule() (deeprank.learn.DataSet.DataSet method)
MinMaxParam (class in deeprank.generate.NormalizeData)
N
neighbor_count() (deeprank.tools.sasa.SASA method)
neighbor_vector() (deeprank.tools.sasa.SASA method)
neighbor_weight() (deeprank.tools.sasa.SASA static method)
NetworkGenerator (class in deeprank.learn.modelGenerator)
NeuralNet (class in deeprank.learn.NeuralNet)
NormalizeData (class in deeprank.generate.NormalizeData)
NormParam (class in deeprank.generate.NormalizeData)
P
plot_hit_rate() (deeprank.learn.NeuralNet.NeuralNet method)
pool (class in deeprank.learn.modelGenerator)
precompute_grid() (deeprank.generate.DataGenerator.DataGenerator method)
print() (deeprank.learn.modelGenerator.NetworkGenerator method)
print_possible_features() (deeprank.learn.DataSet.DataSet method)
process() (deeprank.generate.NormalizeData.NormParam method)
process_dataset() (deeprank.learn.DataSet.DataSet method)
PSSM_IC (class in deeprank.features.PSSM_IC)
R
read_charge_file() (deeprank.features.AtomicFeature.AtomicFeature method)
read_patch() (deeprank.features.AtomicFeature.AtomicFeature method)
read_pdb() (deeprank.generate.GridTools.GridTools method)
read_PSSM_data() (deeprank.features.FullPSSM.FullPSSM method)
read_vdw_file() (deeprank.features.AtomicFeature.AtomicFeature method)
realign_complexes() (deeprank.generate.DataGenerator.DataGenerator method)
remove() (deeprank.generate.DataGenerator.DataGenerator method)
residue_pair (class in deeprank.features.ResidueDensity)
ResidueDensity (class in deeprank.features.ResidueDensity)
S
SASA (class in deeprank.tools.sasa)
save_model() (deeprank.learn.NeuralNet.NeuralNet method)
T
test() (deeprank.learn.NeuralNet.NeuralNet method)
to_dense() (deeprank.tools.sparse.FLANgrid method)
train() (deeprank.learn.NeuralNet.NeuralNet method)
U
update() (deeprank.generate.NormalizeData.MinMaxParam method)
update_feature() (deeprank.generate.GridTools.GridTools method)
W
write() (deeprank.learn.modelGenerator.NetworkGenerator method)
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