Index

A

ae (class in diffnets.nnutils) Analysis (class in diffnets.analysis) apply_exmax() (diffnets.training.Trainer method) apply_unwhitening() (diffnets.data_processing.WhitenTraj method)

apply_whitening() (diffnets.data_processing.WhitenTraj method) apply_whitening_xtc_dir() (diffnets.data_processing.WhitenTraj method) assert_matrix_is_identity() (in module diffnets.tests.test_api) assign_labels_to_variants() (diffnets.analysis.Analysis method)

C

chunks() (in module diffnets.nnutils) classify() (diffnets.nnutils.classify_ae method) (diffnets.nnutils.sae method) (diffnets.nnutils.split_sae method) (diffnets.nnutils.svae method)

classify_ae (class in diffnets.nnutils)

D

Dataset (class in diffnets.training) decode() (diffnets.nnutils.ae method) (diffnets.nnutils.split_ae method) diffnets (module) diffnets.data_processing (module) diffnets.exmax (module) diffnets.nnutils (module)

diffnets.tests (module) diffnets.tests.test_api (module) diffnets.tests.test_cli (module) diffnets.tests.test_diffnets (module) diffnets.training (module) diffnets.utils (module) distribution_of_sum() (in module diffnets.exmax)

E

em_parallel() (diffnets.training.Trainer method) encode() (diffnets.nnutils.ae method) (diffnets.nnutils.split_ae method) (diffnets.nnutils.vae method) encode_data() (diffnets.analysis.Analysis method) expectation_E_EXP() (in module diffnets.exmax)

expectation_or() (in module diffnets.exmax) expectation_or_CUBIC() (in module diffnets.exmax) expectation_or_LINEAR() (in module diffnets.exmax) expectation_range() (in module diffnets.exmax) expectation_range_CUBIC() (in module diffnets.exmax) expectation_range_EXP() (in module diffnets.exmax) extract_default_inds() (diffnets.data_processing.ProcessTraj method)

F

find_feats() (diffnets.analysis.Analysis method) forward() (diffnets.nnutils.ae method) (diffnets.nnutils.classify_ae method) (diffnets.nnutils.sae method) (diffnets.nnutils.split_ae method) (diffnets.nnutils.split_sae method) (diffnets.nnutils.svae method) (diffnets.nnutils.vae method)

freeze_weights() (diffnets.nnutils.ae method) (diffnets.nnutils.split_ae method)

G

get_c00() (diffnets.data_processing.WhitenTraj method) get_c00_xtc_list() (diffnets.data_processing.WhitenTraj method) get_fns() (in module diffnets.utils)

get_labels() (diffnets.analysis.Analysis method) get_rmsd() (diffnets.analysis.Analysis method) get_targets() (diffnets.training.Trainer method) get_wuw_mats() (diffnets.data_processing.WhitenTraj method)

I

ImproperlyConfigured

L

load_npy_dir() (in module diffnets.utils)

load_traj_coords_dir() (in module diffnets.utils)

M

make_master_pdb() (diffnets.data_processing.ProcessTraj method) make_traj_list() (diffnets.data_processing.ProcessTraj method) mkdir() (in module diffnets.utils)

morph() (diffnets.analysis.Analysis method) my_l1() (in module diffnets.nnutils) my_mse() (in module diffnets.nnutils)

P

preprocess_traj() (diffnets.data_processing.ProcessTraj method)

ProcessTraj (class in diffnets.data_processing)

R

rand() (in module diffnets.exmax) recon_traj() (diffnets.analysis.Analysis method) reparameterize() (diffnets.nnutils.vae method)

run() (diffnets.data_processing.ProcessTraj method) (diffnets.data_processing.WhitenTraj method) (diffnets.training.Trainer method) run_core() (diffnets.analysis.Analysis method)

S

sae (class in diffnets.nnutils) set_training_data() (diffnets.training.Trainer method) split_ae (class in diffnets.nnutils) split_inds (diffnets.nnutils.split_ae attribute)

split_inds() (in module diffnets.nnutils) split_sae (class in diffnets.nnutils) split_test_train() (diffnets.training.Trainer method) svae (class in diffnets.nnutils)

T

test_analyze() (in module diffnets.tests.test_cli) test_default_inds() (in module diffnets.tests.test_api) test_diffnets_imported() (in module diffnets.tests.test_diffnets) test_preprocess_custom_inds() (in module diffnets.tests.test_cli) test_preprocess_default_inds() (in module diffnets.tests.test_cli) test_train() (in module diffnets.tests.test_cli)

test_whitening_correctness1() (in module diffnets.tests.test_api) test_whitening_correctness2() (in module diffnets.tests.test_api) test_whitening_correctness3() (in module diffnets.tests.test_api) train() (diffnets.training.Trainer method) Trainer (class in diffnets.training) traj2samples() (diffnets.data_processing.ProcessTraj method)

U

unfreeze_weights() (diffnets.nnutils.ae method) (diffnets.nnutils.split_ae method)

V

vae (class in diffnets.nnutils)

W

WhitenTraj (class in diffnets.data_processing)