deepfold.config.AlphaFoldConfig

class deepfold.config.AlphaFoldConfig(is_multimer: 'bool' = False, input_embedder_config: 'InputEmbedderConfig' = InputEmbedderConfig(tf_dim=22, msa_dim=49, c_z=128, c_m=256, relpos_k=32, max_relative_chain=2, max_relative_index=32, use_chain_relative=True), recycling_embedder_config: 'RecyclingEmbedderConfig' = RecyclingEmbedderConfig(c_m=256, c_z=128, min_bin=3.25, max_bin=20.75, num_bins=15, inf=100000000.0), template_angle_embedder_config: 'TemplateAngleEmbedderConfig' = TemplateAngleEmbedderConfig(ta_dim=57, c_m=256), template_pair_embedder_config: 'TemplatePairEmbedderConfig' = TemplatePairEmbedderConfig(tp_dim=88, c_t=64, c_z=128, c_dgram=39, c_aatype=22), template_pair_stack_config: 'TemplatePairStackConfig' = TemplatePairStackConfig(c_t=64, c_hidden_tri_att=16, c_hidden_tri_mul=64, num_blocks=2, num_heads_tri=4, pair_transition_n=2, dropout_rate=0.25, inf=1000000000.0, chunk_size_tri_att=None, block_size_tri_mul=None, tri_att_first=True), template_pointwise_attention_config: 'TemplatePointwiseAttentionConfig' = TemplatePointwiseAttentionConfig(c_t=64, c_z=128, c_hidden=16, num_heads=4, inf=100000.0, chunk_size=None), template_projection_config: 'TemplateProjectionConfig' = TemplateProjectionConfig(c_t=64, c_z=128), extra_msa_embedder_config: 'ExtraMSAEmbedderConfig' = ExtraMSAEmbedderConfig(emsa_dim=25, c_e=64), extra_msa_stack_config: 'ExtraMSAStackConfig' = ExtraMSAStackConfig(c_e=64, c_z=128, c_hidden_msa_att=8, c_hidden_opm=32, c_hidden_tri_mul=128, c_hidden_tri_att=32, num_heads_msa=8, num_heads_tri=4, num_blocks=4, transition_n=4, msa_dropout=0.15, pair_dropout=0.25, inf=1000000000.0, eps=1e-08, eps_opm=0.001, chunk_size_msa_att=None, chunk_size_opm=None, chunk_size_tri_att=None, block_size_tri_mul=None, outer_product_mean_first=False), evoformer_stack_config: 'EvoformerStackConfig' = EvoformerStackConfig(c_m=256, c_z=128, c_hidden_msa_att=32, c_hidden_opm=32, c_hidden_tri_mul=128, c_hidden_tri_att=32, c_s=384, num_heads_msa=8, num_heads_tri=4, num_blocks=48, transition_n=4, msa_dropout=0.15, pair_dropout=0.25, inf=1000000000.0, eps_opm=0.001, chunk_size_msa_att=None, chunk_size_opm=None, chunk_size_tri_att=None, block_size_tri_mul=None, outer_product_mean_first=False), structure_module_config: 'StructureModuleConfig' = StructureModuleConfig(c_s=384, c_z=128, c_hidden_ipa=16, c_hidden_ang_res=128, num_heads_ipa=12, num_qk_points=4, num_v_points=8, is_multimer=False, dropout_rate=0.1, num_blocks=8, num_ang_res_blocks=2, num_angles=7, scale_factor=10.0, inf=100000.0, eps=1e-08), auxiliary_heads_config: 'AuxiliaryHeadsConfig' = AuxiliaryHeadsConfig(per_residue_lddt_ca_predictor_config=PerResidueLDDTCaPredictorConfig(c_s=384, c_hidden=128, num_bins=50), distogram_head_config=DistogramHeadConfig(c_z=128, num_bins=64), masked_msa_head_config=MaskedMSAHeadConfig(c_m=256, c_out=23), experimentally_resolved_head_config=ExperimentallyResolvedHeadConfig(c_s=384, c_out=37), tm_score_head_config=TMScoreHeadConfig(c_z=128, num_bins=64, max_bin=31), tm_score_head_enabled=False, ptm_weight=0.2, iptm_weight=0.8), loss_config: 'LossConfig' = LossConfig(fape_loss_config=FAPELossConfig(weight=1.0, backbone_clamp_distance=10.0, backbone_loss_unit_distance=10.0, backbone_weight=0.5, interface_clamp_distance=30.0, interface_loss_unit_distance=20.0, interface_weight=0.5, sidechain_clamp_distance=10.0, sidechain_length_scale=10.0, sidechain_weight=0.5, eps=0.0001), supervised_chi_loss_config=SupervisedChiLossConfig(weight=1.0, chi_weight=0.5, angle_norm_weight=0.01, eps=1e-08), distogram_loss_config=DistogramLossConfig(weight=0.3, min_bin=2.3125, max_bin=21.6875, num_bins=64, eps=1e-08), masked_msa_loss_config=MaskedMSALossConfig(weight=2.0, eps=1e-08, num_classes=23), plddt_loss_config=PLDDTLossConfig(weight=0.01, cutoff=15.0, min_resolution=0.1, max_resolution=3.0, num_bins=50, eps=1e-08), experimentally_resolved_loss_config=ExperimentallyResolvedLossConfig(weight=0.0, min_resolution=0.1, max_resolution=3.0, eps=1e-08), violation_loss_config=ViolationLossConfig(weight=0.0, violation_tolerance_factor=12.0, average_clashes=False, clash_overlap_tolerance=1.5, eps=1e-06), tm_loss_config=TMLossConfig(enabled=False, weight=0.0, min_resolution=0.1, max_resolution=3.0, num_bins=64, max_bin=31, eps=1e-08), chain_center_of_mass_config=CenterOfMassConfig(enabled=False, clamp_distance=-4.0, eps=1e-10, weight=0.05)), recycle_early_stop_enabled: 'bool' = False, recycle_early_stop_tolerance: 'float' = 0.5, templates_enabled: 'bool' = True, embed_template_torsion_angles: 'bool' = True, template_pair_feat_distogram_min_bin: 'float' = 3.25, template_pair_feat_distogram_max_bin: 'float' = 50.75, template_pair_feat_distogram_num_bins: 'int' = 39, template_pair_feat_use_unit_vector: 'bool' = False, template_pair_feat_inf: 'float' = 100000.0, template_pair_feat_eps: 'float' = 1e-06)

__init__(is_multimer: bool = False, input_embedder_config: InputEmbedderConfig = InputEmbedderConfig(tf_dim=22, msa_dim=49, c_z=128, c_m=256, relpos_k=32, max_relative_chain=2, max_relative_index=32, use_chain_relative=True), recycling_embedder_config: RecyclingEmbedderConfig = RecyclingEmbedderConfig(c_m=256, c_z=128, min_bin=3.25, max_bin=20.75, num_bins=15, inf=100000000.0), template_angle_embedder_config: TemplateAngleEmbedderConfig = TemplateAngleEmbedderConfig(ta_dim=57, c_m=256), template_pair_embedder_config: TemplatePairEmbedderConfig = TemplatePairEmbedderConfig(tp_dim=88, c_t=64, c_z=128, c_dgram=39, c_aatype=22), template_pair_stack_config: TemplatePairStackConfig = TemplatePairStackConfig(c_t=64, c_hidden_tri_att=16, c_hidden_tri_mul=64, num_blocks=2, num_heads_tri=4, pair_transition_n=2, dropout_rate=0.25, inf=1000000000.0, chunk_size_tri_att=None, block_size_tri_mul=None, tri_att_first=True), template_pointwise_attention_config: TemplatePointwiseAttentionConfig = TemplatePointwiseAttentionConfig(c_t=64, c_z=128, c_hidden=16, num_heads=4, inf=100000.0, chunk_size=None), template_projection_config: TemplateProjectionConfig = TemplateProjectionConfig(c_t=64, c_z=128), extra_msa_embedder_config: ExtraMSAEmbedderConfig = ExtraMSAEmbedderConfig(emsa_dim=25, c_e=64), extra_msa_stack_config: ExtraMSAStackConfig = ExtraMSAStackConfig(c_e=64, c_z=128, c_hidden_msa_att=8, c_hidden_opm=32, c_hidden_tri_mul=128, c_hidden_tri_att=32, num_heads_msa=8, num_heads_tri=4, num_blocks=4, transition_n=4, msa_dropout=0.15, pair_dropout=0.25, inf=1000000000.0, eps=1e-08, eps_opm=0.001, chunk_size_msa_att=None, chunk_size_opm=None, chunk_size_tri_att=None, block_size_tri_mul=None, outer_product_mean_first=False), evoformer_stack_config: EvoformerStackConfig = EvoformerStackConfig(c_m=256, c_z=128, c_hidden_msa_att=32, c_hidden_opm=32, c_hidden_tri_mul=128, c_hidden_tri_att=32, c_s=384, num_heads_msa=8, num_heads_tri=4, num_blocks=48, transition_n=4, msa_dropout=0.15, pair_dropout=0.25, inf=1000000000.0, eps_opm=0.001, chunk_size_msa_att=None, chunk_size_opm=None, chunk_size_tri_att=None, block_size_tri_mul=None, outer_product_mean_first=False), structure_module_config: StructureModuleConfig = StructureModuleConfig(c_s=384, c_z=128, c_hidden_ipa=16, c_hidden_ang_res=128, num_heads_ipa=12, num_qk_points=4, num_v_points=8, is_multimer=False, dropout_rate=0.1, num_blocks=8, num_ang_res_blocks=2, num_angles=7, scale_factor=10.0, inf=100000.0, eps=1e-08), auxiliary_heads_config: AuxiliaryHeadsConfig = AuxiliaryHeadsConfig(per_residue_lddt_ca_predictor_config=PerResidueLDDTCaPredictorConfig(c_s=384, c_hidden=128, num_bins=50), distogram_head_config=DistogramHeadConfig(c_z=128, num_bins=64), masked_msa_head_config=MaskedMSAHeadConfig(c_m=256, c_out=23), experimentally_resolved_head_config=ExperimentallyResolvedHeadConfig(c_s=384, c_out=37), tm_score_head_config=TMScoreHeadConfig(c_z=128, num_bins=64, max_bin=31), tm_score_head_enabled=False, ptm_weight=0.2, iptm_weight=0.8), loss_config: LossConfig = LossConfig(fape_loss_config=FAPELossConfig(weight=1.0, backbone_clamp_distance=10.0, backbone_loss_unit_distance=10.0, backbone_weight=0.5, interface_clamp_distance=30.0, interface_loss_unit_distance=20.0, interface_weight=0.5, sidechain_clamp_distance=10.0, sidechain_length_scale=10.0, sidechain_weight=0.5, eps=0.0001), supervised_chi_loss_config=SupervisedChiLossConfig(weight=1.0, chi_weight=0.5, angle_norm_weight=0.01, eps=1e-08), distogram_loss_config=DistogramLossConfig(weight=0.3, min_bin=2.3125, max_bin=21.6875, num_bins=64, eps=1e-08), masked_msa_loss_config=MaskedMSALossConfig(weight=2.0, eps=1e-08, num_classes=23), plddt_loss_config=PLDDTLossConfig(weight=0.01, cutoff=15.0, min_resolution=0.1, max_resolution=3.0, num_bins=50, eps=1e-08), experimentally_resolved_loss_config=ExperimentallyResolvedLossConfig(weight=0.0, min_resolution=0.1, max_resolution=3.0, eps=1e-08), violation_loss_config=ViolationLossConfig(weight=0.0, violation_tolerance_factor=12.0, average_clashes=False, clash_overlap_tolerance=1.5, eps=1e-06), tm_loss_config=TMLossConfig(enabled=False, weight=0.0, min_resolution=0.1, max_resolution=3.0, num_bins=64, max_bin=31, eps=1e-08), chain_center_of_mass_config=CenterOfMassConfig(enabled=False, clamp_distance=-4.0, eps=1e-10, weight=0.05)), recycle_early_stop_enabled: bool = False, recycle_early_stop_tolerance: float = 0.5, templates_enabled: bool = True, embed_template_torsion_angles: bool = True, template_pair_feat_distogram_min_bin: float = 3.25, template_pair_feat_distogram_max_bin: float = 50.75, template_pair_feat_distogram_num_bins: int = 39, template_pair_feat_use_unit_vector: bool = False, template_pair_feat_inf: float = 100000.0, template_pair_feat_eps: float = 1e-06) → None

Methods

__init__([is_multimer, ...])
from_dict(cfg)
from_preset([is_multimer, precision, ...])
to_dict()

Attributes

auxiliary_heads_config
embed_template_torsion_angles
evoformer_stack_config
extra_msa_embedder_config
extra_msa_stack_config
input_embedder_config
is_multimer
loss_config
recycle_early_stop_enabled
recycle_early_stop_tolerance
recycling_embedder_config
structure_module_config
template_angle_embedder_config
template_pair_embedder_config
template_pair_feat_distogram_max_bin
template_pair_feat_distogram_min_bin
template_pair_feat_distogram_num_bins
template_pair_feat_eps
template_pair_feat_inf
template_pair_feat_use_unit_vector
template_pair_stack_config
template_pointwise_attention_config
template_projection_config
templates_enabled