Index

_

__init__() (mdlearn.data.datasets.contact_map.ContactMapDataset method) (mdlearn.data.datasets.contact_map.ContactMapHDF5Dataset method) (mdlearn.data.datasets.feature_vector.FeatureVectorDataset method) (mdlearn.data.datasets.feature_vector.FeatureVectorHDF5Dataset method) (mdlearn.data.datasets.feature_vector.TimeFeatureVectorDataset method) (mdlearn.data.datasets.point_cloud.CenterOfMassTransform method) (mdlearn.data.datasets.point_cloud.PointCloudDataset method) (mdlearn.data.datasets.point_cloud.PointCloudDatasetInMemory method) (mdlearn.data.datasets.time_contact_map.ContactMapTimeSeriesDataset method) (mdlearn.nn.models.aae.point_3d_aae.AAE3d method) (mdlearn.nn.models.ae.linear.LinearAE method) (mdlearn.nn.models.ae.linear.LinearAETrainer method) (mdlearn.nn.models.ae.lstm.LSTMAE method) (mdlearn.nn.models.ae.lstm.LSTMAETrainer method) (mdlearn.nn.models.ae.model.AE method) (mdlearn.nn.models.lstm.LSTM method) (mdlearn.nn.models.lstm.LSTMTrainer method) (mdlearn.nn.models.vae.model.VAE method) (mdlearn.nn.models.vae.symmetric_conv2d_vae.SymmetricConv2dVAE method) (mdlearn.nn.models.vae.symmetric_conv2d_vae.SymmetricConv2dVAETrainer method) (mdlearn.nn.models.vde.symmetric_conv2d_vde.SymmetricConv2dVDE method) (mdlearn.nn.models.wae.symmetric_conv2d_wae.SymmetricConv2dWAE method) (mdlearn.nn.modules.conv1d_encoder.Conv1dEncoder method) (mdlearn.nn.modules.dense_net.DenseNet method) (mdlearn.nn.modules.linear_decoder.LinearDecoder method) (mdlearn.nn.modules.linear_discriminator.LinearDiscriminator method) (mdlearn.nn.modules.lstm_net.LSTMNet method) (mdlearn.nn.utils.Trainer method)

A

AAE (class in mdlearn.nn.models.aae.model) AAE3d (class in mdlearn.nn.models.aae.point_3d_aae)

ac_loss() (mdlearn.nn.models.vde.model.VDE method) AE (class in mdlearn.nn.models.ae.model)

B

batch_pairwise_dist() (mdlearn.nn.models.aae.model.ChamferLoss method)

C

CenterOfMassTransform (class in mdlearn.data.datasets.point_cloud) ChamferLoss (class in mdlearn.nn.models.aae.model) ContactMapDataset (class in mdlearn.data.datasets.contact_map) ContactMapHDF5Dataset (class in mdlearn.data.datasets.contact_map) ContactMapTimeSeriesDataset (class in mdlearn.data.datasets.time_contact_map)

Conv1dEncoder (class in mdlearn.nn.modules.conv1d_encoder) Conv2dDecoder (class in mdlearn.nn.modules.conv2d_decoder) Conv2dEncoder (class in mdlearn.nn.modules.conv2d_encoder) conv_output_dim() (in module mdlearn.nn.utils) conv_output_shape() (in module mdlearn.nn.utils) critic_loss() (mdlearn.nn.models.aae.point_3d_aae.AAE3d method)

D

decode() (mdlearn.nn.models.ae.model.AE method) decoder_loss() (mdlearn.nn.models.aae.point_3d_aae.AAE3d method)

DenseNet (class in mdlearn.nn.modules.dense_net) discriminate() (mdlearn.nn.models.aae.model.AAE method) dump_yaml() (mdlearn.utils.BaseSettings method)

E

encode() (mdlearn.nn.models.ae.model.AE method) (mdlearn.nn.models.vae.model.VAE method)

F

FeatureVectorDataset (class in mdlearn.data.datasets.feature_vector) FeatureVectorHDF5Dataset (class in mdlearn.data.datasets.feature_vector) fit() (mdlearn.nn.models.ae.linear.LinearAETrainer method) (mdlearn.nn.models.ae.lstm.LSTMAETrainer method) (mdlearn.nn.models.lstm.LSTMTrainer method) (mdlearn.nn.models.vae.symmetric_conv2d_vae.SymmetricConv2dVAETrainer method) (mdlearn.nn.utils.Trainer method) forward() (mdlearn.nn.models.aae.model.ChamferLoss method) (mdlearn.nn.models.aae.point_3d_aae.AAE3d method) (mdlearn.nn.models.ae.linear.LinearAE method) (mdlearn.nn.models.ae.lstm.LSTMAE method) (mdlearn.nn.models.lstm.LSTM method) (mdlearn.nn.models.vae.symmetric_conv2d_vae.SymmetricConv2dVAE method) (mdlearn.nn.models.vde.symmetric_conv2d_vde.SymmetricConv2dVDE method) (mdlearn.nn.models.wae.symmetric_conv2d_wae.SymmetricConv2dWAE method) (mdlearn.nn.modules.conv1d_encoder.Conv1dEncoder method) (mdlearn.nn.modules.conv2d_decoder.Conv2dDecoder method) (mdlearn.nn.modules.conv2d_encoder.Conv2dEncoder method) (mdlearn.nn.modules.dense_net.DenseNet method) (mdlearn.nn.modules.linear_decoder.LinearDecoder method) (mdlearn.nn.modules.linear_discriminator.LinearDiscriminator method) (mdlearn.nn.modules.lstm_net.LSTMNet method)

from_yaml() (mdlearn.utils.BaseSettings class method)

G

get_activation() (in module mdlearn.nn.utils) get_torch_optimizer() (in module mdlearn.utils)

get_torch_scheduler() (in module mdlearn.utils) gp_loss() (mdlearn.nn.models.aae.point_3d_aae.AAE3d method)

H

hparams (mdlearn.utils.OptimizerConfig attribute) (mdlearn.utils.SchedulerConfig attribute)

I

init() (mdlearn.utils.WandbConfig method) init_weights() (mdlearn.nn.modules.conv2d_decoder.Conv2dDecoder method) (mdlearn.nn.modules.conv2d_encoder.Conv2dEncoder method)

iterative_means_align() (in module mdlearn.data.preprocess.align)

K

kabsch() (in module mdlearn.data.preprocess.align.kabsch_align)

kld_loss() (mdlearn.nn.models.vae.model.VAE method)

L

LinearAE (class in mdlearn.nn.models.ae.linear) LinearAETrainer (class in mdlearn.nn.models.ae.linear) LinearDecoder (class in mdlearn.nn.modules.linear_decoder) LinearDiscriminator (class in mdlearn.nn.modules.linear_discriminator) log_checkpoint() (in module mdlearn.utils)

log_latent_visualization() (in module mdlearn.visualize) LSTM (class in mdlearn.nn.models.lstm) LSTMAE (class in mdlearn.nn.models.ae.lstm) LSTMAETrainer (class in mdlearn.nn.models.ae.lstm) LSTMNet (class in mdlearn.nn.modules.lstm_net) LSTMTrainer (class in mdlearn.nn.models.lstm)

M

mdlearn module mdlearn.data module mdlearn.data.datasets module mdlearn.data.datasets.contact_map module mdlearn.data.datasets.feature_vector module mdlearn.data.datasets.point_cloud module mdlearn.data.datasets.time_contact_map module mdlearn.data.preprocess module mdlearn.data.preprocess.align module mdlearn.data.preprocess.align.kabsch_align module mdlearn.data.preprocess.decorrelation module mdlearn.data.preprocess.decorrelation.spatial module mdlearn.data.preprocess.decorrelation.temporal module mdlearn.data.utils module mdlearn.metrics module mdlearn.nn module mdlearn.nn.models module mdlearn.nn.models.aae module mdlearn.nn.models.aae.model module mdlearn.nn.models.aae.point_3d_aae module mdlearn.nn.models.ae module mdlearn.nn.models.ae.linear module mdlearn.nn.models.ae.lstm module mdlearn.nn.models.ae.model module mdlearn.nn.models.lstm module mdlearn.nn.models.vae module mdlearn.nn.models.vae.model module mdlearn.nn.models.vae.symmetric_conv2d_vae module mdlearn.nn.models.vde module mdlearn.nn.models.vde.model module mdlearn.nn.models.vde.symmetric_conv2d_vde module mdlearn.nn.models.wae module mdlearn.nn.models.wae.model module mdlearn.nn.models.wae.symmetric_conv2d_wae module mdlearn.nn.modules module

mdlearn.nn.modules.conv1d_encoder module mdlearn.nn.modules.conv2d_decoder module mdlearn.nn.modules.conv2d_encoder module mdlearn.nn.modules.dense_net module mdlearn.nn.modules.linear_decoder module mdlearn.nn.modules.linear_discriminator module mdlearn.nn.modules.lstm_net module mdlearn.nn.utils module mdlearn.utils module mdlearn.visualize module metric_cluster_quality() (in module mdlearn.metrics) mmdrf_loss() (mdlearn.nn.models.wae.model.WAE method) model_tag (mdlearn.utils.WandbConfig attribute) module mdlearn mdlearn.data mdlearn.data.datasets mdlearn.data.datasets.contact_map mdlearn.data.datasets.feature_vector mdlearn.data.datasets.point_cloud mdlearn.data.datasets.time_contact_map mdlearn.data.preprocess mdlearn.data.preprocess.align mdlearn.data.preprocess.align.kabsch_align mdlearn.data.preprocess.decorrelation mdlearn.data.preprocess.decorrelation.spatial mdlearn.data.preprocess.decorrelation.temporal mdlearn.data.utils mdlearn.metrics mdlearn.nn mdlearn.nn.models mdlearn.nn.models.aae mdlearn.nn.models.aae.model mdlearn.nn.models.aae.point_3d_aae mdlearn.nn.models.ae mdlearn.nn.models.ae.linear mdlearn.nn.models.ae.lstm mdlearn.nn.models.ae.model mdlearn.nn.models.lstm mdlearn.nn.models.vae mdlearn.nn.models.vae.model mdlearn.nn.models.vae.symmetric_conv2d_vae mdlearn.nn.models.vde mdlearn.nn.models.vde.model mdlearn.nn.models.vde.symmetric_conv2d_vde mdlearn.nn.models.wae mdlearn.nn.models.wae.model mdlearn.nn.models.wae.symmetric_conv2d_wae mdlearn.nn.modules mdlearn.nn.modules.conv1d_encoder mdlearn.nn.modules.conv2d_decoder mdlearn.nn.modules.conv2d_encoder mdlearn.nn.modules.dense_net mdlearn.nn.modules.linear_decoder mdlearn.nn.modules.linear_discriminator mdlearn.nn.modules.lstm_net mdlearn.nn.utils mdlearn.utils mdlearn.visualize mse_loss() (mdlearn.nn.models.ae.lstm.LSTMAE method) (mdlearn.nn.models.lstm.LSTM method)

N

name (mdlearn.utils.OptimizerConfig attribute) (mdlearn.utils.SchedulerConfig attribute)

P

parse_args() (in module mdlearn.utils) plot_scatter() (in module mdlearn.visualize) point_cloud_size (mdlearn.data.datasets.point_cloud.PointCloudDataset property) PointCloudDataset (class in mdlearn.data.datasets.point_cloud) PointCloudDatasetInMemory (class in mdlearn.data.datasets.point_cloud)

predict() (mdlearn.nn.models.ae.linear.LinearAETrainer method) (mdlearn.nn.models.ae.lstm.LSTMAETrainer method) (mdlearn.nn.models.lstm.LSTMTrainer method) (mdlearn.nn.models.vae.symmetric_conv2d_vae.SymmetricConv2dVAETrainer method) (mdlearn.nn.utils.Trainer method)

R

recon_loss() (mdlearn.nn.models.aae.point_3d_aae.AAE3d method) (mdlearn.nn.models.ae.linear.LinearAE method) (mdlearn.nn.models.ae.model.AE method) reparametrize() (mdlearn.nn.models.vae.model.VAE method)

reset() (in module mdlearn.nn.utils) reset_parameters() (mdlearn.nn.models.aae.model.AAE method) (mdlearn.nn.models.ae.model.AE method) resume_checkpoint() (in module mdlearn.utils)

S

same_padding() (in module mdlearn.nn.utils) SD2() (in module mdlearn.data.preprocess.decorrelation.spatial) SD4() (in module mdlearn.data.preprocess.decorrelation.spatial) step_scheduler() (mdlearn.nn.utils.Trainer method)

SymmetricConv2dVAE (class in mdlearn.nn.models.vae.symmetric_conv2d_vae) SymmetricConv2dVAETrainer (class in mdlearn.nn.models.vae.symmetric_conv2d_vae) SymmetricConv2dVDE (class in mdlearn.nn.models.vde.symmetric_conv2d_vde) SymmetricConv2dWAE (class in mdlearn.nn.models.wae.symmetric_conv2d_wae)

T

TimeFeatureVectorDataset (class in mdlearn.data.datasets.feature_vector) train_valid_split() (in module mdlearn.data.utils)

Trainer (class in mdlearn.nn.utils) transform() (mdlearn.data.datasets.point_cloud.CenterOfMassTransform method)

V

VAE (class in mdlearn.nn.models.vae.model)

VDE (class in mdlearn.nn.models.vde.model)

W

WAE (class in mdlearn.nn.models.wae.model)

wandb_entity_name (mdlearn.utils.WandbConfig attribute) wandb_project_name (mdlearn.utils.WandbConfig attribute)