Functions — github.com/google-deepmind/alphafold3

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Functions889 in github.com/google-deepmind/alphafold3

⨍ Functions 889◇ Types & classes 165↳ Endpoints 1

Method__hash__

(self)

src/alphafold3/common/folding_input.py:547

Method__hash__

(self)

src/alphafold3/common/folding_input.py:734

Method__hash__

(self)

src/alphafold3/constants/chemical_components.py:98

Method__init__

( self, config: model.Model.Config, device: jax.Device, model_dir: pathlib.Path, )

run_alphafold.py:419

Method__init__

(self, files: list[pathlib.Path])

src/alphafold3/model/params.py:98

Method__init__

(self, config: Config, name: str = 'diffuser')

src/alphafold3/model/model.py:241

Method__init__

( self, *, axis: int = -1, create_scale: bool = True, create_offset: bool = True

src/alphafold3/model/components/haiku_modules.py:62

Method__init__

( self, config: Config, global_config: model_config.GlobalConfig, name='evoformer',

src/alphafold3/model/network/evoformer.py:76

Method__init__

( self, config: Config, global_config: model_config.GlobalConfig, name: str = 'transfo

src/alphafold3/model/network/diffusion_transformer.py:348

Method__init__

( self, config: Config, global_config: model_config.GlobalConfig, *, name )

src/alphafold3/model/network/modules.py:57

Method__init__

( self, config: Config, global_config: model_config.GlobalConfig, transpose: bool,

src/alphafold3/model/network/modules.py:146

Method__init__

( self, config: Config, global_config: model_config.GlobalConfig, *, name )

src/alphafold3/model/network/modules.py:261

Method__init__

( self, config: Config, global_config: model_config.GlobalConfig, num_output_channel,

src/alphafold3/model/network/modules.py:350

Method__init__

( self, config: Config, global_config: model_config.GlobalConfig, with_single=False,

src/alphafold3/model/network/modules.py:443

Method__init__

( self, config: Config, global_config: model_config.GlobalConfig, name='evoformer_iter

src/alphafold3/model/network/modules.py:564

Method__init__

( self, config: Config, global_config: model_config.GlobalConfig, name='confidence_hea

src/alphafold3/model/network/confidence_head.py:62

Method__init__

( self, config: Config, global_config: model_config.GlobalConfig, name='diffusion_head

src/alphafold3/model/network/diffusion_head.py:132

Method__init__

( self, config: Config, global_config: model_config.GlobalConfig, name='distogram_head

src/alphafold3/model/network/distogram_head.py:45

Method__init__

( self, config: TemplateEmbedding.Config, global_config: model_config.GlobalConfig, na

src/alphafold3/model/network/template_modules.py:220

Method__init__

Initializes WholePdb data pipeline. Args: config: Pipeline configuration.

src/alphafold3/model/pipeline/pipeline.py:161

Method__init__

( self, *, query_sequence: str, hits: Sequence[Hit], max_template_date: datetime

src/alphafold3/data/templates.py:414

Method__init__

Initializes the data pipeline with default configurations.

src/alphafold3/data/pipeline.py:304

Method__init__

Raw constructor, prefer using the from_{a3m,multiple_msas} class methods. The first sequence must be equal (in featurised form) to the query sequ

src/alphafold3/data/msa.py:64

Method__init__

Initialises the instance. Args: structures: Path of the directory where the mmCIF files are or a Mapping from target name to mmCIF

src/alphafold3/data/structure_stores.py:36

Method__init__

Initializes the Python hmmalign wrapper. Args: binary_path: Path to the hmmalign binary. Raises: RuntimeError: If hmmalign binar

src/alphafold3/data/tools/hmmalign.py:40

Method__init__

Initializes the Python hmmsearch wrapper. Args: binary_path: The path to the hmmsearch executable. hmmbuild_binary_path: The path to

src/alphafold3/data/tools/hmmsearch.py:34

Method__init__

Initializes the Python Nhmmer wrapper. NOTE: The MSA obtained by running against sharded dbs won't be always exactly the same as the MSA obta

src/alphafold3/data/tools/nhmmer.py:47

Method__init__

Initializes the Python Jackhmmer wrapper. NOTE: The MSA obtained by running against sharded dbs won't be always exactly the same as the MSA o

src/alphafold3/data/tools/jackhmmer.py:41

Method__init__

Initializes the Python hmmbuild wrapper. Args: binary_path: The path to the hmmbuild executable. singlemx: Whether to use --singlemx

src/alphafold3/data/tools/hmmbuild.py:34

Method__init__

( self, *, name: str = 'unset', release_date: datetime.date | None = None, resol

src/alphafold3/structure/structure.py:317

Method__init__

(self, struc: Structure)

src/alphafold3/structure/structure.py:2995

Method__init__

(self, table: Table, column_name_map: Mapping[str, str])

src/alphafold3/structure/table.py:445

Method__init__

( self, *, pdbx_struct_assembly: Mapping[str, Mapping[str, str]], pdbx_struct_assembly

src/alphafold3/structure/bioassemblies.py:117

Method__init__

( self, *, chain_key_by_chain_id: Mapping[str, int], entity_id_by_chain_id: Mapping[st

src/alphafold3/structure/parsing.py:854

Method__init__

(self, same_dtype=True)

src/alphafold3/jax/geometry/struct_of_array.py:202

Method__init__

Initializes the template. Args: mmcif: The structural template in mmCIF format. The mmCIF should have only one protein chain.

src/alphafold3/common/folding_input.py:100

Method__init__

Initializes a single protein chain input. Args: id: Unique protein chain identifier. sequence: The amino acid sequence of the chain.

src/alphafold3/common/folding_input.py:147

Method__init__

Initializes a single strand RNA chain input. Args: id: Unique RNA chain identifier. sequence: The RNA sequence of the chain. mo

src/alphafold3/common/folding_input.py:467

Method__init__

Initializes a single strand DNA chain input. Args: id: Unique DNA chain identifier. sequence: The DNA sequence of the chain. mo

src/alphafold3/common/folding_input.py:670

Method__init__

(self, **defaults: Any)

src/alphafold3/common/base_config.py:48

Method__init__

Initiailizes data wrapper, providing users with high level data access. Args: data_dir: Directory containing test data.

src/alphafold3/common/testing/data.py:32

Method__init__

Initialises the chemical components dictionary. Args: ccd_pickle_path: Path to the CCD pickle file. If None, uses the default CCD p

src/alphafold3/constants/chemical_components.py:57

Method__iter__

(self)

src/alphafold3/constants/chemical_components.py:92

Method__len__

(self)

src/alphafold3/structure/table.py:128

Method__len__

(self)

src/alphafold3/common/folding_input.py:232

Method__len__

(self)

src/alphafold3/common/folding_input.py:533

Method__len__

(self)

src/alphafold3/common/folding_input.py:721

Method__len__

(self)

src/alphafold3/common/folding_input.py:840

Method__len__

(self)

src/alphafold3/constants/chemical_components.py:95

Method__matmul__

(self, other: Self)

src/alphafold3/jax/geometry/rigid_matrix_vector.py:115

Method__matmul__

Composes two Rot3Arrays.

src/alphafold3/jax/geometry/rotation_matrix.py:153

Method__mul__

(self, other: Float)

src/alphafold3/jax/geometry/vector.py:72

Method__neg__

(self)

src/alphafold3/jax/geometry/vector.py:81

Method__new__

(mcs, name, bases, classdict)

src/alphafold3/common/base_config.py:77

Method__pos__

(self)

src/alphafold3/jax/geometry/vector.py:84

Method__post_init__

(self)

src/alphafold3/model/confidence_types.py:103

Method__post_init__

Assert all arrays have the same shape.

src/alphafold3/model/atom_layout/atom_layout.py:84

Method__post_init__

Assert all arrays are 1D have the same shape.

src/alphafold3/model/atom_layout/atom_layout.py:268

Method__post_init__

(self)

src/alphafold3/model/atom_layout/atom_layout.py:335

Method__post_init__

(self)

src/alphafold3/data/templates.py:291

Method__post_init__

(self)

src/alphafold3/data/msa_config.py:126

Method__post_init__

(self)

src/alphafold3/data/msa_config.py:160

Method__post_init__

(self)

src/alphafold3/structure/chemical_components.py:111

Method__post_init__

(self)

src/alphafold3/structure/structure_tables.py:109

Method__post_init__

(self)

src/alphafold3/structure/table.py:76

Method__post_init__

(self)

src/alphafold3/jax/geometry/vector.py:55

Method__post_init__

(self)

src/alphafold3/common/folding_input.py:827

Method__post_init__

(self)

src/alphafold3/common/folding_input.py:979

Method__repr__

(self)

src/alphafold3/data/templates.py:607

Method__repr__

(self)

src/alphafold3/data/msa.py:252

Method__repr__

(self)

src/alphafold3/structure/structure.py:651

Method__rmul__

(self, other: Float)

src/alphafold3/jax/geometry/vector.py:75

Method__setstate__

(self, state)

src/alphafold3/jax/geometry/rigid_matrix_vector.py:229

Method__setstate__

(self, state)

src/alphafold3/jax/geometry/rotation_matrix.py:296

Method__setstate__

(self, state)

src/alphafold3/jax/geometry/vector.py:135

Method__sub__

(self, other: Self)

src/alphafold3/jax/geometry/vector.py:69

Method__truediv__

(self, other: Float)

src/alphafold3/jax/geometry/vector.py:78

Method_attention

( self, act, mask, bias, )

src/alphafold3/model/network/modules.py:160

Function_clone_field

( field: dataclasses.Field[_T], new_default: _T )

src/alphafold3/common/base_config.py:57

Method_coercable_fields

(self)

src/alphafold3/common/base_config.py:80

Method_coercable_fields

(self)

src/alphafold3/common/base_config.py:149

Method_copy_and_update

Performs a shallow copy but with specified fields updated.

src/alphafold3/structure/structure.py:1205

Function_generate_diff

(actual: str, expected: str)

run_alphafold_test.py:63

Method_iter_residues

(struc: Self)

src/alphafold3/structure/structure.py:1083

Method_keep

(atom_index: int)

src/alphafold3/structure/structure.py:1871

Function_maybe_get_size

(array, axis)

src/alphafold3/model/components/mapping.py:49

Method_post_init

(self)

src/alphafold3/common/base_config.py:98

Method_query_shard_fn

( shard_path: str, )

src/alphafold3/data/tools/nhmmer.py:161

Method_query_shard_fn

( shard_path: str, )

src/alphafold3/data/tools/jackhmmer.py:160

Function_safe_norm

(x, keepdims, axis, eps=1e-8)

src/alphafold3/model/network/confidence_head.py:34

Function_set_docstring

Decorator for setting the docstring of a function.

src/alphafold3/model/components/mapping.py:96

Method_tar_members

(self)

src/alphafold3/data/structure_stores.py:61

Method_to_internal_res_id

( bonded_atom_id: tuple[str, int, str], )

src/alphafold3/structure/structure.py:1938

Functionadd_legal_comment

Adds legal comment at the top of the mmCIF.

src/alphafold3/model/mmcif_metadata.py:225

Functionadd_metadata_to_mmcif

Adds metadata to a mmCIF to make it ModelCIF-conformant.

src/alphafold3/model/mmcif_metadata.py:56

Methodalign_ratio

Ratio of the number of aligned residues to the query length.

src/alphafold3/data/templates.py:271

Methodalign_sequences

Aligns sequence list to the profile and returns the alignment in A3M.

src/alphafold3/data/tools/hmmalign.py:55

Methodall_residues

(self)

src/alphafold3/structure/structure.py:495

Methodall_unset

(fields)

src/alphafold3/structure/structure.py:1162

Functionallocate_buffer

(dtype, shape)

src/alphafold3/model/components/mapping.py:209

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