Index

_

__getitem__() (spurs.datamodules.datasets.ddgbench.ddgBenchDataset method) __init__() (spurs.datamodules.datasets.ddgbench.ddgBenchDataset method) (spurs.datamodules.datasets.ddggeo.ddgGeo method) (spurs.datamodules.datasets.domainome.domainome method) (spurs.datamodules.datasets.fireport.FireProtDataset method) (spurs.datamodules.datasets.megascale.Featurizer method) (spurs.datamodules.datasets.megascale.MegaScaleDataset method) (spurs.datamodules.datasets.megascale.MegaScaleTestDatasets method) (spurs.datamodules.datasets.megascale_multi.Featurizer method) (spurs.datamodules.datasets.megascale_multi.MegaScaleDoubleDataset method) (spurs.functional_site_annotation.SigmoidRegressor method) (spurs.models.stability.esm.ESM method) (spurs.models.stability.mpnn.MPNN method) (spurs.models.stability.org_transfer_model.TransferModel method) (spurs.models.stability.org_transfer_model.TransferModelConfig method) (spurs.models.stability.spurs.SPURS method) (spurs.models.stability.spurs.SPURSConfig method)

A

adapter_layer_indices (spurs.models.stability.spurs.SPURSConfig attribute)

C

cal_index2mt() (spurs.datamodules.datasets.megascale.MegaScaleDataset method)

collect_func() (spurs.datamodules.datasets.megascale.MegaScaleDataset method)

D

ddgBenchDataset (class in spurs.datamodules.datasets.ddgbench) ddgGeo (class in spurs.datamodules.datasets.ddggeo)

domainome (class in spurs.datamodules.datasets.domainome) dropout (spurs.models.stability.spurs.SPURSConfig attribute)

E

encoder (spurs.models.stability.org_transfer_model.TransferModelConfig attribute) (spurs.models.stability.spurs.SPURSConfig attribute)

ESM (class in spurs.models.stability.esm)

F

Featurizer (class in spurs.datamodules.datasets.megascale) (class in spurs.datamodules.datasets.megascale_multi) FireProtDataset (class in spurs.datamodules.datasets.fireport) fit() (spurs.functional_site_annotation.SigmoidRegressor method) forward() (spurs.models.stability.esm.ESM method) (spurs.models.stability.mpnn.MPNN method) (spurs.models.stability.org_transfer_model.TransferModel method) (spurs.models.stability.spurs.SPURS method)

forward_encoder() (spurs.models.stability.esm.ESM method) (spurs.models.stability.mpnn.MPNN method) (spurs.models.stability.spurs.SPURS method)

G

get_sigmoid_results() (in module spurs.functional_site_annotation) get_SPURS() (in module spurs.inference)

get_SPURS_from_hub() (in module spurs.inference) get_SPURS_multi_from_hub() (in module spurs.inference) get_wt_aa_logit_differences() (in module spurs.functional_site_annotation)

I

inference_wt_seq() (in module spurs.functional_site_annotation)

M

MegaScaleDataset (class in spurs.datamodules.datasets.megascale) MegaScaleDoubleDataset (class in spurs.datamodules.datasets.megascale_multi) MegaScaleTestDatasets (class in spurs.datamodules.datasets.megascale) mlp (spurs.models.stability.spurs.SPURSConfig attribute) module spurs.datamodules.datasets.ddgbench spurs.datamodules.datasets.ddggeo spurs.datamodules.datasets.domainome spurs.datamodules.datasets.fireport spurs.datamodules.datasets.megascale spurs.datamodules.datasets.megascale_multi spurs.functional_site_annotation spurs.inference spurs.models.stability.esm spurs.models.stability.mpnn spurs.models.stability.org_transfer_model spurs.models.stability.spurs

MPNN (class in spurs.models.stability.mpnn)

N

name (spurs.models.stability.spurs.SPURSConfig attribute)

normalize() (in module spurs.functional_site_annotation)

P

parse_pdb() (in module spurs.inference) parse_pdb_for_mutation() (in module spurs.inference)

plot_sigmoid_results() (in module spurs.functional_site_annotation) predict() (spurs.functional_site_annotation.SigmoidRegressor method)

S

separate_loss (spurs.models.stability.spurs.SPURSConfig attribute) sigmoid_function() (in module spurs.functional_site_annotation) SigmoidRegressor (class in spurs.functional_site_annotation) SPURS (class in spurs.models.stability.spurs) spurs.datamodules.datasets.ddgbench module spurs.datamodules.datasets.ddggeo module spurs.datamodules.datasets.domainome module spurs.datamodules.datasets.fireport module spurs.datamodules.datasets.megascale module

spurs.datamodules.datasets.megascale_multi module spurs.functional_site_annotation module spurs.inference module spurs.models.stability.esm module spurs.models.stability.mpnn module spurs.models.stability.org_transfer_model module spurs.models.stability.spurs module SPURSConfig (class in spurs.models.stability.spurs)

T

training (spurs.models.stability.esm.ESM attribute) (spurs.models.stability.mpnn.MPNN attribute) (spurs.models.stability.org_transfer_model.TransferModel attribute) (spurs.models.stability.spurs.SPURS attribute)

TransferModel (class in spurs.models.stability.org_transfer_model) TransferModelConfig (class in spurs.models.stability.org_transfer_model)