Index

A

activation (tensorclouds.nn.attention.EquivariantSelfAttention attribute) (tensorclouds.nn.spatial.CompleteSpatialConvolution attribute) (tensorclouds.nn.spatial.kNNSpatialConvolution attribute) align_with_rotation() (in module tensorclouds.utils) ApproximateTimeEmbed (class in tensorclouds.nn.embed)

assembly_to_tensor_cloud() (in module tensorclouds.data.protein) atom_perm_loss (tensorclouds.nn.utils.ModelOutput attribute) attention (tensorclouds.nn.spatial.CompleteSpatialConvolution attribute) attn_bias (tensorclouds.nn.attention.EquivariantSelfAttention attribute) (tensorclouds.nn.transformer.Transformer attribute) (tensorclouds.nn.transformer.TransformerBlock attribute)

B

base (tensorclouds.nn.self_interaction.SelfInteraction attribute)

basis (tensorclouds.nn.embed.SpatialDistanceEmbed attribute)

C

CA_INDEX (in module tensorclouds.loss.losses) centralize() (tensorclouds.nn.TensorCloud method) (tensorclouds.TensorCloud method) (tensorclouds.tensorcloud.TensorCloud method) ChannelWiseTensorSquareSelfInteraction (class in tensorclouds.nn.self_interaction) clip_grads() (in module tensorclouds.nn.utils) CompleteSpatialConvolution (class in tensorclouds.nn.spatial) compute_constants() (in module tensorclouds.transport.diffusion) compute_rotation_for_alignment() (in module tensorclouds.utils) compute_xt() (tensorclouds.transport.mirror_interpolant.TensorCloudMirrorInterpolant method) (tensorclouds.transport.one_sided_interpolant.TensorCloudOneSidedInterpolant method) (tensorclouds.transport.two_sided_interpolant.TensorCloudTwoSidedInterpolant method)

concatenate() (tensorclouds.nn.TensorCloud class method) (tensorclouds.TensorCloud class method) (tensorclouds.tensorcloud.TensorCloud class method) convolution_indices() (in module tensorclouds.nn.sequence) coord (tensorclouds.nn.TensorCloud attribute), [1] (tensorclouds.TensorCloud attribute), [1] (tensorclouds.tensorcloud.TensorCloud attribute), [1] coords_mean (tensorclouds.random.normal.NormalDistribution attribute) coords_scale (tensorclouds.random.normal.NormalDistribution attribute) create() (tensorclouds.tensorcloud.TensorClouds class method) create_radius_graph() (in module tensorclouds.nn.radius_graph) cut (tensorclouds.nn.embed.SpatialDistanceEmbed attribute)

D

datum (tensorclouds.nn.utils.ModelOutput attribute) decoder_internals (tensorclouds.nn.utils.ModelOutput attribute) depth (tensorclouds.nn.self_interaction.SelfInteraction attribute) (tensorclouds.nn.transformer.Transformer attribute) diff_loss (tensorclouds.nn.utils.ModelOutput attribute) dim (tensorclouds.nn.embed.SequenceDistanceEmbed attribute) (tensorclouds.nn.embed.SpatialDistanceEmbed attribute)

dot() (tensorclouds.nn.TensorCloud method) (tensorclouds.TensorCloud method) (tensorclouds.tensorcloud.TensorCloud method) dotdict (class in tensorclouds.nn.utils) down_conv_seq_len() (in module tensorclouds.nn.utils) Downsample (class in tensorclouds.nn.pooling) DriftPrediction (class in tensorclouds.transport.one_sided_interpolant) (class in tensorclouds.transport.two_sided_interpolant)

E

edge_irreps (tensorclouds.nn.spatial.CompleteSpatialConvolution attribute) (tensorclouds.nn.spatial.kNNSpatialConvolution attribute) Embed (class in tensorclouds.nn.embed) EmbeddingsDataset (class in tensorclouds.nn.utils) empty() (tensorclouds.nn.TensorCloud class method) (tensorclouds.TensorCloud class method) (tensorclouds.tensorcloud.TensorCloud class method)

encoder_internals (tensorclouds.nn.utils.ModelOutput attribute) envelope (tensorclouds.nn.spatial.kNNSpatialConvolution attribute) EquivariantLayerNorm (class in tensorclouds.nn.layer_norm) EquivariantSelfAttention (class in tensorclouds.nn.attention)

F

factor (tensorclouds.nn.feed_forward.FeedForward attribute) FeedForward (class in tensorclouds.nn.feed_forward) ff_factor (tensorclouds.nn.transformer.Transformer attribute) (tensorclouds.nn.transformer.TransformerBlock attribute)

FullTensorSquareSelfInteraction (class in tensorclouds.nn.self_interaction) function (tensorclouds.nn.residual.Residual attribute)

H

HarmonicDistribution (class in tensorclouds.random.harmonic)

I

inner_split() (in module tensorclouds.nn.utils) inner_stack() (in module tensorclouds.nn.utils) InternalVectorLoss (class in tensorclouds.loss.losses) irreps (tensorclouds.nn.feed_forward.FeedForward attribute) (tensorclouds.nn.self_interaction.ChannelWiseTensorSquareSelfInteraction attribute) (tensorclouds.nn.self_interaction.FullTensorSquareSelfInteraction attribute) (tensorclouds.nn.self_interaction.SegmentedTensorSquareSelfInteraction attribute) (tensorclouds.nn.self_interaction.SelfInteraction attribute) (tensorclouds.nn.TensorCloud property) (tensorclouds.nn.transformer.Transformer attribute) (tensorclouds.nn.transformer.TransformerBlock attribute) (tensorclouds.random.harmonic.HarmonicDistribution attribute) (tensorclouds.TensorCloud property) (tensorclouds.tensorcloud.TensorCloud property) (tensorclouds.tensorcloud.TensorClouds attribute) (tensorclouds.transport.diffusion.TensorCloudDiffuser attribute) (tensorclouds.transport.flow_matching.TensorCloudFlowMatcher attribute)

irreps_array (tensorclouds.nn.TensorCloud attribute), [1] (tensorclouds.TensorCloud attribute), [1] (tensorclouds.tensorcloud.TensorCloud attribute), [1] irreps_in (tensorclouds.random.normal.NormalDistribution attribute) irreps_mean (tensorclouds.random.normal.NormalDistribution attribute) irreps_out (tensorclouds.nn.attention.EquivariantSelfAttention attribute) (tensorclouds.nn.pooling.Downsample attribute) (tensorclouds.nn.pooling.Upsample attribute) (tensorclouds.nn.self_interaction.SelfInteraction attribute) (tensorclouds.nn.sequence.SequenceConvolution attribute) (tensorclouds.nn.sequence.TransposeSequenceConvolution attribute) (tensorclouds.nn.spatial.CompleteSpatialConvolution attribute) (tensorclouds.nn.spatial.kNNSpatialConvolution attribute) irreps_scale (tensorclouds.random.normal.NormalDistribution attribute)

K

k (tensorclouds.nn.embed.SequenceDistanceEmbed attribute) (tensorclouds.nn.spatial.kNNSpatialConvolution attribute) k_seq (tensorclouds.nn.spatial.CompleteSpatialConvolution attribute) (tensorclouds.nn.spatial.kNNSpatialConvolution attribute) kernel_size (tensorclouds.nn.pooling.Downsample attribute) (tensorclouds.nn.pooling.Upsample attribute) (tensorclouds.nn.sequence.SequenceConvolution attribute) (tensorclouds.nn.sequence.TransposeSequenceConvolution attribute)

knn() (in module tensorclouds.nn.spatial) kNNSpatialConvolution (class in tensorclouds.nn.spatial)

L

l2_norm() (in module tensorclouds.nn.utils) label (tensorclouds.nn.TensorCloud attribute), [1] (tensorclouds.TensorCloud attribute), [1] (tensorclouds.tensorcloud.TensorCloud attribute), [1] leading_shape (tensorclouds.transport.diffusion.TensorCloudDiffuser attribute) (tensorclouds.transport.flow_matching.TensorCloudFlowMatcher attribute) (tensorclouds.transport.mirror_interpolant.TensorCloudMirrorInterpolant attribute) (tensorclouds.transport.one_sided_interpolant.TensorCloudOneSidedInterpolant attribute) (tensorclouds.transport.two_sided_interpolant.TensorCloudTwoSidedInterpolant attribute)

ligand_to_point_cloud() (in module tensorclouds.data.protein) linear_beta_schedule() (in module tensorclouds.transport.diffusion) log_likelihood() (tensorclouds.random.normal.NormalDistribution method)

M

mask (tensorclouds.nn.TensorCloud property) (tensorclouds.TensorCloud property) (tensorclouds.tensorcloud.TensorCloud property) mask_coord (tensorclouds.nn.TensorCloud attribute), [1] (tensorclouds.TensorCloud attribute), [1] (tensorclouds.tensorcloud.TensorCloud attribute), [1] (tensorclouds.tensorcloud.TensorClouds property) mask_irreps_array (tensorclouds.nn.TensorCloud attribute), [1] (tensorclouds.TensorCloud attribute), [1] (tensorclouds.tensorcloud.TensorCloud attribute), [1] (tensorclouds.tensorcloud.TensorClouds property) mode (tensorclouds.nn.pooling.Downsample attribute) (tensorclouds.nn.pooling.Upsample attribute) (tensorclouds.nn.sequence.SequenceConvolution attribute) (tensorclouds.nn.sequence.TransposeSequenceConvolution attribute) ModelOutput (class in tensorclouds.nn.utils) ModelPrediction (class in tensorclouds.transport.diffusion) (class in tensorclouds.transport.flow_matching) (class in tensorclouds.transport.utils) module tensorclouds tensorclouds.data tensorclouds.data.protein tensorclouds.data.rna tensorclouds.loss tensorclouds.loss.losses tensorclouds.loss.matching tensorclouds.loss.stochastic_interpolant tensorclouds.nn tensorclouds.nn.attention tensorclouds.nn.egnn tensorclouds.nn.embed tensorclouds.nn.feed_forward tensorclouds.nn.layer_norm tensorclouds.nn.pooling tensorclouds.nn.radius_graph tensorclouds.nn.residual tensorclouds.nn.self_interaction tensorclouds.nn.sequence tensorclouds.nn.spatial tensorclouds.nn.tensor_fields tensorclouds.nn.transformer tensorclouds.nn.utils tensorclouds.random tensorclouds.random.harmonic tensorclouds.random.normal tensorclouds.tensorcloud tensorclouds.transport tensorclouds.transport.diffusion tensorclouds.transport.flow_matching tensorclouds.transport.mirror_interpolant tensorclouds.transport.one_sided_interpolant tensorclouds.transport.transport tensorclouds.transport.two_sided_interpolant tensorclouds.transport.utils tensorclouds.utils

move (tensorclouds.nn.attention.EquivariantSelfAttention attribute) (tensorclouds.nn.spatial.CompleteSpatialConvolution attribute) (tensorclouds.nn.spatial.kNNSpatialConvolution attribute) (tensorclouds.nn.transformer.Transformer attribute) (tensorclouds.nn.transformer.TransformerBlock attribute) moving_window() (in module tensorclouds.nn.sequence) multiscale_irreps() (in module tensorclouds.nn.utils)

N

N (tensorclouds.random.harmonic.HarmonicDistribution attribute) network (tensorclouds.transport.diffusion.TensorCloudDiffuser attribute) (tensorclouds.transport.flow_matching.TensorCloudFlowMatcher attribute) (tensorclouds.transport.mirror_interpolant.TensorCloudMirrorInterpolant attribute) (tensorclouds.transport.one_sided_interpolant.TensorCloudOneSidedInterpolant attribute) (tensorclouds.transport.two_sided_interpolant.TensorCloudTwoSidedInterpolant attribute) next_multiple() (in module tensorclouds.nn.utils) NoisePrediction (class in tensorclouds.transport.one_sided_interpolant) (class in tensorclouds.transport.two_sided_interpolant) norm (tensorclouds.nn.residual.Residual attribute) (tensorclouds.nn.self_interaction.ChannelWiseTensorSquareSelfInteraction attribute) (tensorclouds.nn.self_interaction.FullTensorSquareSelfInteraction attribute) (tensorclouds.nn.self_interaction.SegmentedTensorSquareSelfInteraction attribute) (tensorclouds.nn.sequence.SequenceConvolution attribute) (tensorclouds.nn.sequence.TransposeSequenceConvolution attribute) (tensorclouds.nn.spatial.CompleteSpatialConvolution attribute) (tensorclouds.nn.spatial.kNNSpatialConvolution attribute)

norm() (tensorclouds.nn.TensorCloud method) (tensorclouds.TensorCloud method) (tensorclouds.tensorcloud.TensorCloud method) norm_last (tensorclouds.nn.self_interaction.SelfInteraction attribute) norm_only (tensorclouds.loss.losses.InternalVectorLoss attribute) NormalDistribution (class in tensorclouds.random.normal) nuc_to_tensor_cloud() (in module tensorclouds.data.rna) num_heads (tensorclouds.nn.attention.EquivariantSelfAttention attribute)

O

OnehotTimeEmbed (class in tensorclouds.nn.embed) ones_like() (tensorclouds.nn.TensorCloud class method) (tensorclouds.TensorCloud class method) (tensorclouds.tensorcloud.TensorCloud class method)

P

p_t() (tensorclouds.transport.flow_matching.TensorCloudFlowMatcher method) PairwiseEmbed (class in tensorclouds.nn.embed) path (tensorclouds.nn.utils.EmbeddingsDataset attribute) plot() (tensorclouds.nn.TensorCloud method) (tensorclouds.TensorCloud method) (tensorclouds.tensorcloud.TensorCloud method) prediction (tensorclouds.transport.diffusion.ModelPrediction attribute) (tensorclouds.transport.flow_matching.ModelPrediction attribute) (tensorclouds.transport.one_sided_interpolant.DriftPrediction attribute) (tensorclouds.transport.one_sided_interpolant.NoisePrediction attribute) (tensorclouds.transport.two_sided_interpolant.DriftPrediction attribute) (tensorclouds.transport.two_sided_interpolant.NoisePrediction attribute) (tensorclouds.transport.utils.ModelPrediction attribute)

protein_to_tensor_cloud() (in module tensorclouds.data.protein)

Q

q_sample() (tensorclouds.transport.diffusion.TensorCloudDiffuser method)

R

radial_basis (tensorclouds.nn.spatial.CompleteSpatialConvolution attribute) (tensorclouds.nn.spatial.kNNSpatialConvolution attribute) radial_bins (tensorclouds.nn.spatial.CompleteSpatialConvolution attribute) (tensorclouds.nn.spatial.kNNSpatialConvolution attribute) radial_cut (tensorclouds.nn.spatial.CompleteSpatialConvolution attribute) (tensorclouds.nn.spatial.kNNSpatialConvolution attribute) replace() (tensorclouds.nn.TensorCloud method) (tensorclouds.TensorCloud method) (tensorclouds.tensorcloud.TensorCloud method) (tensorclouds.tensorcloud.TensorClouds method)

rescale_irreps() (in module tensorclouds.nn.utils) Residual (class in tensorclouds.nn.residual) reweight (tensorclouds.transport.diffusion.ModelPrediction attribute) (tensorclouds.transport.flow_matching.ModelPrediction attribute) (tensorclouds.transport.utils.ModelPrediction attribute) rms() (in module tensorclouds.nn.layer_norm)

S

safe_norm() (in module tensorclouds.nn.utils) safe_normalize() (in module tensorclouds.nn.utils) sample() (tensorclouds.random.harmonic.HarmonicDistribution method) (tensorclouds.random.normal.NormalDistribution method) (tensorclouds.transport.diffusion.TensorCloudDiffuser method) (tensorclouds.transport.flow_matching.TensorCloudFlowMatcher method) (tensorclouds.transport.mirror_interpolant.TensorCloudMirrorInterpolant method) (tensorclouds.transport.one_sided_interpolant.TensorCloudOneSidedInterpolant method) (tensorclouds.transport.two_sided_interpolant.TensorCloudTwoSidedInterpolant method) sample_like() (tensorclouds.random.normal.NormalDistribution method) segment_size (tensorclouds.nn.self_interaction.SegmentedTensorSquareSelfInteraction attribute) SegmentedTensorSquareSelfInteraction (class in tensorclouds.nn.self_interaction) SelfInteraction (class in tensorclouds.nn.self_interaction) SequenceConvolution (class in tensorclouds.nn.sequence) SequenceDistanceEmbed (class in tensorclouds.nn.embed) setup() (tensorclouds.transport.diffusion.TensorCloudDiffuser method) (tensorclouds.transport.flow_matching.TensorCloudFlowMatcher method) (tensorclouds.transport.one_sided_interpolant.TensorCloudOneSidedInterpolant method) (tensorclouds.transport.two_sided_interpolant.TensorCloudTwoSidedInterpolant method)

shape (tensorclouds.nn.TensorCloud property) (tensorclouds.TensorCloud property) (tensorclouds.tensorcloud.TensorCloud property) shapes (tensorclouds.tensorcloud.TensorClouds property) sigmoid_beta_schedule() (in module tensorclouds.transport.diffusion) SpatialDistanceEmbed (class in tensorclouds.nn.embed) split() (tensorclouds.nn.TensorCloud method) (tensorclouds.TensorCloud method) (tensorclouds.tensorcloud.TensorCloud method) stack() (tensorclouds.nn.TensorCloud class method) (tensorclouds.TensorCloud class method) (tensorclouds.tensorcloud.TensorCloud class method) StochasticInterpolantLoss (class in tensorclouds.loss.stochastic_interpolant) stride (tensorclouds.nn.pooling.Downsample attribute) (tensorclouds.nn.pooling.Upsample attribute) (tensorclouds.nn.sequence.SequenceConvolution attribute) (tensorclouds.nn.sequence.TransposeSequenceConvolution attribute)

T

target (tensorclouds.transport.diffusion.ModelPrediction attribute) (tensorclouds.transport.flow_matching.ModelPrediction attribute) (tensorclouds.transport.one_sided_interpolant.DriftPrediction attribute) (tensorclouds.transport.one_sided_interpolant.NoisePrediction attribute) (tensorclouds.transport.two_sided_interpolant.DriftPrediction attribute) (tensorclouds.transport.two_sided_interpolant.NoisePrediction attribute) (tensorclouds.transport.utils.ModelPrediction attribute) tensor_cloud_to_assembly() (in module tensorclouds.data.protein) tensor_cloud_to_ligand() (in module tensorclouds.data.protein) tensor_cloud_to_nuc() (in module tensorclouds.data.rna) tensor_cloud_to_protein() (in module tensorclouds.data.protein) TensorCloud (class in tensorclouds) (class in tensorclouds.nn) (class in tensorclouds.tensorcloud) TensorCloudDiffuser (class in tensorclouds.transport.diffusion) TensorCloudFlowMatcher (class in tensorclouds.transport.flow_matching) TensorCloudMatchingLoss (class in tensorclouds.loss.matching) TensorCloudMirrorInterpolant (class in tensorclouds.transport.mirror_interpolant) TensorCloudOneSidedInterpolant (class in tensorclouds.transport.one_sided_interpolant) tensorclouds module TensorClouds (class in tensorclouds.tensorcloud) tensorclouds.data module tensorclouds.data.protein module tensorclouds.data.rna module tensorclouds.loss module tensorclouds.loss.losses module tensorclouds.loss.matching module tensorclouds.loss.stochastic_interpolant module tensorclouds.nn module tensorclouds.nn.attention module tensorclouds.nn.egnn module tensorclouds.nn.embed module tensorclouds.nn.feed_forward module tensorclouds.nn.layer_norm module tensorclouds.nn.pooling module

tensorclouds.nn.radius_graph module tensorclouds.nn.residual module tensorclouds.nn.self_interaction module tensorclouds.nn.sequence module tensorclouds.nn.spatial module tensorclouds.nn.tensor_fields module tensorclouds.nn.transformer module tensorclouds.nn.utils module tensorclouds.random module tensorclouds.random.harmonic module tensorclouds.random.normal module tensorclouds.tensorcloud module tensorclouds.transport module tensorclouds.transport.diffusion module tensorclouds.transport.flow_matching module tensorclouds.transport.mirror_interpolant module tensorclouds.transport.one_sided_interpolant module tensorclouds.transport.transport module tensorclouds.transport.two_sided_interpolant module tensorclouds.transport.utils module tensorclouds.utils module TensorCloudTwoSidedInterpolant (class in tensorclouds.transport.two_sided_interpolant) time_range (tensorclouds.nn.embed.OnehotTimeEmbed attribute) timesteps (tensorclouds.nn.embed.ApproximateTimeEmbed attribute) (tensorclouds.nn.embed.OnehotTimeEmbed attribute) (tensorclouds.transport.diffusion.TensorCloudDiffuser attribute) Transformer (class in tensorclouds.nn.transformer) TransformerBlock (class in tensorclouds.nn.transformer) TransposeSequenceConvolution (class in tensorclouds.nn.sequence)

U

up_conv_seq_len() (in module tensorclouds.nn.utils)

Upsample (class in tensorclouds.nn.pooling)

V

var_coords (tensorclouds.transport.diffusion.TensorCloudDiffuser attribute) (tensorclouds.transport.flow_matching.TensorCloudFlowMatcher attribute) (tensorclouds.transport.mirror_interpolant.TensorCloudMirrorInterpolant attribute) (tensorclouds.transport.one_sided_interpolant.TensorCloudOneSidedInterpolant attribute) (tensorclouds.transport.two_sided_interpolant.TensorCloudTwoSidedInterpolant attribute) var_features (tensorclouds.random.harmonic.HarmonicDistribution attribute) (tensorclouds.transport.diffusion.TensorCloudDiffuser attribute) (tensorclouds.transport.flow_matching.TensorCloudFlowMatcher attribute) (tensorclouds.transport.mirror_interpolant.TensorCloudMirrorInterpolant attribute) (tensorclouds.transport.one_sided_interpolant.TensorCloudOneSidedInterpolant attribute) (tensorclouds.transport.two_sided_interpolant.TensorCloudTwoSidedInterpolant attribute)

vector_cloud_matching_loss() (in module tensorclouds.loss.losses)

W

weighted (tensorclouds.nn.sequence.SequenceConvolution attribute) (tensorclouds.nn.sequence.TransposeSequenceConvolution attribute)

Z

zeros() (tensorclouds.nn.TensorCloud class method) (tensorclouds.TensorCloud class method) (tensorclouds.tensorcloud.TensorCloud class method)

zeros_like() (tensorclouds.nn.TensorCloud class method) (tensorclouds.TensorCloud class method) (tensorclouds.tensorcloud.TensorCloud class method)