Index

_

__init__() (terminator.data.data.TERMBatchSampler method) (terminator.data.data.TERMDataset method) (terminator.data.data.TERMLazyBatchSampler method) (terminator.data.data.TERMLazyDataset method) (terminator.models.layers.condense.CondenseTERM method) (terminator.models.layers.condense.ContactIndexEncoding method) (terminator.models.layers.condense.EdgeFeatures method) (terminator.models.layers.condense.ResidueFeatures method) (terminator.models.layers.energies.gvp.EdgeLayer method) (terminator.models.layers.energies.gvp.GVPPairEnergies method) (terminator.models.layers.energies.s2s.AblatedPairEnergies method) (terminator.models.layers.energies.s2s.PairEnergies method) (terminator.models.layers.graph_features.IndexDiffEncoding method) (terminator.models.layers.graph_features.MultiChainProteinFeatures method) (terminator.models.layers.graph_features.PositionalEncodings method) (terminator.models.layers.graph_features.ProteinFeatures method) (terminator.models.layers.gvp.Dropout method) (terminator.models.layers.gvp.GVP method) (terminator.models.layers.gvp.GVPConv method) (terminator.models.layers.gvp.GVPConvLayer method) (terminator.models.layers.gvp.LayerNorm method) (terminator.models.layers.s2s_modules.EdgeEndpointAttention method) (terminator.models.layers.s2s_modules.EdgeMPNNLayer method) (terminator.models.layers.s2s_modules.EdgeTransformerLayer method) (terminator.models.layers.s2s_modules.NeighborAttention method) (terminator.models.layers.s2s_modules.NodeMPNNLayer method) (terminator.models.layers.s2s_modules.NodeTransformerLayer method) (terminator.models.layers.s2s_modules.Normalize method) (terminator.models.layers.s2s_modules.PositionWiseFeedForward method) (terminator.models.layers.term.graph.s2s.TERMEdgeEndpointAttention method) (terminator.models.layers.term.graph.s2s.TERMEdgeMPNNLayer method) (terminator.models.layers.term.graph.s2s.TERMEdgeTransformerLayer method) (terminator.models.layers.term.graph.s2s.TERMGraphTransformerEncoder method) (terminator.models.layers.term.graph.s2s.TERMNeighborAttention method) (terminator.models.layers.term.graph.s2s.TERMNodeMPNNLayer method) (terminator.models.layers.term.graph.s2s.TERMNodeTransformerLayer method) (terminator.models.layers.term.matches.attn.TERMMatchAttention method) (terminator.models.layers.term.matches.attn.TERMMatchTransformerEncoder method) (terminator.models.layers.term.matches.attn.TERMMatchTransformerLayer method) (terminator.models.layers.term.matches.cnn.Conv1DResidual method) (terminator.models.layers.term.matches.cnn.Conv1DResNet method) (terminator.models.TERMinator.TERMinator method) (terminator.utils.model.optim.NoamOpt method)

_agg_nodes() (terminator.models.layers.condense.CondenseTERM method) _cluster() (terminator.data.data.TERMBatchSampler method) (terminator.data.data.TERMLazyBatchSampler method) _contacts() (terminator.models.layers.graph_features.ProteinFeatures method) _dist() (terminator.models.layers.graph_features.ProteinFeatures method) _edges() (terminator.models.layers.condense.CondenseTERM method) _from_gvp_outputs() (terminator.models.TERMinator.TERMinator method) _hbonds() (terminator.models.layers.graph_features.ProteinFeatures method) _masked_softmax() (terminator.models.layers.s2s_modules.EdgeEndpointAttention method) (terminator.models.layers.s2s_modules.NeighborAttention method) (terminator.models.layers.term.graph.s2s.TERMEdgeEndpointAttention method) (terminator.models.layers.term.graph.s2s.TERMNeighborAttention method) (terminator.models.layers.term.matches.attn.TERMMatchAttention method) _matches() (terminator.models.layers.condense.CondenseTERM method) _quaternions() (terminator.models.layers.graph_features.ProteinFeatures method) _term_mpnn() (terminator.models.layers.condense.CondenseTERM method) _to_gvp_input() (terminator.models.TERMinator.TERMinator method)

A

aa_three_to_one() (in module terminator.utils.common)

AblatedPairEnergies (class in terminator.models.layers.energies.s2s) aggregate_edges() (in module terminator.models.layers.utils)

B

batchify() (in module terminator.models.layers.utils)

C

cat_edge_endpoints() (in module terminator.models.layers.utils) cat_neighbors_nodes() (in module terminator.models.layers.utils) cat_term_edge_endpoints() (in module terminator.models.layers.utils) cat_term_neighbors_nodes() (in module terminator.models.layers.utils) CondenseTERM (class in terminator.models.layers.condense) construct_loss_fn() (in module terminator.utils.model.loss_fn)

contact_idx() (in module scripts.data.preprocessing.parseTERM) ContactIndexEncoding (class in terminator.models.layers.condense) Conv1DResidual (class in terminator.models.layers.term.matches.cnn) Conv1DResNet (class in terminator.models.layers.term.matches.cnn) conv1xN() (in module terminator.models.layers.term.matches.cnn) convert() (in module terminator.data.data) covariation_features() (in module terminator.models.layers.condense)

D

dataGen() (in module scripts.data.preprocessing.cleanStructs) (in module scripts.data.preprocessing.generateDataset)

Dropout (class in terminator.models.layers.gvp) dumpCoordsTensors() (in module scripts.data.preprocessing.packageTensors) dumpTrainingTensors() (in module scripts.data.preprocessing.packageTensors)

E

EdgeEndpointAttention (class in terminator.models.layers.s2s_modules) EdgeFeatures (class in terminator.models.layers.condense) EdgeLayer (class in terminator.models.layers.energies.gvp) EdgeMPNNLayer (class in terminator.models.layers.s2s_modules)

EdgeTransformerLayer (class in terminator.models.layers.s2s_modules) eprint() (in module scripts.data.postprocessing.to_etab) etab_l1_norm_penalty() (in module terminator.utils.model.loss_fn) etab_norm_penalty() (in module terminator.utils.model.loss_fn) extractBackbone() (in module scripts.data.preprocessing.cleanStructs)

F

find_dtermen_folder() (in module scripts.data.postprocessing.search_utils) find_pdb_path() (in module scripts.data.postprocessing.search_utils) forward() (terminator.models.layers.condense.CondenseTERM method) (terminator.models.layers.condense.ContactIndexEncoding method) (terminator.models.layers.condense.EdgeFeatures method) (terminator.models.layers.condense.ResidueFeatures method) (terminator.models.layers.energies.gvp.EdgeLayer method) (terminator.models.layers.energies.gvp.GVPPairEnergies method) (terminator.models.layers.energies.s2s.AblatedPairEnergies method) (terminator.models.layers.energies.s2s.PairEnergies method) (terminator.models.layers.graph_features.IndexDiffEncoding method) (terminator.models.layers.graph_features.MultiChainProteinFeatures method) (terminator.models.layers.graph_features.PositionalEncodings method) (terminator.models.layers.graph_features.ProteinFeatures method) (terminator.models.layers.gvp.Dropout method) (terminator.models.layers.gvp.GVP method) (terminator.models.layers.gvp.GVPConv method) (terminator.models.layers.gvp.GVPConvLayer method) (terminator.models.layers.gvp.LayerNorm method) (terminator.models.layers.s2s_modules.EdgeEndpointAttention method) (terminator.models.layers.s2s_modules.EdgeMPNNLayer method) (terminator.models.layers.s2s_modules.EdgeTransformerLayer method) (terminator.models.layers.s2s_modules.NeighborAttention method) (terminator.models.layers.s2s_modules.NodeMPNNLayer method) (terminator.models.layers.s2s_modules.NodeTransformerLayer method) (terminator.models.layers.s2s_modules.Normalize method) (terminator.models.layers.s2s_modules.PositionWiseFeedForward method) (terminator.models.layers.term.graph.s2s.TERMEdgeEndpointAttention method) (terminator.models.layers.term.graph.s2s.TERMEdgeMPNNLayer method) (terminator.models.layers.term.graph.s2s.TERMEdgeTransformerLayer method) (terminator.models.layers.term.graph.s2s.TERMGraphTransformerEncoder method) (terminator.models.layers.term.graph.s2s.TERMNeighborAttention method) (terminator.models.layers.term.graph.s2s.TERMNodeMPNNLayer method) (terminator.models.layers.term.graph.s2s.TERMNodeTransformerLayer method) (terminator.models.layers.term.matches.attn.TERMMatchAttention method) (terminator.models.layers.term.matches.attn.TERMMatchTransformerEncoder method) (terminator.models.layers.term.matches.attn.TERMMatchTransformerLayer method) (terminator.models.layers.term.matches.cnn.Conv1DResidual method) (terminator.models.layers.term.matches.cnn.Conv1DResNet method) (terminator.models.TERMinator.TERMinator method)

G

gather_edges() (in module terminator.models.layers.utils) gather_nodes() (in module terminator.models.layers.utils) gather_pairEs() (in module terminator.models.layers.utils) gather_term_edges() (in module terminator.models.layers.utils) gather_term_nodes() (in module terminator.models.layers.utils) generateCoordsDir() (in module scripts.data.preprocessing.cleanStructs)

generateDatasetParallel() (in module scripts.data.preprocessing.generateDataset) get_idx_dict() (in module scripts.data.postprocessing.to_etab) get_std_opt() (in module terminator.utils.model.optim) GVP (class in terminator.models.layers.gvp) GVPConv (class in terminator.models.layers.gvp) GVPConvLayer (class in terminator.models.layers.gvp) GVPPairEnergies (class in terminator.models.layers.energies.gvp)

I

IndexDiffEncoding (class in terminator.models.layers.graph_features)

ints_to_seq() (in module terminator.utils.common)

L

LayerNorm (class in terminator.models.layers.gvp)

load_file() (in module terminator.data.data)

M

main() (in module scripts.data.preprocessing.split_datasets) merge_duplicate_edges() (in module terminator.models.layers.utils) merge_duplicate_edges_geometric() (in module terminator.models.layers.utils) merge_duplicate_pairE() (in module terminator.models.layers.utils) merge_duplicate_pairE_dense() (in module terminator.models.layers.utils) merge_duplicate_pairE_geometric() (in module terminator.models.layers.utils) merge_duplicate_pairE_sparse() (in module terminator.models.layers.utils) merge_duplicate_term_edges() (in module terminator.models.layers.utils) message() (terminator.models.layers.gvp.GVPConv method) mindren_etab_norm_penalty() (in module terminator.utils.model.loss_fn) module scripts.analysis scripts.data.postprocessing scripts.data.postprocessing.batch_arr_dTERMen scripts.data.postprocessing.fix_dTERMen scripts.data.postprocessing.search_utils scripts.data.postprocessing.summarize_results scripts.data.postprocessing.to_etab scripts.data.preprocessing scripts.data.preprocessing.cleanStructs scripts.data.preprocessing.generateDataset scripts.data.preprocessing.packageTensors scripts.data.preprocessing.parseCoords scripts.data.preprocessing.parseEtab scripts.data.preprocessing.parseTERM scripts.data.preprocessing.split_datasets scripts.models.eval scripts.models.eval.eval scripts.models.train terminator terminator.data terminator.data.data terminator.models terminator.models.layers terminator.models.layers.condense terminator.models.layers.energies terminator.models.layers.energies.gvp terminator.models.layers.energies.s2s terminator.models.layers.graph_features terminator.models.layers.gvp terminator.models.layers.s2s_modules terminator.models.layers.term terminator.models.layers.term.graph terminator.models.layers.term.graph.s2s terminator.models.layers.term.matches terminator.models.layers.term.matches.attn terminator.models.layers.term.matches.cnn terminator.models.layers.utils terminator.models.TERMinator terminator.utils terminator.utils.common terminator.utils.model terminator.utils.model.default_hparams terminator.utils.model.loop_utils terminator.utils.model.loss_fn terminator.utils.model.optim

MultiChainProteinFeatures (class in terminator.models.layers.graph_features)

N

NeighborAttention (class in terminator.models.layers.s2s_modules) nlcpl() (in module terminator.utils.model.loss_fn) nlcpl_full() (in module terminator.utils.model.loss_fn) nlcpl_test() (in module terminator.utils.model.loss_fn)

nlpl() (in module terminator.utils.model.loss_fn) NoamOpt (class in terminator.utils.model.optim) NodeMPNNLayer (class in terminator.models.layers.s2s_modules) NodeTransformerLayer (class in terminator.models.layers.s2s_modules) Normalize (class in terminator.models.layers.s2s_modules)

P

package() (terminator.data.data.TERMBatchSampler method) (terminator.data.data.TERMLazyBatchSampler method) pad_sequence_12() (in module terminator.models.layers.utils) pair_self_energy_ratio() (in module terminator.utils.model.loss_fn) PairEnergies (class in terminator.models.layers.energies.s2s)

parseCoords() (in module scripts.data.preprocessing.parseCoords) parseEtab() (in module scripts.data.preprocessing.parseEtab) parseTERMdata() (in module scripts.data.preprocessing.parseTERM) PositionalEncodings (class in terminator.models.layers.graph_features) PositionWiseFeedForward (class in terminator.models.layers.s2s_modules) ProteinFeatures (class in terminator.models.layers.graph_features)

R

randn() (in module terminator.models.layers.gvp) rate() (terminator.utils.model.optim.NoamOpt method)

read_lens() (in module terminator.data.data) ResidueFeatures (class in terminator.models.layers.condense) run_epoch() (in module terminator.utils.model.loop_utils)

S

scripts.analysis module scripts.data.postprocessing module scripts.data.postprocessing.batch_arr_dTERMen module scripts.data.postprocessing.fix_dTERMen module scripts.data.postprocessing.search_utils module scripts.data.postprocessing.summarize_results module scripts.data.postprocessing.to_etab module scripts.data.preprocessing module scripts.data.preprocessing.cleanStructs module scripts.data.preprocessing.generateDataset module scripts.data.preprocessing.packageTensors module

scripts.data.preprocessing.parseCoords module scripts.data.preprocessing.parseEtab module scripts.data.preprocessing.parseTERM module scripts.data.preprocessing.split_datasets module scripts.models.eval module scripts.models.eval.eval module scripts.models.train module seq_to_ints() (in module terminator.utils.common) shuffle() (terminator.data.data.TERMDataset method) (terminator.data.data.TERMLazyDataset method) sortcery_loss() (in module terminator.utils.model.loss_fn) step() (terminator.models.layers.s2s_modules.NeighborAttention method) (terminator.models.layers.s2s_modules.NodeTransformerLayer method) (terminator.utils.model.optim.NoamOpt method)

T

TERMBatchSampler (class in terminator.data.data) TERMDataset (class in terminator.data.data) TERMEdgeEndpointAttention (class in terminator.models.layers.term.graph.s2s) TERMEdgeMPNNLayer (class in terminator.models.layers.term.graph.s2s) TERMEdgeTransformerLayer (class in terminator.models.layers.term.graph.s2s) TERMGraphTransformerEncoder (class in terminator.models.layers.term.graph.s2s) terminator module TERMinator (class in terminator.models.TERMinator) terminator.data module terminator.data.data module terminator.models module terminator.models.layers module terminator.models.layers.condense module terminator.models.layers.energies module terminator.models.layers.energies.gvp module terminator.models.layers.energies.s2s module terminator.models.layers.graph_features module terminator.models.layers.gvp module terminator.models.layers.s2s_modules module terminator.models.layers.term module terminator.models.layers.term.graph module terminator.models.layers.term.graph.s2s module

terminator.models.layers.term.matches module terminator.models.layers.term.matches.attn module terminator.models.layers.term.matches.cnn module terminator.models.layers.utils module terminator.models.TERMinator module terminator.utils module terminator.utils.common module terminator.utils.model module terminator.utils.model.default_hparams module terminator.utils.model.loop_utils module terminator.utils.model.loss_fn module terminator.utils.model.optim module TERMLazyBatchSampler (class in terminator.data.data) TERMLazyDataset (class in terminator.data.data) TERMMatchAttention (class in terminator.models.layers.term.matches.attn) TERMMatchTransformerEncoder (class in terminator.models.layers.term.matches.attn) TERMMatchTransformerLayer (class in terminator.models.layers.term.matches.attn) TERMNeighborAttention (class in terminator.models.layers.term.graph.s2s) TERMNodeMPNNLayer (class in terminator.models.layers.term.graph.s2s) TERMNodeTransformerLayer (class in terminator.models.layers.term.graph.s2s) to_etab_file() (in module scripts.data.postprocessing.to_etab) tuple_cat() (in module terminator.models.layers.gvp) tuple_index() (in module terminator.models.layers.gvp) tuple_sum() (in module terminator.models.layers.gvp)