deepfold.config.FeaturePipelineConfig

class deepfold.config.FeaturePipelineConfig(preset: 'str' = '', is_multimer: 'bool' = False, seed: 'int' = 0, num_chunks: 'int' = 8, fixed_size: 'bool' = True, max_msa_clusters: 'int' = 128, max_extra_msa: 'int' = 1024, sample_msa_distillation_enabled: 'bool' = False, max_distillation_msa_clusters: 'int' = 1000, block_delete_msa_enabled: 'bool' = True, msa_fraction_per_deletion_block: 'float' = 0.3, randomize_num_msa_deletion_blocks: 'bool' = False, num_msa_deletion_blocks: 'int' = 5, masked_msa_enabled: 'bool' = True, masked_msa_profile_prob: 'float' = 0.1, masked_msa_same_prob: 'float' = 0.1, masked_msa_uniform_prob: 'float' = 0.1, masked_msa_replace_fraction: 'float' = 0.15, max_recycling_iters: 'int' = 3, resample_msa_in_recycling: 'bool' = True, residue_cropping_enabled: 'bool' = False, crop_size: 'int' = 256, spatial_crop_prob: 'float' = 0.5, interface_threshold: 'float' = 10.0, primary_raw_feature_names: 'List[str]' = <factory>, msa_cluster_features_enabled: 'bool' = True, templates_enabled: 'bool' = True, embed_template_torsion_angles: 'bool' = True, max_templates: 'int' = 4, shuffle_top_k_prefiltered: 'int' = 20, subsample_templates: 'bool' = False, template_raw_feature_names: 'List[str]' = <factory>, supervised_features_enabled: 'bool' = False, supervised_raw_feature_names: 'List[str]' = <factory>, clamped_fape_enabled: 'bool' = False, clamped_fape_probability: 'float' = 0.9, self_distillation_plddt_threshold: 'float' = 50.0)

__init__(preset: str = '', is_multimer: bool = False, seed: int = 0, num_chunks: int = 8, fixed_size: bool = True, max_msa_clusters: int = 128, max_extra_msa: int = 1024, sample_msa_distillation_enabled: bool = False, max_distillation_msa_clusters: int = 1000, block_delete_msa_enabled: bool = True, msa_fraction_per_deletion_block: float = 0.3, randomize_num_msa_deletion_blocks: bool = False, num_msa_deletion_blocks: int = 5, masked_msa_enabled: bool = True, masked_msa_profile_prob: float = 0.1, masked_msa_same_prob: float = 0.1, masked_msa_uniform_prob: float = 0.1, masked_msa_replace_fraction: float = 0.15, max_recycling_iters: int = 3, resample_msa_in_recycling: bool = True, residue_cropping_enabled: bool = False, crop_size: int = 256, spatial_crop_prob: float = 0.5, interface_threshold: float = 10.0, primary_raw_feature_names: ~typing.List[str] = <factory>, msa_cluster_features_enabled: bool = True, templates_enabled: bool = True, embed_template_torsion_angles: bool = True, max_templates: int = 4, shuffle_top_k_prefiltered: int = 20, subsample_templates: bool = False, template_raw_feature_names: ~typing.List[str] = <factory>, supervised_features_enabled: bool = False, supervised_raw_feature_names: ~typing.List[str] = <factory>, clamped_fape_enabled: bool = False, clamped_fape_probability: float = 0.9, self_distillation_plddt_threshold: float = 50.0) → None

Methods

__init__([preset, is_multimer, seed, ...])
feature_names()
from_dict(cfg)
from_preset(preset, seed[, is_multimer])
to_dict()

Attributes

block_delete_msa_enabled
clamped_fape_enabled
clamped_fape_probability
crop_size
embed_template_torsion_angles
fixed_size
interface_threshold
is_multimer
masked_msa_enabled
masked_msa_profile_prob
masked_msa_replace_fraction
masked_msa_same_prob
masked_msa_uniform_prob
max_distillation_msa_clusters
max_extra_msa
max_msa_clusters
max_recycling_iters
max_templates
msa_cluster_features_enabled
msa_fraction_per_deletion_block
num_chunks
num_msa_deletion_blocks
preset
randomize_num_msa_deletion_blocks
resample_msa_in_recycling
residue_cropping_enabled
sample_msa_distillation_enabled
seed
self_distillation_plddt_threshold
shuffle_top_k_prefiltered
spatial_crop_prob
subsample_templates
supervised_features_enabled
templates_enabled
primary_raw_feature_names
template_raw_feature_names
supervised_raw_feature_names