Index

_

_check_atom_array_length() (in module prxteinmpnn.io) _check_enums() (in module prxteinmpnn.model.decoder) _check_if_file_empty() (in module prxteinmpnn.io) _fill_in_cb_coordinates() (in module prxteinmpnn.io) _from_fcz() (in module prxteinmpnn.utils.foldcomp_utils)

_get_chain_index() (in module prxteinmpnn.io) _make_rigid_group_constants() (in module prxteinmpnn.utils.residue_constants) _make_rigid_transformation_4x4() (in module prxteinmpnn.utils.residue_constants) _make_standard_atom_mask() (in module prxteinmpnn.utils.residue_constants) _process_chain_id() (in module prxteinmpnn.io) _setup_foldcomp_database() (in module prxteinmpnn.utils.foldcomp_utils)

A

aatype (prxteinmpnn.utils.data_structures.ProteinStructure attribute), [1] af_to_mpnn() (in module prxteinmpnn.utils.aa_convert) AFDB_A_THALIANA (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) AFDB_C_ALBICANS (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) AFDB_C_ELEGANS (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) AFDB_D_DISCOIDEUM (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) AFDB_D_MELANOGASTER (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) AFDB_D_RERIO (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) AFDB_E_COLI (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) AFDB_G_MAX (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) AFDB_H_SAPIENS (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) AFDB_M_JANNASCHII (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) AFDB_M_MUSCULUS (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) AFDB_O_SATIVA (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) AFDB_R_NORVEGICUS (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) AFDB_REP_DARK_V4 (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) AFDB_REP_V4 (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute)

AFDB_S_CEREVISIAE (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) AFDB_S_POMBE (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) AFDB_SWISSPROT_V4 (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) AFDB_UNIPROT_V4 (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) AFDB_Z_MAYS (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) angle_rad (prxteinmpnn.utils.residue_constants.BondAngle attribute) apply_noise_to_coordinates() (in module prxteinmpnn.utils.coordinates) atom1_name (prxteinmpnn.utils.residue_constants.Bond attribute) (prxteinmpnn.utils.residue_constants.BondAngle attribute) atom2_name (prxteinmpnn.utils.residue_constants.Bond attribute) (prxteinmpnn.utils.residue_constants.BondAngle attribute) atom3name (prxteinmpnn.utils.residue_constants.BondAngle attribute) atom_mask (prxteinmpnn.utils.data_structures.ProteinStructure attribute), [1] atom_names_to_index() (in module prxteinmpnn.io) augment_eps (prxteinmpnn.utils.data_structures.ModelInputs attribute) (prxteinmpnn.utils.data_structures.SamplingInputs attribute) AUTOREGRESSIVE (prxteinmpnn.model.decoder.DecodingEnum attribute)

B

BEAM_SEARCH (prxteinmpnn.sampling.SamplingEnum attribute) bias (prxteinmpnn.utils.data_structures.ModelInputs attribute), [1] (prxteinmpnn.utils.data_structures.SamplingInputs attribute)

Bond (class in prxteinmpnn.utils.residue_constants) BondAngle (class in prxteinmpnn.utils.residue_constants)

C

chain_index (prxteinmpnn.utils.data_structures.ModelInputs attribute), [1] (prxteinmpnn.utils.data_structures.ProteinStructure attribute) (prxteinmpnn.utils.data_structures.SamplingInputs attribute) chi_angle_atom() (in module prxteinmpnn.utils.residue_constants) compute_backbone_coordinates() (in module prxteinmpnn.utils.coordinates) compute_backbone_distance() (in module prxteinmpnn.utils.coordinates) compute_c_beta() (in module prxteinmpnn.utils.coordinates) compute_cb_precise() (in module prxteinmpnn.utils.coordinates)

compute_neighbor_offsets() (in module prxteinmpnn.utils.graph) compute_radial_basis() (in module prxteinmpnn.utils.radial_basis) concatenate_neighbor_nodes() (in module prxteinmpnn.utils.concatenate) CONDITIONAL (prxteinmpnn.model.decoder.DecodingEnum attribute) (prxteinmpnn.model.masked_attention.MaskedAttentionEnum attribute) (prxteinmpnn.model.MaskedAttentionEnum attribute) coordinates (prxteinmpnn.utils.data_structures.ProteinStructure attribute), [1] CROSS (prxteinmpnn.model.masked_attention.MaskedAttentionEnum attribute) (prxteinmpnn.model.MaskedAttentionEnum attribute)

D

decode_message() (in module prxteinmpnn.model.decoder) decoder_normalize() (in module prxteinmpnn.model.decoder) decoder_parameter_pytree() (in module prxteinmpnn.model.decoder) DecodingEnum (class in prxteinmpnn.model.decoder)

DEFAULT (prxteinmpnn.mpnn.ModelWeights attribute) dense_layer() (in module prxteinmpnn.model) (in module prxteinmpnn.model.dense) dihedrals (prxteinmpnn.utils.data_structures.ProteinStructure attribute)

E

embed_edges() (in module prxteinmpnn.model.features) embed_sequence() (in module prxteinmpnn.model.decoder) encode() (in module prxteinmpnn.model.encoder) encode_positions() (in module prxteinmpnn.model.features) encoder_normalize() (in module prxteinmpnn.model.encoder) encoder_parameter_pytree() (in module prxteinmpnn.model.encoder)

ESMATLAS_FULL (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) ESMATLAS_HIGH_QUALITY (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) ESMATLAS_v2023_02 (prxteinmpnn.utils.foldcomp_utils.FoldCompDatabaseEnum attribute) extend_coordinate() (in module prxteinmpnn.utils.coordinates) extract_features() (in module prxteinmpnn.model) (in module prxteinmpnn.model.features)

F

final_projection() (in module prxteinmpnn.model) (in module prxteinmpnn.model.projection) FoldCompDatabaseEnum (class in prxteinmpnn.utils.foldcomp_utils)

from_string() (in module prxteinmpnn.io) from_structure_file() (in module prxteinmpnn.io) from_trajectory() (in module prxteinmpnn.io)

G

generate_ar_mask() (in module prxteinmpnn.utils.autoregression) get_edge_chains_neighbors() (in module prxteinmpnn.model.features)

get_mpnn_model() (in module prxteinmpnn.mpnn) get_protein_structures() (in module prxteinmpnn.utils.foldcomp_utils) GREEDY (prxteinmpnn.sampling.SamplingEnum attribute)

H

HETEROMER (prxteinmpnn.utils.data_structures.OligomerType attribute)

HOMOOLIGOMER (prxteinmpnn.utils.data_structures.OligomerType attribute) hyperparameters (prxteinmpnn.utils.data_structures.SamplingInputs attribute), [1]

I

initial_sequence (prxteinmpnn.utils.data_structures.SamplingInputs attribute) initialize_conditional_decoder() (in module prxteinmpnn.model.decoder)

initialize_node_features() (in module prxteinmpnn.model.encoder) iterations (prxteinmpnn.sampling.SamplingConfig attribute) (prxteinmpnn.utils.data_structures.SamplingInputs attribute), [1]

K

k_neighbors (prxteinmpnn.utils.data_structures.ModelInputs attribute) (prxteinmpnn.utils.data_structures.SamplingInputs attribute)

L

layer_normalization() (in module prxteinmpnn.utils.normalize) learning_rate (prxteinmpnn.sampling.SamplingConfig attribute)

length (prxteinmpnn.utils.residue_constants.Bond attribute) lengths (prxteinmpnn.utils.data_structures.ModelInputs attribute), [1] load_stereo_chemical_props() (in module prxteinmpnn.utils.residue_constants)

M

make_atom14_dists_bounds() (in module prxteinmpnn.utils.residue_constants) make_decode_layer() (in module prxteinmpnn.model.decoder) make_decoder() (in module prxteinmpnn.model) (in module prxteinmpnn.model.decoder) make_encode_layer() (in module prxteinmpnn.model.encoder) make_encoder() (in module prxteinmpnn.model) (in module prxteinmpnn.model.encoder) make_sample_sequences() (in module prxteinmpnn.sampling) (in module prxteinmpnn.sampling.sample) make_score_sequence() (in module prxteinmpnn.scoring.score) mask (prxteinmpnn.utils.data_structures.ModelInputs attribute), [1] (prxteinmpnn.utils.data_structures.SamplingInputs attribute) mask_attention() (in module prxteinmpnn.model.masked_attention) MaskedAttentionEnum (class in prxteinmpnn.model) (class in prxteinmpnn.model.masked_attention) model_from_id() (in module prxteinmpnn.utils.foldcomp_utils) ModelInputs (class in prxteinmpnn.utils.data_structures) ModelWeights (class in prxteinmpnn.mpnn) module prxteinmpnn prxteinmpnn.io prxteinmpnn.model prxteinmpnn.model.decoder prxteinmpnn.model.dense prxteinmpnn.model.encoder prxteinmpnn.model.features prxteinmpnn.model.masked_attention prxteinmpnn.model.projection prxteinmpnn.mpnn prxteinmpnn.sampling prxteinmpnn.sampling.initialize prxteinmpnn.sampling.sample prxteinmpnn.sampling.sampling_step prxteinmpnn.sampling.ste prxteinmpnn.scoring prxteinmpnn.scoring.score prxteinmpnn.utils prxteinmpnn.utils.aa_convert prxteinmpnn.utils.autoregression prxteinmpnn.utils.concatenate prxteinmpnn.utils.coordinates prxteinmpnn.utils.data_structures prxteinmpnn.utils.decoding_order prxteinmpnn.utils.foldcomp_utils prxteinmpnn.utils.gelu prxteinmpnn.utils.graph prxteinmpnn.utils.normalize prxteinmpnn.utils.radial_basis prxteinmpnn.utils.residue_constants prxteinmpnn.utils.types

MONOMER (prxteinmpnn.utils.data_structures.OligomerType attribute) mpnn_to_af() (in module prxteinmpnn.utils.aa_convert)

N

NONE (prxteinmpnn.model.masked_attention.MaskedAttentionEnum attribute) (prxteinmpnn.model.MaskedAttentionEnum attribute)

normalize() (in module prxteinmpnn.utils.normalize)

O

OligomerType (class in prxteinmpnn.utils.data_structures)

P

preload_sampling_step_decoder() (in module prxteinmpnn.sampling.sampling_step) prng_key (prxteinmpnn.utils.data_structures.SamplingInputs attribute), [1] process_atom_array() (in module prxteinmpnn.io) process_lines_iter_chemical_props() (in module prxteinmpnn.utils.residue_constants) project_features() (in module prxteinmpnn.model.features) protein_sequence_to_string() (in module prxteinmpnn.io) protein_structure_to_model_inputs() (in module prxteinmpnn.io) ProteinMPNNModelVersion (class in prxteinmpnn.mpnn) ProteinStructure (class in prxteinmpnn.utils.data_structures) prxteinmpnn module prxteinmpnn.io module prxteinmpnn.model module prxteinmpnn.model.decoder module prxteinmpnn.model.dense module prxteinmpnn.model.encoder module prxteinmpnn.model.features module prxteinmpnn.model.masked_attention module prxteinmpnn.model.projection module prxteinmpnn.mpnn module prxteinmpnn.sampling module prxteinmpnn.sampling.initialize module prxteinmpnn.sampling.sample module

prxteinmpnn.sampling.sampling_step module prxteinmpnn.sampling.ste module prxteinmpnn.scoring module prxteinmpnn.scoring.score module prxteinmpnn.utils module prxteinmpnn.utils.aa_convert module prxteinmpnn.utils.autoregression module prxteinmpnn.utils.concatenate module prxteinmpnn.utils.coordinates module prxteinmpnn.utils.data_structures module prxteinmpnn.utils.decoding_order module prxteinmpnn.utils.foldcomp_utils module prxteinmpnn.utils.gelu module prxteinmpnn.utils.graph module prxteinmpnn.utils.normalize module prxteinmpnn.utils.radial_basis module prxteinmpnn.utils.residue_constants module prxteinmpnn.utils.types module

R

random_decoding_order() (in module prxteinmpnn.utils.decoding_order) replace() (prxteinmpnn.sampling.SamplingConfig method) (prxteinmpnn.utils.data_structures.ModelInputs method) (prxteinmpnn.utils.data_structures.ProteinStructure method) (prxteinmpnn.utils.data_structures.SamplingInputs method)

residue_index (prxteinmpnn.utils.data_structures.ModelInputs attribute), [1] (prxteinmpnn.utils.data_structures.ProteinStructure attribute), [1] (prxteinmpnn.utils.data_structures.SamplingInputs attribute) residue_names_to_aatype() (in module prxteinmpnn.io)

S

sampling_encode() (in module prxteinmpnn.sampling.initialize) sampling_strategy (prxteinmpnn.sampling.SamplingConfig attribute) SamplingConfig (class in prxteinmpnn.sampling) SamplingEnum (class in prxteinmpnn.sampling) SamplingInputs (class in prxteinmpnn.utils.data_structures) sequence (prxteinmpnn.utils.data_structures.ModelInputs attribute), [1] setup_decoder() (in module prxteinmpnn.model.decoder) setup_encoder() (in module prxteinmpnn.model.encoder) single_decoding_order() (in module prxteinmpnn.utils.decoding_order) SOLUBLE (prxteinmpnn.mpnn.ModelWeights attribute)

stddev (prxteinmpnn.utils.residue_constants.Bond attribute) (prxteinmpnn.utils.residue_constants.BondAngle attribute) ste_loss() (in module prxteinmpnn.sampling.ste) ste_sample() (in module prxteinmpnn.sampling.sampling_step) STRAIGHT_THROUGH (prxteinmpnn.sampling.SamplingEnum attribute) straight_through_estimator() (in module prxteinmpnn.sampling.ste) string_key_to_index() (in module prxteinmpnn.io) string_to_protein_sequence() (in module prxteinmpnn.io) structure_coordinates (prxteinmpnn.utils.data_structures.ModelInputs attribute), [1] (prxteinmpnn.utils.data_structures.SamplingInputs attribute)

T

target_logits (prxteinmpnn.sampling.SamplingConfig attribute) temperature (prxteinmpnn.sampling.SamplingConfig attribute) TEMPERATURE (prxteinmpnn.sampling.SamplingEnum attribute)

temperature_sample() (in module prxteinmpnn.sampling.sampling_step) TIED_HOMOOLIGOMER (prxteinmpnn.utils.data_structures.OligomerType attribute) TOP_K (prxteinmpnn.sampling.SamplingEnum attribute) TOP_P (prxteinmpnn.sampling.SamplingEnum attribute)

U

UNCONDITIONAL (prxteinmpnn.model.decoder.DecodingEnum attribute)

V

V_48_002 (prxteinmpnn.mpnn.ProteinMPNNModelVersion attribute) V_48_010 (prxteinmpnn.mpnn.ProteinMPNNModelVersion attribute)

V_48_020 (prxteinmpnn.mpnn.ProteinMPNNModelVersion attribute) V_48_030 (prxteinmpnn.mpnn.ProteinMPNNModelVersion attribute)