Welcome to PPI Integration Toolkit’s documentation!

Table of Contents

• Backbone Models
  • DeepFold
    • deepfold
      • deepfold.common
        • deepfold.common.protein
          • deepfold.common.protein.add_pdb_headers
            • add_pdb_headers()
          • deepfold.common.protein.from_pdb_string
            • from_pdb_string()
          • deepfold.common.protein.from_prediction
            • from_prediction()
          • deepfold.common.protein.from_relaxation
            • from_relaxation()
          • deepfold.common.protein.get_pdb_headers
            • get_pdb_headers()
          • deepfold.common.protein.ideal_atom_mask
            • ideal_atom_mask()
          • deepfold.common.protein.to_modelcif
            • to_modelcif()
          • deepfold.common.protein.to_pdb
            • to_pdb()
          • deepfold.common.protein.Protein
            • Protein
              • Protein.__init__()
        • deepfold.common.residue_constants
          • deepfold.common.residue_constants.aatype_to_str_sequence
            • aatype_to_str_sequence()
          • deepfold.common.residue_constants.chi_angle_atom
            • chi_angle_atom()
          • deepfold.common.residue_constants.load_stereo_chemical_props
            • load_stereo_chemical_props()
          • deepfold.common.residue_constants.make_atom14_dists_bounds
            • make_atom14_dists_bounds()
          • deepfold.common.residue_constants.map_structure_with_atom_order
            • map_structure_with_atom_order()
          • deepfold.common.residue_constants.sequence_to_onehot
            • sequence_to_onehot()
          • deepfold.common.residue_constants.Bond
            • Bond
              • Bond.__init__()
          • deepfold.common.residue_constants.BondAngle
            • BondAngle
              • BondAngle.__init__()
      • deepfold.config
        • deepfold.config.AlphaFoldConfig
          • AlphaFoldConfig
            • AlphaFoldConfig.__init__()
        • deepfold.config.AuxiliaryHeadsConfig
          • AuxiliaryHeadsConfig
            • AuxiliaryHeadsConfig.__init__()
        • deepfold.config.CenterOfMassConfig
          • CenterOfMassConfig
            • CenterOfMassConfig.__init__()
        • deepfold.config.DistogramHeadConfig
          • DistogramHeadConfig
            • DistogramHeadConfig.__init__()
        • deepfold.config.DistogramLossConfig
          • DistogramLossConfig
            • DistogramLossConfig.__init__()
        • deepfold.config.EvoformerStackConfig
          • EvoformerStackConfig
            • EvoformerStackConfig.__init__()
        • deepfold.config.ExperimentallyResolvedHeadConfig
          • ExperimentallyResolvedHeadConfig
            • ExperimentallyResolvedHeadConfig.__init__()
        • deepfold.config.ExperimentallyResolvedLossConfig
          • ExperimentallyResolvedLossConfig
            • ExperimentallyResolvedLossConfig.__init__()
        • deepfold.config.ExtraMSAEmbedderConfig
          • ExtraMSAEmbedderConfig
            • ExtraMSAEmbedderConfig.__init__()
        • deepfold.config.ExtraMSAStackConfig
          • ExtraMSAStackConfig
            • ExtraMSAStackConfig.__init__()
        • deepfold.config.FAPELossConfig
          • FAPELossConfig
            • FAPELossConfig.__init__()
        • deepfold.config.FeaturePipelineConfig
          • FeaturePipelineConfig
            • FeaturePipelineConfig.__init__()
        • deepfold.config.InputEmbedderConfig
          • InputEmbedderConfig
            • InputEmbedderConfig.__init__()
        • deepfold.config.LossConfig
          • LossConfig
            • LossConfig.__init__()
        • deepfold.config.MaskedMSAHeadConfig
          • MaskedMSAHeadConfig
            • MaskedMSAHeadConfig.__init__()
        • deepfold.config.MaskedMSALossConfig
          • MaskedMSALossConfig
            • MaskedMSALossConfig.__init__()
        • deepfold.config.PLDDTLossConfig
          • PLDDTLossConfig
            • PLDDTLossConfig.__init__()
        • deepfold.config.PerResidueLDDTCaPredictorConfig
          • PerResidueLDDTCaPredictorConfig
            • PerResidueLDDTCaPredictorConfig.__init__()
        • deepfold.config.RecyclingEmbedderConfig
          • RecyclingEmbedderConfig
            • RecyclingEmbedderConfig.__init__()
        • deepfold.config.StructureModuleConfig
          • StructureModuleConfig
            • StructureModuleConfig.__init__()
        • deepfold.config.SupervisedChiLossConfig
          • SupervisedChiLossConfig
            • SupervisedChiLossConfig.__init__()
        • deepfold.config.TMLossConfig
          • TMLossConfig
            • TMLossConfig.__init__()
        • deepfold.config.TMScoreHeadConfig
          • TMScoreHeadConfig
            • TMScoreHeadConfig.__init__()
        • deepfold.config.TemplateAngleEmbedderConfig
          • TemplateAngleEmbedderConfig
            • TemplateAngleEmbedderConfig.__init__()
        • deepfold.config.TemplatePairEmbedderConfig
          • TemplatePairEmbedderConfig
            • TemplatePairEmbedderConfig.__init__()
        • deepfold.config.TemplatePairStackConfig
          • TemplatePairStackConfig
            • TemplatePairStackConfig.__init__()
        • deepfold.config.TemplatePointwiseAttentionConfig
          • TemplatePointwiseAttentionConfig
            • TemplatePointwiseAttentionConfig.__init__()
        • deepfold.config.TemplateProjectionConfig
          • TemplateProjectionConfig
            • TemplateProjectionConfig.__init__()
        • deepfold.config.TrainingConfig
          • TrainingConfig
            • TrainingConfig.__init__()
        • deepfold.config.ViolationLossConfig
          • ViolationLossConfig
            • ViolationLossConfig.__init__()
      • deepfold.data
        • deepfold.data.errors
        • deepfold.data.modules
          • deepfold.data.modules.dataloaders
          • deepfold.data.modules.mmcif_dataset
          • deepfold.data.modules.samplers
          • deepfold.data.modules.single_dataset
        • deepfold.data.monomer
          • deepfold.data.monomer.build_atom_map
            • build_atom_map()
          • deepfold.data.monomer.fetch_ligand
            • fetch_ligand()
          • deepfold.data.monomer.get_ligand
            • get_ligand()
          • deepfold.data.monomer.read_ligand
            • read_ligand()
          • deepfold.data.monomer.AtomMap
            • AtomMap
              • AtomMap.__init__()
          • deepfold.data.monomer.Ligand
            • Ligand
              • Ligand.__init__()
        • deepfold.data.multimer
          • deepfold.data.multimer.input_features
            • deepfold.data.multimer.input_features.add_assembly_features
              • add_assembly_features()
            • deepfold.data.multimer.input_features.convert_monomer_features
              • convert_monomer_features()
            • deepfold.data.multimer.input_features.create_all_seq_msa_features
              • create_all_seq_msa_features()
            • deepfold.data.multimer.input_features.create_all_seq_msa_features_from_a3m
              • create_all_seq_msa_features_from_a3m()
            • deepfold.data.multimer.input_features.create_multimer_features
              • create_multimer_features()
            • deepfold.data.multimer.input_features.crop_chains
              • crop_chains()
            • deepfold.data.multimer.input_features.int_id_to_str_id
              • int_id_to_str_id()
            • deepfold.data.multimer.input_features.pad_msa
              • pad_msa()
            • deepfold.data.multimer.input_features.pair_and_merge
              • pair_and_merge()
            • deepfold.data.multimer.input_features.process_final
              • process_final()
            • deepfold.data.multimer.input_features.process_multimer_features
              • process_multimer_features()
            • deepfold.data.multimer.input_features.process_single_chain
              • process_single_chain()
            • deepfold.data.multimer.input_features.process_unmerged_features
              • process_unmerged_features()
            • deepfold.data.multimer.input_features.ComplexInfo
              • ComplexInfo
          • deepfold.data.multimer.msa_pairing
            • deepfold.data.multimer.msa_pairing.block_diag
              • block_diag()
            • deepfold.data.multimer.msa_pairing.create_paired_features
              • create_paired_features()
            • deepfold.data.multimer.msa_pairing.deduplicate_unpaired_sequences
              • deduplicate_unpaired_sequences()
            • deepfold.data.multimer.msa_pairing.merge_chain_features
              • merge_chain_features()
            • deepfold.data.multimer.msa_pairing.pad_features
              • pad_features()
            • deepfold.data.multimer.msa_pairing.pair_sequences
              • pair_sequences()
            • deepfold.data.multimer.msa_pairing.reorder_paired_rows
              • reorder_paired_rows()
        • deepfold.data.pdbio
          • deepfold.data.pdbio.IO
            • IO
              • IO.__init__()
          • deepfold.data.pdbio.PDBIO
            • PDBIO
              • PDBIO.__init__()
        • deepfold.data.pdbx_parsing
          • deepfold.data.pdbx_parsing.fetch_mmcif
            • fetch_mmcif()
          • deepfold.data.pdbx_parsing.get_assemblies
            • get_assemblies()
          • deepfold.data.pdbx_parsing.get_chain_features
            • get_chain_features()
          • deepfold.data.pdbx_parsing.get_fasta
            • get_fasta()
          • deepfold.data.pdbx_parsing.loop_to_dict
            • loop_to_dict()
          • deepfold.data.pdbx_parsing.loop_to_list
            • loop_to_list()
          • deepfold.data.pdbx_parsing.print_amap
            • print_amap()
          • deepfold.data.pdbx_parsing.print_chain_features
            • print_chain_features()
          • deepfold.data.pdbx_parsing.read_mmcif
            • read_mmcif()
          • deepfold.data.pdbx_parsing.AssemblyGenerator
            • AssemblyGenerator
              • AssemblyGenerator.__init__()
          • deepfold.data.pdbx_parsing.AtomSite
            • AtomSite
              • AtomSite.__init__()
          • deepfold.data.pdbx_parsing.ModResidue
            • ModResidue
              • ModResidue.__init__()
          • deepfold.data.pdbx_parsing.Monomer
            • Monomer
              • Monomer.__init__()
          • deepfold.data.pdbx_parsing.Op
            • Op
              • Op.__init__()
          • deepfold.data.pdbx_parsing.PDBxHeader
            • PDBxHeader
              • PDBxHeader.__init__()
          • deepfold.data.pdbx_parsing.PDBxObject
            • PDBxObject
              • PDBxObject.__init__()
          • deepfold.data.pdbx_parsing.PDBxParser
            • PDBxParser
              • PDBxParser.__init__()
          • deepfold.data.pdbx_parsing.ParsingResult
            • ParsingResult
              • ParsingResult.__init__()
          • deepfold.data.pdbx_parsing.ResidueAtPosition
            • ResidueAtPosition
              • ResidueAtPosition.__init__()
          • deepfold.data.pdbx_parsing.ResiduePosition
            • ResiduePosition
              • ResiduePosition.__init__()
        • deepfold.data.search
          • deepfold.data.search.crfalign
            • deepfold.data.search.crfalign.parse_crf
              • parse_crf()
            • deepfold.data.search.crfalign.parse_pir
              • parse_pir()
          • deepfold.data.search.input_features
            • deepfold.data.search.input_features.create_mmcif_features
              • create_mmcif_features()
            • deepfold.data.search.input_features.create_msa_features
              • create_msa_features()
            • deepfold.data.search.input_features.create_pdb_features
              • create_pdb_features()
            • deepfold.data.search.input_features.create_protein_features
              • create_protein_features()
            • deepfold.data.search.input_features.create_sequence_features
              • create_sequence_features()
            • deepfold.data.search.input_features.create_template_features
              • create_template_features()
            • deepfold.data.search.input_features.create_template_features_from_hhr_string
              • create_template_features_from_hhr_string()
            • deepfold.data.search.input_features.create_template_features_from_hmmsearch_sto_string
              • create_template_features_from_hmmsearch_sto_string()
          • deepfold.data.search.mmcif
            • deepfold.data.search.mmcif.load_mmcif_file
              • load_mmcif_file()
            • deepfold.data.search.mmcif.parse_mmcif_string
              • parse_mmcif_string()
            • deepfold.data.search.mmcif.zero_center_atom_positions
              • zero_center_atom_positions()
          • deepfold.data.search.msa_identifiers
            • deepfold.data.search.msa_identifiers.get_identifiers
              • get_identifiers()
          • deepfold.data.search.parsers
            • deepfold.data.search.parsers.convert_stockholm_to_a3m
              • convert_stockholm_to_a3m()
            • deepfold.data.search.parsers.deduplicate_stockholm_msa
              • deduplicate_stockholm_msa()
            • deepfold.data.search.parsers.parse_a3m
              • parse_a3m()
            • deepfold.data.search.parsers.parse_e_values_from_tblout
              • parse_e_values_from_tblout()
            • deepfold.data.search.parsers.parse_fasta
              • parse_fasta()
            • deepfold.data.search.parsers.parse_hhr
              • parse_hhr()
            • deepfold.data.search.parsers.parse_hmmsearch_a3m
              • parse_hmmsearch_a3m()
            • deepfold.data.search.parsers.parse_hmmsearch_sto
              • parse_hmmsearch_sto()
            • deepfold.data.search.parsers.parse_stockholm
              • parse_stockholm()
            • deepfold.data.search.parsers.remove_empty_columns_from_stockholm_msa
              • remove_empty_columns_from_stockholm_msa()
            • deepfold.data.search.parsers.truncate_stockholm_msa
              • truncate_stockholm_msa()
            • deepfold.data.search.parsers.HitMetadata
              • HitMetadata
            • deepfold.data.search.parsers.TemplateHit
              • TemplateHit
          • deepfold.data.search.templates
            • deepfold.data.search.templates.build_query_to_hit_index_mapping
              • build_query_to_hit_index_mapping()
            • deepfold.data.search.templates.create_empty_template_feats
              • create_empty_template_feats()
            • deepfold.data.search.templates.extract_template_features
              • extract_template_features()
            • deepfold.data.search.templates.get_atom_positions
              • get_atom_positions()
            • deepfold.data.search.templates.load_mmcif_dict
              • load_mmcif_dict()
            • deepfold.data.search.templates.load_pdb_obsolete_mapping
              • load_pdb_obsolete_mapping()
            • deepfold.data.search.templates.TemplateFeaturesResult
              • TemplateFeaturesResult
            • deepfold.data.search.templates.TemplateHitFeaturizer
              • TemplateHitFeaturizer
        • deepfold.data.tools
          • deepfold.data.tools.hhblits
            • deepfold.data.tools.hhblits.HHBlits
              • HHBlits
          • deepfold.data.tools.hhsearch
            • deepfold.data.tools.hhsearch.HHSearch
              • HHSearch
          • deepfold.data.tools.hmmbuild
            • deepfold.data.tools.hmmbuild.Hmmbuild
              • Hmmbuild
          • deepfold.data.tools.hmmsearch
            • deepfold.data.tools.hmmsearch.Hmmsearch
              • Hmmsearch
          • deepfold.data.tools.jackhmmer
            • deepfold.data.tools.jackhmmer.Jackhmmer
              • Jackhmmer
          • deepfold.data.tools.kalign
            • deepfold.data.tools.kalign.Kalign
              • Kalign
          • deepfold.data.tools.utils
            • deepfold.data.tools.utils.timing
              • timing()
            • deepfold.data.tools.utils.tmpdir_manager
              • tmpdir_manager()
            • deepfold.data.tools.utils.to_date
              • to_date()
      • deepfold.distributed
        • deepfold.distributed.model_parallel
          • deepfold.distributed.model_parallel.all_to_all
            • all_to_all()
          • deepfold.distributed.model_parallel.broadcast
            • broadcast()
          • deepfold.distributed.model_parallel.broadcast_on_model_parallel_region
            • broadcast_on_model_parallel_region()
          • deepfold.distributed.model_parallel.col_to_row
            • col_to_row()
          • deepfold.distributed.model_parallel.copy_to_model_parallel_reigon
            • copy_to_model_parallel_reigon()
          • deepfold.distributed.model_parallel.disable
            • disable()
          • deepfold.distributed.model_parallel.enable
            • enable()
          • deepfold.distributed.model_parallel.gather
            • gather()
          • deepfold.distributed.model_parallel.gather_from_model_parallel_region
            • gather_from_model_parallel_region()
          • deepfold.distributed.model_parallel.group
            • group()
          • deepfold.distributed.model_parallel.group_rank
            • group_rank()
          • deepfold.distributed.model_parallel.initialize
            • initialize()
          • deepfold.distributed.model_parallel.is_enabled
            • is_enabled()
          • deepfold.distributed.model_parallel.is_initialized
            • is_initialized()
          • deepfold.distributed.model_parallel.rank
            • rank()
          • deepfold.distributed.model_parallel.reduce
            • reduce()
          • deepfold.distributed.model_parallel.reduce_from_model_parallel_region
            • reduce_from_model_parallel_region()
          • deepfold.distributed.model_parallel.row_to_col
            • row_to_col()
          • deepfold.distributed.model_parallel.scatter
            • scatter()
          • deepfold.distributed.model_parallel.scatter_to_model_parallel_region
            • scatter_to_model_parallel_region()
          • deepfold.distributed.model_parallel.size
            • size()
          • deepfold.distributed.model_parallel.transpose_on_model_parallel_region
            • transpose_on_model_parallel_region()
          • deepfold.distributed.model_parallel.Disable
            • Disable
              • Disable.__init__()
          • deepfold.distributed.model_parallel.Enable
            • Enable
              • Enable.__init__()
        • deepfold.distributed.utils
          • deepfold.distributed.utils.assert_viewless_tensor
            • assert_viewless_tensor()
          • deepfold.distributed.utils.divide
            • divide()
          • deepfold.distributed.utils.ensure_divisibility
            • ensure_divisibility()
          • deepfold.distributed.utils.safely_set_viewless_tensor_data
            • safely_set_viewless_tensor_data()
          • deepfold.distributed.utils.GlobalMemoryBuffer
            • GlobalMemoryBuffer
              • GlobalMemoryBuffer.__init__()
      • deepfold.eval
        • deepfold.eval.cell_lists
          • deepfold.eval.cell_lists.CellLists
            • CellLists
              • CellLists.__init__()
          • deepfold.eval.cell_lists.Particle
            • Particle
              • Particle.__init__()
        • deepfold.eval.contact
          • deepfold.eval.contact.contact_map
            • contact_map()
          • deepfold.eval.contact.Atom
            • Atom
              • Atom.__init__()
        • deepfold.eval.distogram
          • deepfold.eval.distogram.bin_edges_np
            • bin_edges_np()
          • deepfold.eval.distogram.calculate_bin_centers_np
            • calculate_bin_centers_np()
          • deepfold.eval.distogram.compute_distogram
            • compute_distogram()
          • deepfold.eval.distogram.compute_predicted_distogram
            • compute_predicted_distogram()
          • deepfold.eval.distogram.undigitize
            • undigitize()
        • deepfold.eval.msa
          • deepfold.eval.msa.compute_neff_v1
            • compute_neff_v1()
          • deepfold.eval.msa.compute_neff_v2
            • compute_neff_v2()
        • deepfold.eval.plot
          • deepfold.eval.plot.find_cluster_boundaries
            • find_cluster_boundaries()
          • deepfold.eval.plot.plot_distogram
            • plot_distogram()
          • deepfold.eval.plot.plot_msa
            • plot_msa()
          • deepfold.eval.plot.plot_plddt
            • plot_plddt()
          • deepfold.eval.plot.plot_predicted_alignment_error
            • plot_predicted_alignment_error()
        • deepfold.eval.pseudo_3d
          • deepfold.eval.pseudo_3d.kabsch
            • kabsch()
          • deepfold.eval.pseudo_3d.plot_protein
            • plot_protein()
          • deepfold.eval.pseudo_3d.plot_protein_bb
            • plot_protein_bb()
      • deepfold.loss
        • deepfold.loss.AlphaFoldLoss
          • AlphaFoldLoss
            • AlphaFoldLoss.__init__()
      • deepfold.losses
        • deepfold.losses.auxillary
          • deepfold.losses.auxillary.chain_centre_mass_loss
            • chain_centre_mass_loss()
          • deepfold.losses.auxillary.experimentally_resolved_loss
            • experimentally_resolved_loss()
          • deepfold.losses.auxillary.get_asym_mask
            • get_asym_mask()
          • deepfold.losses.auxillary.repr_norm_loss
            • repr_norm_loss()
        • deepfold.losses.confidence
          • deepfold.losses.confidence.compute_plddt
            • compute_plddt()
          • deepfold.losses.confidence.compute_predicted_aligned_error
            • compute_predicted_aligned_error()
          • deepfold.losses.confidence.compute_tm
            • compute_tm()
          • deepfold.losses.confidence.lddt
            • lddt()
          • deepfold.losses.confidence.lddt_ca
            • lddt_ca()
          • deepfold.losses.confidence.plddt_loss
            • plddt_loss()
          • deepfold.losses.confidence.tm_loss
            • tm_loss()
        • deepfold.losses.geometry
          • deepfold.losses.geometry.backbone_loss
            • backbone_loss()
          • deepfold.losses.geometry.compute_distogram
            • compute_distogram()
          • deepfold.losses.geometry.compute_fape
            • compute_fape()
          • deepfold.losses.geometry.compute_renamed_ground_truth
            • compute_renamed_ground_truth()
          • deepfold.losses.geometry.distogram_loss
            • distogram_loss()
          • deepfold.losses.geometry.fape_loss
            • fape_loss()
          • deepfold.losses.geometry.get_optimal_transform
            • get_optimal_transform()
          • deepfold.losses.geometry.kabsch_rmsd
            • kabsch_rmsd()
          • deepfold.losses.geometry.sidechain_loss
            • sidechain_loss()
          • deepfold.losses.geometry.superimpose
            • superimpose()
          • deepfold.losses.geometry.supervised_chi_loss
            • supervised_chi_loss()
        • deepfold.losses.masked_msa
          • deepfold.losses.masked_msa.masked_msa_loss
            • masked_msa_loss()
        • deepfold.losses.procrustes
          • deepfold.losses.procrustes.flatten_batch_dims
            • flatten_batch_dims()
          • deepfold.losses.procrustes.kabsch
            • kabsch()
          • deepfold.losses.procrustes.procrustes
            • procrustes()
          • deepfold.losses.procrustes.rigid_points_registration
            • rigid_points_registration()
          • deepfold.losses.procrustes.rigid_vectors_registration
            • rigid_vectors_registration()
          • deepfold.losses.procrustes.speical_procrustes
            • speical_procrustes()
          • deepfold.losses.procrustes.svd
            • svd()
          • deepfold.losses.procrustes.unflatten_batch_dims
            • unflatten_batch_dims()
          • deepfold.losses.procrustes.Procrustes
            • Procrustes
              • Procrustes.__init__()
        • deepfold.losses.utils
          • deepfold.losses.utils.calculate_bin_centers
            • calculate_bin_centers()
          • deepfold.losses.utils.sigmoid_cross_entropy
            • sigmoid_cross_entropy()
          • deepfold.losses.utils.softmax_cross_entropy
            • softmax_cross_entropy()
        • deepfold.losses.violation
          • deepfold.losses.violation.between_residue_bond_loss
            • between_residue_bond_loss()
          • deepfold.losses.violation.between_residue_clash_loss
            • between_residue_clash_loss()
          • deepfold.losses.violation.compute_violation_metrics
            • compute_violation_metrics()
          • deepfold.losses.violation.compute_violation_metrics_np
            • compute_violation_metrics_np()
          • deepfold.losses.violation.extreme_ca_ca_distance_violations
            • extreme_ca_ca_distance_violations()
          • deepfold.losses.violation.find_structural_violations
            • find_structural_violations()
          • deepfold.losses.violation.find_structural_violations_np
            • find_structural_violations_np()
          • deepfold.losses.violation.violation_loss
            • violation_loss()
          • deepfold.losses.violation.within_residue_violations
            • within_residue_violations()
      • deepfold.modules
        • deepfold.modules.alphafold
          • deepfold.modules.alphafold.AlphaFold
            • AlphaFold
              • AlphaFold.__init__()
        • deepfold.modules.angle_resnet
          • deepfold.modules.angle_resnet.AngleResnet
            • AngleResnet
              • AngleResnet.__init__()
          • deepfold.modules.angle_resnet.AngleResnetBlock
            • AngleResnetBlock
              • AngleResnetBlock.__init__()
        • deepfold.modules.attention
          • deepfold.modules.attention.CrossAttentionNoGate
            • CrossAttentionNoGate
              • CrossAttentionNoGate.__init__()
          • deepfold.modules.attention.SelfAttentionWithGate
            • SelfAttentionWithGate
              • SelfAttentionWithGate.__init__()
        • deepfold.modules.auxiliary_heads
          • deepfold.modules.auxiliary_heads.AuxiliaryHeads
            • AuxiliaryHeads
              • AuxiliaryHeads.__init__()
          • deepfold.modules.auxiliary_heads.DistogramHead
            • DistogramHead
              • DistogramHead.__init__()
          • deepfold.modules.auxiliary_heads.ExperimentallyResolvedHead
            • ExperimentallyResolvedHead
              • ExperimentallyResolvedHead.__init__()
          • deepfold.modules.auxiliary_heads.MaskedMSAHead
            • MaskedMSAHead
              • MaskedMSAHead.__init__()
          • deepfold.modules.auxiliary_heads.PerResidueLDDTCaPredictor
            • PerResidueLDDTCaPredictor
              • PerResidueLDDTCaPredictor.__init__()
          • deepfold.modules.auxiliary_heads.TMScoreHead
            • TMScoreHead
              • TMScoreHead.__init__()
        • deepfold.modules.backbone_update
          • deepfold.modules.backbone_update.BackboneUpdate
            • BackboneUpdate
              • BackboneUpdate.__init__()
        • deepfold.modules.dropout
          • deepfold.modules.dropout.Dropout
            • Dropout
              • Dropout.__init__()
          • deepfold.modules.dropout.DropoutColumnwise
            • DropoutColumnwise
              • DropoutColumnwise.__init__()
          • deepfold.modules.dropout.DropoutRowwise
            • DropoutRowwise
              • DropoutRowwise.__init__()
        • deepfold.modules.evoformer_block
          • deepfold.modules.evoformer_block.EvoformerBlock
            • EvoformerBlock
              • EvoformerBlock.__init__()
        • deepfold.modules.evoformer_block_pair_core
          • deepfold.modules.evoformer_block_pair_core.EvoformerBlockPairCore
            • EvoformerBlockPairCore
              • EvoformerBlockPairCore.__init__()
        • deepfold.modules.evoformer_stack
          • deepfold.modules.evoformer_stack.EvoformerStack
            • EvoformerStack
              • EvoformerStack.__init__()
        • deepfold.modules.extra_msa_block
          • deepfold.modules.extra_msa_block.ExtraMSABlock
            • ExtraMSABlock
              • ExtraMSABlock.__init__()
        • deepfold.modules.extra_msa_embedder
          • deepfold.modules.extra_msa_embedder.ExtraMSAEmbedder
            • ExtraMSAEmbedder
              • ExtraMSAEmbedder.__init__()
        • deepfold.modules.extra_msa_stack
          • deepfold.modules.extra_msa_stack.ExtraMSAStack
            • ExtraMSAStack
              • ExtraMSAStack.__init__()
        • deepfold.modules.global_attention
          • deepfold.modules.global_attention.GlobalAttention
            • GlobalAttention
              • GlobalAttention.__init__()
        • deepfold.modules.inductor
          • deepfold.modules.inductor.disable
            • disable()
          • deepfold.modules.inductor.enable
            • enable()
          • deepfold.modules.inductor.is_enabled
            • is_enabled()
          • deepfold.modules.inductor.is_enabled_and_autograd_off
            • is_enabled_and_autograd_off()
        • deepfold.modules.input_embedder
          • deepfold.modules.input_embedder.InputEmbedder
            • InputEmbedder
              • InputEmbedder.__init__()
          • deepfold.modules.input_embedder.InputEmbedderMultimer
            • InputEmbedderMultimer
              • InputEmbedderMultimer.__init__()
        • deepfold.modules.invariant_point_attention
          • deepfold.modules.invariant_point_attention.ipa_point_weights_init_
            • ipa_point_weights_init_()
          • deepfold.modules.invariant_point_attention.InvariantPointAttention
            • InvariantPointAttention
              • InvariantPointAttention.__init__()
          • deepfold.modules.invariant_point_attention.InvariantPointAttentionMultimer
            • InvariantPointAttentionMultimer
              • InvariantPointAttentionMultimer.__init__()
          • deepfold.modules.invariant_point_attention.PointProjection
            • PointProjection
              • PointProjection.__init__()
        • deepfold.modules.layer_norm
          • deepfold.modules.layer_norm.LayerNorm
            • LayerNorm
              • LayerNorm.__init__()
        • deepfold.modules.linear
          • deepfold.modules.linear.final_init_
            • final_init_()
          • deepfold.modules.linear.gating_init_
            • gating_init_()
          • deepfold.modules.linear.glorot_uniform_init_
            • glorot_uniform_init_()
          • deepfold.modules.linear.he_normal_init_
            • he_normal_init_()
          • deepfold.modules.linear.lecun_normal_init_
            • lecun_normal_init_()
          • deepfold.modules.linear.normal_init_
            • normal_init_()
          • deepfold.modules.linear.trunc_normal_init_
            • trunc_normal_init_()
          • deepfold.modules.linear.Linear
            • Linear
              • Linear.__init__()
        • deepfold.modules.msa_column_attention
          • deepfold.modules.msa_column_attention.MSAColumnAttention
            • MSAColumnAttention
              • MSAColumnAttention.__init__()
        • deepfold.modules.msa_column_global_attention
          • deepfold.modules.msa_column_global_attention.MSAColumnGlobalAttention
            • MSAColumnGlobalAttention
              • MSAColumnGlobalAttention.__init__()
        • deepfold.modules.msa_row_attention_with_pair_bias
          • deepfold.modules.msa_row_attention_with_pair_bias.MSARowAttentionWithPairBias
            • MSARowAttentionWithPairBias
              • MSARowAttentionWithPairBias.__init__()
        • deepfold.modules.msa_transition
          • deepfold.modules.msa_transition.MSATransition
            • MSATransition
              • MSATransition.__init__()
        • deepfold.modules.outer_product_mean
          • deepfold.modules.outer_product_mean.OuterProductMean
            • OuterProductMean
              • OuterProductMean.__init__()
        • deepfold.modules.pair_transition
          • deepfold.modules.pair_transition.PairTransition
            • PairTransition
              • PairTransition.__init__()
        • deepfold.modules.recycling_embedder
          • deepfold.modules.recycling_embedder.RecyclingEmbedder
            • RecyclingEmbedder
              • RecyclingEmbedder.__init__()
        • deepfold.modules.single_transition
          • deepfold.modules.single_transition.SingleTransition
            • SingleTransition
              • SingleTransition.__init__()
        • deepfold.modules.structure_module
          • deepfold.modules.structure_module.StructureModule
            • StructureModule
              • StructureModule.__init__()
        • deepfold.modules.template_angle_embedder
          • deepfold.modules.template_angle_embedder.TemplateAngleEmbedder
            • TemplateAngleEmbedder
              • TemplateAngleEmbedder.__init__()
        • deepfold.modules.template_pair_block
          • deepfold.modules.template_pair_block.TemplatePairBlock
            • TemplatePairBlock
              • TemplatePairBlock.__init__()
        • deepfold.modules.template_pair_embedder
          • deepfold.modules.template_pair_embedder.TemplatePairEmbedder
            • TemplatePairEmbedder
              • TemplatePairEmbedder.__init__()
          • deepfold.modules.template_pair_embedder.TemplatePairEmbedderMultimer
            • TemplatePairEmbedderMultimer
              • TemplatePairEmbedderMultimer.__init__()
        • deepfold.modules.template_pair_stack
          • deepfold.modules.template_pair_stack.TemplatePairStack
            • TemplatePairStack
              • TemplatePairStack.__init__()
        • deepfold.modules.template_pointwise_attention
          • deepfold.modules.template_pointwise_attention.TemplatePointwiseAttention
            • TemplatePointwiseAttention
              • TemplatePointwiseAttention.__init__()
        • deepfold.modules.template_projection
          • deepfold.modules.template_projection.TemplateProjection
            • TemplateProjection
              • TemplateProjection.__init__()
        • deepfold.modules.triangular_attention
          • deepfold.modules.triangular_attention.TriangleAttention
            • TriangleAttention
              • TriangleAttention.__init__()
          • deepfold.modules.triangular_attention.TriangleAttentionEndingNode
            • TriangleAttentionEndingNode
              • TriangleAttentionEndingNode.__init__()
          • deepfold.modules.triangular_attention.TriangleAttentionStartingNode
            • TriangleAttentionStartingNode
              • TriangleAttentionStartingNode.__init__()
        • deepfold.modules.triangular_multiplicative_update
          • deepfold.modules.triangular_multiplicative_update.TriangleMultiplicationIncoming
            • TriangleMultiplicationIncoming
              • TriangleMultiplicationIncoming.__init__()
          • deepfold.modules.triangular_multiplicative_update.TriangleMultiplicationOutgoing
            • TriangleMultiplicationOutgoing
              • TriangleMultiplicationOutgoing.__init__()
          • deepfold.modules.triangular_multiplicative_update.TriangleMultiplicativeUpdate
            • TriangleMultiplicativeUpdate
              • TriangleMultiplicativeUpdate.__init__()
        • deepfold.modules.tweaks
          • deepfold.modules.tweaks.evo_attn
            • deepfold.modules.tweaks.evo_attn.disable
              • disable()
            • deepfold.modules.tweaks.evo_attn.enable
              • enable()
            • deepfold.modules.tweaks.evo_attn.is_enabled
              • is_enabled()
      • deepfold.ops
        • deepfold.ops.evoformer_attention
          • deepfold.ops.evoformer_attention.deepspeed_evo_attn
            • deepspeed_evo_attn()
      • deepfold.package_info
      • deepfold.relax
        • deepfold.relax.amber_minimize
          • deepfold.relax.amber_minimize.clean_protein
            • clean_protein()
          • deepfold.relax.amber_minimize.find_violations
            • find_violations()
          • deepfold.relax.amber_minimize.get_violation_metrics
            • get_violation_metrics()
          • deepfold.relax.amber_minimize.make_atom14_positions
            • make_atom14_positions()
          • deepfold.relax.amber_minimize.run_pipeline
            • run_pipeline()
          • deepfold.relax.amber_minimize.will_restrain
            • will_restrain()
        • deepfold.relax.cleanup
          • deepfold.relax.cleanup.clean_structure
            • clean_structure()
          • deepfold.relax.cleanup.fix_pdb
            • fix_pdb()
        • deepfold.relax.relax
          • deepfold.relax.relax.AmberRelaxation
            • AmberRelaxation
              • AmberRelaxation.__init__()
        • deepfold.relax.utils
          • deepfold.relax.utils.assert_equal_nonterminal_atom_types
            • assert_equal_nonterminal_atom_types()
          • deepfold.relax.utils.overwrite_b_factors
            • overwrite_b_factors()
          • deepfold.relax.utils.overwrite_pdb_coordinates
            • overwrite_pdb_coordinates()
      • deepfold.runner
        • deepfold.runner.config_utils
          • deepfold.runner.config_utils.load
            • load()
        • deepfold.runner.parser
          • deepfold.runner.parser.Lexer
            • Lexer
              • Lexer.__init__()
          • deepfold.runner.parser.Parser
            • Parser
              • Parser.__init__()
        • deepfold.runner.utils
          • deepfold.runner.utils.safe_filename
            • safe_filename()
      • deepfold.testing
        • deepfold.testing.common
          • deepfold.testing.common.skip_if_lt_x_gpu
            • skip_if_lt_x_gpu()
          • deepfold.testing.common.skip_if_no_gpu
            • skip_if_no_gpu()
          • deepfold.testing.common.with_nccl_blocking_wait
            • with_nccl_blocking_wait()
          • deepfold.testing.common.MultiProcessTestCase
            • MultiProcessTestCase
              • MultiProcessTestCase.__init__()
        • deepfold.testing.utils
          • deepfold.testing.utils.find_free_port
            • find_free_port()
      • deepfold.train
        • deepfold.train.gradient_clipping
          • deepfold.train.gradient_clipping.update_norm_from_buckets
            • update_norm_from_buckets()
          • deepfold.train.gradient_clipping.AsyncGradientClipping
            • AsyncGradientClipping
              • AsyncGradientClipping.__init__()
        • deepfold.train.lr_scheduler
          • deepfold.train.lr_scheduler.get_learning_rate
            • get_learning_rate()
          • deepfold.train.lr_scheduler.set_learning_rate
            • set_learning_rate()
          • deepfold.train.lr_scheduler.AlphaFoldLRScheduler
            • AlphaFoldLRScheduler
              • AlphaFoldLRScheduler.__init__()
          • deepfold.train.lr_scheduler.OpenFoldBenchmarkLRScheduler
            • OpenFoldBenchmarkLRScheduler
              • OpenFoldBenchmarkLRScheduler.__init__()
        • deepfold.train.validation_metrics
          • deepfold.train.validation_metrics.compute_validation_metrics
            • compute_validation_metrics()
          • deepfold.train.validation_metrics.drmsd
            • drmsd()
          • deepfold.train.validation_metrics.gdt
            • gdt()
          • deepfold.train.validation_metrics.gdt_ha
            • gdt_ha()
          • deepfold.train.validation_metrics.gdt_ts
            • gdt_ts()
      • deepfold.utils
        • deepfold.utils.checkpoint_utils
          • deepfold.utils.checkpoint_utils.map_init_state_dicts
            • map_init_state_dicts()
          • deepfold.utils.checkpoint_utils.resume_checkpoint
            • resume_checkpoint()
          • deepfold.utils.checkpoint_utils.resume_from_latest_checkpoint
            • resume_from_latest_checkpoint()
          • deepfold.utils.checkpoint_utils.save_checkpoint
            • save_checkpoint()
          • deepfold.utils.checkpoint_utils.save_last_checkpoint
            • save_last_checkpoint()
          • deepfold.utils.checkpoint_utils.save_val_checkpoint
            • save_val_checkpoint()
        • deepfold.utils.chunk_utils
          • deepfold.utils.chunk_utils.chunk_layer
            • chunk_layer()
        • deepfold.utils.crop_utils
          • deepfold.utils.crop_utils.unpad_to_schema_shape_
            • unpad_to_schema_shape_()
        • deepfold.utils.datetime_utils
          • deepfold.utils.datetime_utils.datetime_from_string
            • datetime_from_string()
          • deepfold.utils.datetime_utils.datetime_to_string
            • datetime_to_string()
          • deepfold.utils.datetime_utils.get_timestamp_string
            • get_timestamp_string()
        • deepfold.utils.dist_utils
          • deepfold.utils.dist_utils.get_pad_size
            • get_pad_size()
          • deepfold.utils.dist_utils.pad_tensor
            • pad_tensor()
        • deepfold.utils.feats_utils
          • deepfold.utils.feats_utils.crop_a3m_string
            • crop_a3m_string()
          • deepfold.utils.feats_utils.crop_features
            • crop_features()
        • deepfold.utils.file_utils
          • deepfold.utils.file_utils.dump_pickle
            • dump_pickle()
          • deepfold.utils.file_utils.find_paths
            • find_paths()
          • deepfold.utils.file_utils.get_file_content_and_extension
            • get_file_content_and_extension()
          • deepfold.utils.file_utils.load_pickle
            • load_pickle()
          • deepfold.utils.file_utils.read_text
            • read_text()
          • deepfold.utils.file_utils.restore_wrapper
            • restore_wrapper()
        • deepfold.utils.geometry
          • deepfold.utils.geometry.quat_rigid
            • deepfold.utils.geometry.quat_rigid.QuatRigid
              • QuatRigid
          • deepfold.utils.geometry.rigid_matrix_vector
            • deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array
              • Rigid3Array
          • deepfold.utils.geometry.rotation_matrix
            • deepfold.utils.geometry.rotation_matrix.Rot3Array
              • Rot3Array
          • deepfold.utils.geometry.utils
            • deepfold.utils.geometry.utils.get_field_names
              • get_field_names()
          • deepfold.utils.geometry.vector
            • deepfold.utils.geometry.vector.cross
              • cross()
            • deepfold.utils.geometry.vector.dihedral_angle
              • dihedral_angle()
            • deepfold.utils.geometry.vector.dot
              • dot()
            • deepfold.utils.geometry.vector.euclidean_distance
              • euclidean_distance()
            • deepfold.utils.geometry.vector.norm
              • norm()
            • deepfold.utils.geometry.vector.normalized
              • normalized()
            • deepfold.utils.geometry.vector.square_euclidean_distance
              • square_euclidean_distance()
            • deepfold.utils.geometry.vector.Vec3Array
              • Vec3Array
        • deepfold.utils.hash_utils
          • deepfold.utils.hash_utils.hash_string_into_number
            • hash_string_into_number()
        • deepfold.utils.import_utils
          • deepfold.utils.import_utils.assign
            • assign()
          • deepfold.utils.import_utils.import_jax_weights_
            • import_jax_weights_()
          • deepfold.utils.import_utils.reshape_weight
            • reshape_weight()
          • deepfold.utils.import_utils.stacked
            • stacked()
          • deepfold.utils.import_utils.Param
            • Param
              • Param.__init__()
          • deepfold.utils.import_utils.ParamType
            • ParamType
              • ParamType.__init__()
        • deepfold.utils.iter_utils
          • deepfold.utils.iter_utils.all_equal
            • all_equal()
          • deepfold.utils.iter_utils.flatten_dict
            • flatten_dict()
          • deepfold.utils.iter_utils.list_zip
            • list_zip()
          • deepfold.utils.iter_utils.map_dict_values
            • map_dict_values()
          • deepfold.utils.iter_utils.slice_generator
            • slice_generator()
        • deepfold.utils.log_utils
          • deepfold.utils.log_utils.read_logs
            • read_logs()
          • deepfold.utils.log_utils.save_logs
            • save_logs()
          • deepfold.utils.log_utils.setup_logging
            • setup_logging()
          • deepfold.utils.log_utils.TqdmHandler
            • TqdmHandler
              • TqdmHandler.__init__()
        • deepfold.utils.precision
          • deepfold.utils.precision.is_fp16_enabled
            • is_fp16_enabled()
        • deepfold.utils.random
          • deepfold.utils.random.get_seed_from_string
            • get_seed_from_string()
          • deepfold.utils.random.get_seed_randomly
            • get_seed_randomly()
          • deepfold.utils.random.numpy_seed
            • numpy_seed()
          • deepfold.utils.random.str_hash
            • str_hash()
        • deepfold.utils.rigid_utils
          • deepfold.utils.rigid_utils.identity_quats
            • identity_quats()
          • deepfold.utils.rigid_utils.identity_rot_mats
            • identity_rot_mats()
          • deepfold.utils.rigid_utils.identity_trans
            • identity_trans()
          • deepfold.utils.rigid_utils.invert_quat
            • invert_quat()
          • deepfold.utils.rigid_utils.invert_rot_mat
            • invert_rot_mat()
          • deepfold.utils.rigid_utils.quat_multiply
            • quat_multiply()
          • deepfold.utils.rigid_utils.quat_multiply_by_vec
            • quat_multiply_by_vec()
          • deepfold.utils.rigid_utils.quat_to_rot
            • quat_to_rot()
          • deepfold.utils.rigid_utils.rot_matmul
            • rot_matmul()
          • deepfold.utils.rigid_utils.rot_to_quat
            • rot_to_quat()
          • deepfold.utils.rigid_utils.rot_vec_mul
            • rot_vec_mul()
          • deepfold.utils.rigid_utils.Rigid
            • Rigid
              • Rigid.__init__()
          • deepfold.utils.rigid_utils.Rotation
            • Rotation
              • Rotation.__init__()
        • deepfold.utils.script_utils
          • deepfold.utils.script_utils.get_basename
            • get_basename()
          • deepfold.utils.script_utils.make_output_directory
            • make_output_directory()
          • deepfold.utils.script_utils.parse_fasta
            • parse_fasta()
        • deepfold.utils.swa_utils
          • deepfold.utils.swa_utils.AlphaFoldSWA
            • AlphaFoldSWA
              • AlphaFoldSWA.__init__()
          • deepfold.utils.swa_utils.swa_avg_fn
            • swa_avg_fn
              • swa_avg_fn.__init__()
        • deepfold.utils.tensor_utils
          • deepfold.utils.tensor_utils.add
            • add()
          • deepfold.utils.tensor_utils.batched_gather
            • batched_gather()
          • deepfold.utils.tensor_utils.collate
            • collate()
          • deepfold.utils.tensor_utils.dict_map
            • dict_map()
          • deepfold.utils.tensor_utils.dict_multimap
            • dict_multimap()
          • deepfold.utils.tensor_utils.flatten_final_dims
            • flatten_final_dims()
          • deepfold.utils.tensor_utils.masked_mean
            • masked_mean()
          • deepfold.utils.tensor_utils.one_hot
            • one_hot()
          • deepfold.utils.tensor_utils.permute_final_dims
            • permute_final_dims()
          • deepfold.utils.tensor_utils.pts_to_distogram
            • pts_to_distogram()
          • deepfold.utils.tensor_utils.tree_map
            • tree_map()
  • MiniWorld
    • miniworld
      • miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction
        • miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.a3m_parse
          • a3m_parse()
        • miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.add_weight_decay
          • add_weight_decay()
        • miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.count_parameters
          • count_parameters()
        • miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.visualize_2D_tensor
          • visualize_2D_tensor()
        • miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.EMA
          • EMA
            • EMA.__init__()
        • miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.ModelVisulizer
          • ModelVisulizer
            • ModelVisulizer.__init__()
      • miniworld.feature
        • miniworld.feature.MiniWorld_featuring_species
          • miniworld.feature.MiniWorld_featuring_species.MSA_block_deletion
            • MSA_block_deletion()
          • miniworld.feature.MiniWorld_featuring_species.MSA_featurize_wo_statistics
            • MSA_featurize_wo_statistics()
          • miniworld.feature.MiniWorld_featuring_species.MSA_featurize_wo_statistics_by_chain
            • MSA_featurize_wo_statistics_by_chain()
          • miniworld.feature.MiniWorld_featuring_species.center_and_realign_missing
            • center_and_realign_missing()
          • miniworld.feature.MiniWorld_featuring_species.chain_break_cropping
            • chain_break_cropping()
          • miniworld.feature.MiniWorld_featuring_species.cluster_sum
            • cluster_sum()
          • miniworld.feature.MiniWorld_featuring_species.cutoff_chain_num
            • cutoff_chain_num()
          • miniworld.feature.MiniWorld_featuring_species.display_top
            • display_top()
          • miniworld.feature.MiniWorld_featuring_species.find_chain_combinations
            • find_chain_combinations()
          • miniworld.feature.MiniWorld_featuring_species.generate_combinations
            • generate_combinations()
          • miniworld.feature.MiniWorld_featuring_species.get_STRING_crop
            • get_STRING_crop()
          • miniworld.feature.MiniWorld_featuring_species.get_complex_crop
            • get_complex_crop()
          • miniworld.feature.MiniWorld_featuring_species.get_crop
            • get_crop()
          • miniworld.feature.MiniWorld_featuring_species.get_same_crop_idx
            • get_same_crop_idx()
          • miniworld.feature.MiniWorld_featuring_species.get_spatial_crop
            • get_spatial_crop()
          • miniworld.feature.MiniWorld_featuring_species.getsize
            • getsize()
          • miniworld.feature.MiniWorld_featuring_species.permute_label
            • permute_label()
          • miniworld.feature.MiniWorld_featuring_species.random_split
            • random_split()
          • miniworld.feature.MiniWorld_featuring_species.template_featurize
            • template_featurize()
      • miniworld.models_MiniWorld_v1_5_use_interaction
        • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module
          • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.Attention
            • Attention
              • Attention.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.AttentionWithBias
            • AttentionWithBias
              • AttentionWithBias.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.BiasedAxialAttention
            • BiasedAxialAttention
              • BiasedAxialAttention.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.FeedForwardLayer
            • FeedForwardLayer
              • FeedForwardLayer.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.GraphTriangleAttention
            • GraphTriangleAttention
              • GraphTriangleAttention.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.MSAColAttention
            • MSAColAttention
              • MSAColAttention.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.MSAColGlobalAttention
            • MSAColGlobalAttention
              • MSAColGlobalAttention.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.MSARowAttentionWithBias
            • MSARowAttentionWithBias
              • MSARowAttentionWithBias.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.SequenceWeight
            • SequenceWeight
              • SequenceWeight.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.StateAttentionGate
            • StateAttentionGate
              • StateAttentionGate.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.TriangleMultiplication
            • TriangleMultiplication
              • TriangleMultiplication.__init__()
        • miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor
          • miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor.BinderNetwork
            • BinderNetwork
              • BinderNetwork.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor.DistanceNetwork
            • DistanceNetwork
              • DistanceNetwork.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor.ExpResolvedNetwork
            • ExpResolvedNetwork
              • ExpResolvedNetwork.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor.LDDTNetwork
            • LDDTNetwork
              • LDDTNetwork.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor.MaskedTokenNetwork
            • MaskedTokenNetwork
              • MaskedTokenNetwork.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor.PAENetwork
            • PAENetwork
              • PAENetwork.__init__()
        • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings
          • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.Extra_emb
            • Extra_emb
              • Extra_emb.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.InteractionEmb
            • InteractionEmb
              • InteractionEmb.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.MSA_emb
            • MSA_emb
              • MSA_emb.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.PositionalEncoding2D
            • PositionalEncoding2D
              • PositionalEncoding2D.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.Recycling
            • Recycling
              • Recycling.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.Species_emb
            • Species_emb
              • Species_emb.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.Templ_emb
            • Templ_emb
              • Templ_emb.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.TemplatePairStack
            • TemplatePairStack
              • TemplatePairStack.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.TemplateTorsionStack
            • TemplateTorsionStack
              • TemplateTorsionStack.__init__()
        • miniworld.models_MiniWorld_v1_5_use_interaction.MiniWorld
          • miniworld.models_MiniWorld_v1_5_use_interaction.MiniWorld.MiniWorldModule
            • MiniWorldModule
              • MiniWorldModule.__init__()
        • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module
          • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.update_symm_Rs
            • update_symm_Rs()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.update_symm_subs
            • update_symm_subs()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.IPA
            • IPA
              • IPA.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.IterBlock
            • IterBlock
              • IterBlock.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.IterativeSimulator
            • IterativeSimulator
              • IterativeSimulator.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.MSA2Pair
            • MSA2Pair
              • MSA2Pair.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.MSAPairStr2MSA
            • MSAPairStr2MSA
              • MSAPairStr2MSA.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.PairStr2Pair
            • PairStr2Pair
              • PairStr2Pair.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.SCPred
            • SCPred
              • SCPred.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.SeqSep
            • SeqSep
              • SeqSep.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.Str2Chain_IPA
            • Str2Chain_IPA
              • Str2Chain_IPA.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.Str2Residue_IPA
            • Str2Residue_IPA
              • Str2Residue_IPA.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.UpdatePairByValue
            • UpdatePairByValue
              • UpdatePairByValue.__init__()
        • miniworld.models_MiniWorld_v1_5_use_interaction.value_network
          • miniworld.models_MiniWorld_v1_5_use_interaction.value_network.cat_neighbors_nodes
            • cat_neighbors_nodes()
          • miniworld.models_MiniWorld_v1_5_use_interaction.value_network.gather_edges
            • gather_edges()
          • miniworld.models_MiniWorld_v1_5_use_interaction.value_network.gather_nodes
            • gather_nodes()
          • miniworld.models_MiniWorld_v1_5_use_interaction.value_network.MPNN_block
            • MPNN_block
              • MPNN_block.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.value_network.PositionWiseFeedForward
            • PositionWiseFeedForward
              • PositionWiseFeedForward.__init__()
          • miniworld.models_MiniWorld_v1_5_use_interaction.value_network.StrSeqValueNet
            • StrSeqValueNet
              • StrSeqValueNet.__init__()
      • miniworld.utils
        • miniworld.utils.DataClass
          • miniworld.utils.DataClass.MiniWorldBatchedDataClass
            • MiniWorldBatchedDataClass
              • MiniWorldBatchedDataClass.__init__()
          • miniworld.utils.DataClass.MiniWorldDataClass
            • MiniWorldDataClass
              • MiniWorldDataClass.__init__()
          • miniworld.utils.DataClass.MiniWorldLabelClass
            • MiniWorldLabelClass
              • MiniWorldLabelClass.__init__()
          • miniworld.utils.DataClass.MiniWorldMSAClass
            • MiniWorldMSAClass
              • MiniWorldMSAClass.__init__()
          • miniworld.utils.DataClass.MiniWorldTemplateClass
            • MiniWorldTemplateClass
              • MiniWorldTemplateClass.__init__()
          • miniworld.utils.DataClass.MiniWorldWrongDataClass
            • MiniWorldWrongDataClass
              • MiniWorldWrongDataClass.__init__()
        • miniworld.utils.My_mistake
          • miniworld.utils.My_mistake.MSA_change_idx
            • MSA_change_idx()
          • miniworld.utils.My_mistake.MSA_change_idx_v2
            • MSA_change_idx_v2()
        • miniworld.utils.ProteinClass
          • miniworld.utils.ProteinClass.PDB_parsing
            • PDB_parsing()
          • miniworld.utils.ProteinClass.Protein
            • Protein
              • Protein.__init__()
          • miniworld.utils.ProteinClass.ProteinMSA
            • ProteinMSA
              • ProteinMSA.__init__()
          • miniworld.utils.ProteinClass.ProteinSequence
            • ProteinSequence
              • ProteinSequence.__init__()
          • miniworld.utils.ProteinClass.ProteinStructure
            • ProteinStructure
              • ProteinStructure.__init__()
          • miniworld.utils.ProteinClass.ProteinTemplate
            • ProteinTemplate
              • ProteinTemplate.__init__()
          • miniworld.utils.ProteinClass.ProteinTemplates
            • ProteinTemplates
              • ProteinTemplates.__init__()
        • miniworld.utils.arguments_MiniWorld
          • miniworld.utils.arguments_MiniWorld.get_args
            • get_args()
        • miniworld.utils.chemical
        • miniworld.utils.data_refactoring
          • miniworld.utils.data_refactoring.AF_Results_filtering
            • AF_Results_filtering()
          • miniworld.utils.data_refactoring.AF_Results_json_filtering
            • AF_Results_json_filtering()
          • miniworld.utils.data_refactoring.AF_Results_json_viewer
            • AF_Results_json_viewer()
          • miniworld.utils.data_refactoring.PDB_parsing_from_pt
            • PDB_parsing_from_pt()
          • miniworld.utils.data_refactoring.STRING_refactoring
            • STRING_refactoring()
          • miniworld.utils.data_refactoring.a3m_pickling
            • a3m_pickling()
          • miniworld.utils.data_refactoring.check_hhr_loaded
            • check_hhr_loaded()
          • miniworld.utils.data_refactoring.get_ID_to_source_dict
            • get_ID_to_source_dict()
          • miniworld.utils.data_refactoring.get_csv
            • get_csv()
          • miniworld.utils.data_refactoring.get_hash_dict
            • get_hash_dict()
          • miniworld.utils.data_refactoring.get_query_from_a3m
            • get_query_from_a3m()
          • miniworld.utils.data_refactoring.gzip_files
            • gzip_files()
          • miniworld.utils.data_refactoring.hhr_dir_rerefactoring
            • hhr_dir_rerefactoring()
          • miniworld.utils.data_refactoring.hhr_file_rerefactoring
            • hhr_file_rerefactoring()
          • miniworld.utils.data_refactoring.hhr_refactoring
            • hhr_refactoring()
          • miniworld.utils.data_refactoring.mmcif_Full_sequence_parsing
            • mmcif_Full_sequence_parsing()
          • miniworld.utils.data_refactoring.mmcif_full_sequence
            • mmcif_full_sequence()
          • miniworld.utils.data_refactoring.mmcif_line_parser
            • mmcif_line_parser()
          • miniworld.utils.data_refactoring.mmcif_loop_parser
            • mmcif_loop_parser()
          • miniworld.utils.data_refactoring.mmcif_parsing
            • mmcif_parsing()
          • miniworld.utils.data_refactoring.mmcif_pickling
            • mmcif_pickling()
          • miniworld.utils.data_refactoring.pdb_Sampling
            • pdb_Sampling()
          • miniworld.utils.data_refactoring.pdb_pickling
            • pdb_pickling()
          • miniworld.utils.data_refactoring.print_hhr_pt
            • print_hhr_pt()
          • miniworld.utils.data_refactoring.protein_to_template
            • protein_to_template()
          • miniworld.utils.data_refactoring.refactoring_hhr_file
            • refactoring_hhr_file()
          • miniworld.utils.data_refactoring.test_a3m
            • test_a3m()
          • miniworld.utils.data_refactoring.test_a3m_file
            • test_a3m_file()
        • miniworld.utils.ffindex
          • miniworld.utils.ffindex.finish_db
            • finish_db()
          • miniworld.utils.ffindex.get_entry_by_name
            • get_entry_by_name()
          • miniworld.utils.ffindex.read_data
            • read_data()
          • miniworld.utils.ffindex.read_entry_data
            • read_entry_data()
          • miniworld.utils.ffindex.read_entry_lines
            • read_entry_lines()
          • miniworld.utils.ffindex.read_index
            • read_index()
          • miniworld.utils.ffindex.write_entries_to_db
            • write_entries_to_db()
          • miniworld.utils.ffindex.write_entry
            • write_entry()
          • miniworld.utils.ffindex.write_entry_with_file
            • write_entry_with_file()
          • miniworld.utils.ffindex.FFindexEntry
            • FFindexEntry
              • FFindexEntry.__init__()
        • miniworld.utils.hhpred_parser
          • miniworld.utils.hhpred_parser.hhpred_parser
            • hhpred_parser()
          • miniworld.utils.hhpred_parser.parse_segment
            • parse_segment()
        • miniworld.utils.kalign_mapping
          • miniworld.utils.kalign_mapping.kalign_mapping
            • kalign_mapping()
        • miniworld.utils.kinematics
          • miniworld.utils.kinematics.Qs2Rs
            • Qs2Rs()
          • miniworld.utils.kinematics.Rs2Qs
            • Rs2Qs()
          • miniworld.utils.kinematics.avgQ
            • avgQ()
          • miniworld.utils.kinematics.c6d_to_bins
            • c6d_to_bins()
          • miniworld.utils.kinematics.c6d_to_bins2
            • c6d_to_bins2()
          • miniworld.utils.kinematics.dist_to_bins
            • dist_to_bins()
          • miniworld.utils.kinematics.dist_to_onehot
            • dist_to_onehot()
          • miniworld.utils.kinematics.get_ang
            • get_ang()
          • miniworld.utils.kinematics.get_dih
            • get_dih()
          • miniworld.utils.kinematics.get_pair_dist
            • get_pair_dist()
          • miniworld.utils.kinematics.normQ
            • normQ()
          • miniworld.utils.kinematics.xyz_to_bbtor
            • xyz_to_bbtor()
          • miniworld.utils.kinematics.xyz_to_c6d
            • xyz_to_c6d()
          • miniworld.utils.kinematics.xyz_to_chi1
            • xyz_to_chi1()
          • miniworld.utils.kinematics.xyz_to_t2d
            • xyz_to_t2d()
        • miniworld.utils.output_visualize
          • miniworld.utils.output_visualize.TMalign
            • TMalign()
          • miniworld.utils.output_visualize.align_two_protein
            • align_two_protein()
          • miniworld.utils.output_visualize.atom_to_pdb_line
            • atom_to_pdb_line()
          • miniworld.utils.output_visualize.output_to_pdb
            • output_to_pdb()
          • miniworld.utils.output_visualize.protein_to_pdb
            • protein_to_pdb()
          • miniworld.utils.output_visualize.tensor_to_pdb
            • tensor_to_pdb()
          • miniworld.utils.output_visualize.visualize_2D_heatmap
            • visualize_2D_heatmap()
          • miniworld.utils.output_visualize.visualize_2D_heatmaps
            • visualize_2D_heatmaps()
          • miniworld.utils.output_visualize.visualize_2D_tensor
            • visualize_2D_tensor()
          • miniworld.utils.output_visualize.visualize_t_map
            • visualize_t_map()
        • miniworld.utils.parser_util
          • miniworld.utils.parser_util.center_and_realign_missing
            • center_and_realign_missing()
          • miniworld.utils.parser_util.cross_product_matrix
            • cross_product_matrix()
          • miniworld.utils.parser_util.donorHs
            • donorHs()
          • miniworld.utils.parser_util.get_Cb
            • get_Cb()
          • miniworld.utils.parser_util.make_frame
            • make_frame()
          • miniworld.utils.parser_util.random_rot_trans
            • random_rot_trans()
          • miniworld.utils.parser_util.rigid_from_3_points
            • rigid_from_3_points()
          • miniworld.utils.parser_util.th_ang_v
            • th_ang_v()
          • miniworld.utils.parser_util.th_dih
            • th_dih()
          • miniworld.utils.parser_util.th_dih_v
            • th_dih_v()
          • miniworld.utils.parser_util.writepdb
            • writepdb()
        • miniworld.utils.template_parser
          • miniworld.utils.template_parser.get_args
            • get_args()
          • miniworld.utils.template_parser.parse_a3m
            • parse_a3m()
          • miniworld.utils.template_parser.parse_pdb
            • parse_pdb()
          • miniworld.utils.template_parser.parse_pdb_lines
            • parse_pdb_lines()
          • miniworld.utils.template_parser.parse_pdb_lines_w_seq
            • parse_pdb_lines_w_seq()
          • miniworld.utils.template_parser.parse_pdb_w_seq
            • parse_pdb_w_seq()
          • miniworld.utils.template_parser.parse_templates_raw
            • parse_templates_raw()
          • miniworld.utils.template_parser.read_template_pdb
            • read_template_pdb()
          • miniworld.utils.template_parser.read_templates
            • read_templates()
        • miniworld.utils.util
          • miniworld.utils.util.cal_integrated_frame
            • cal_integrated_frame()
          • miniworld.utils.util.center_and_realign_missing
            • center_and_realign_missing()
          • miniworld.utils.util.centering_RT
            • centering_RT()
          • miniworld.utils.util.cross_product_matrix
            • cross_product_matrix()
          • miniworld.utils.util.donorHs
            • donorHs()
          • miniworld.utils.util.draw_attn
            • draw_attn()
          • miniworld.utils.util.draw_attn_multirow
            • draw_attn_multirow()
          • miniworld.utils.util.draw_pae
            • draw_pae()
          • miniworld.utils.util.extract_tip_atom_xyz
            • extract_tip_atom_xyz()
          • miniworld.utils.util.generate_initial_xyz
            • generate_initial_xyz()
          • miniworld.utils.util.generate_random_xyz
            • generate_random_xyz()
          • miniworld.utils.util.generate_symmetric_operation
            • generate_symmetric_operation()
          • miniworld.utils.util.generate_symmetric_xyz
            • generate_symmetric_xyz()
          • miniworld.utils.util.get_Cb
            • get_Cb()
          • miniworld.utils.util.get_train_valid_data_dir_dictionary
            • get_train_valid_data_dir_dictionary()
          • miniworld.utils.util.make_frame
            • make_frame()
          • miniworld.utils.util.random_rot_trans
            • random_rot_trans()
          • miniworld.utils.util.rigid_from_3_points
            • rigid_from_3_points()
          • miniworld.utils.util.rigid_from_3_points_v2
            • rigid_from_3_points_v2()
          • miniworld.utils.util.th_ang_v
            • th_ang_v()
          • miniworld.utils.util.th_dih
            • th_dih()
          • miniworld.utils.util.th_dih_v
            • th_dih_v()
          • miniworld.utils.util.writepdb
            • writepdb()
        • miniworld.utils.util_module
          • miniworld.utils.util_module.create_custom_forward
            • create_custom_forward()
          • miniworld.utils.util_module.get_clones
            • get_clones()
          • miniworld.utils.util_module.get_seqsep
            • get_seqsep()
          • miniworld.utils.util_module.get_topk
            • get_topk()
          • miniworld.utils.util_module.init_lecun_normal
            • init_lecun_normal()
          • miniworld.utils.util_module.init_lecun_normal_param
            • init_lecun_normal_param()
          • miniworld.utils.util_module.make_rotX
            • make_rotX()
          • miniworld.utils.util_module.make_rotZ
            • make_rotZ()
          • miniworld.utils.util_module.make_rot_axis
            • make_rot_axis()
          • miniworld.utils.util_module.rbf
            • rbf()
          • miniworld.utils.util_module.ComputeAllAtomCoords
            • ComputeAllAtomCoords
              • ComputeAllAtomCoords.__init__()
          • miniworld.utils.util_module.Dropout
            • Dropout
              • Dropout.__init__()
          • miniworld.utils.util_module.XYZConverter
            • XYZConverter
              • XYZConverter.__init__()
  • RoseTTAFold2
• Tools
  • BAPred
    • bapred
      • bapred.cli
        • bapred.cli.main
          • main()
      • bapred.data
        • bapred.data.atom_feature
          • bapred.data.atom_feature.atom_feature
            • atom_feature()
          • bapred.data.atom_feature.bond_feature
            • bond_feature()
          • bapred.data.atom_feature.get_atom_feature
            • get_atom_feature()
          • bapred.data.atom_feature.get_bond_feature
            • get_bond_feature()
          • bapred.data.atom_feature.get_distance_feature
            • get_distance_feature()
          • bapred.data.atom_feature.get_indices
            • get_indices()
          • bapred.data.atom_feature.get_indices_sparse
            • get_indices_sparse()
          • bapred.data.atom_feature.get_interact_feature
            • get_interact_feature()
          • bapred.data.atom_feature.get_mol_coordinate
            • get_mol_coordinate()
          • bapred.data.atom_feature.get_smarts_feature
            • get_smarts_feature()
        • bapred.data.data
          • bapred.data.data.load_ligands
            • load_ligands()
          • bapred.data.data.process_ligand_file
            • process_ligand_file()
          • bapred.data.data.BAPredDataset
            • BAPredDataset
              • BAPredDataset.__init__()
        • bapred.data.utils
          • bapred.data.utils.calculate_pair_distance
            • calculate_pair_distance()
          • bapred.data.utils.is_one
            • is_one()
          • bapred.data.utils.load_obj
            • load_obj()
          • bapred.data.utils.one_hot
            • one_hot()
          • bapred.data.utils.save_obj
            • save_obj()
      • bapred.inference
        • bapred.inference.inference
          • inference()
      • bapred.logger
        • bapred.logger.setup_logger
          • setup_logger()
      • bapred.model
        • bapred.model.GatedGCNLSPE
          • bapred.model.GatedGCNLSPE.GatedGCNLSPELayer
            • GatedGCNLSPELayer
              • GatedGCNLSPELayer.__init__()
        • bapred.model.GraphGPS
          • bapred.model.GraphGPS.GraphGPS
            • GraphGPS
              • GraphGPS.__init__()
        • bapred.model.MHA
          • bapred.model.MHA.MultiHeadAttention
            • MultiHeadAttention
              • MultiHeadAttention.__init__()
        • bapred.model.model
          • bapred.model.model.PredictionPKD
            • PredictionPKD
              • PredictionPKD.__init__()
  • BindingRMSD
    • bindingrmsd
      • bindingrmsd.data
        • bindingrmsd.data.data
          • bindingrmsd.data.data.load_ligands
            • load_ligands()
          • bindingrmsd.data.data.process_ligand_file
            • process_ligand_file()
          • bindingrmsd.data.data.PoseSelectionDataset
            • PoseSelectionDataset
              • PoseSelectionDataset.__init__()
        • bindingrmsd.data.data_bck
          • bindingrmsd.data.data_bck.load_ligands
            • load_ligands()
          • bindingrmsd.data.data_bck.process_dlg
            • process_dlg()
          • bindingrmsd.data.data_bck.process_ligand_file
            • process_ligand_file()
          • bindingrmsd.data.data_bck.PoseSelectionDataset
            • PoseSelectionDataset
              • PoseSelectionDataset.__init__()
        • bindingrmsd.data.ligand_atom_feature
          • bindingrmsd.data.ligand_atom_feature.atom_feature
            • atom_feature()
          • bindingrmsd.data.ligand_atom_feature.bond_feature
            • bond_feature()
          • bindingrmsd.data.ligand_atom_feature.calculate_pair_distance
            • calculate_pair_distance()
          • bindingrmsd.data.ligand_atom_feature.get_atom_feature
            • get_atom_feature()
          • bindingrmsd.data.ligand_atom_feature.get_bond_feature
            • get_bond_feature()
          • bindingrmsd.data.ligand_atom_feature.get_distance_feature
            • get_distance_feature()
          • bindingrmsd.data.ligand_atom_feature.get_indices
            • get_indices()
          • bindingrmsd.data.ligand_atom_feature.get_indices_sparse
            • get_indices_sparse()
          • bindingrmsd.data.ligand_atom_feature.get_interact_feature
            • get_interact_feature()
          • bindingrmsd.data.ligand_atom_feature.get_mol_coordinate
            • get_mol_coordinate()
          • bindingrmsd.data.ligand_atom_feature.get_smarts_feature
            • get_smarts_feature()
          • bindingrmsd.data.ligand_atom_feature.is_one
            • is_one()
          • bindingrmsd.data.ligand_atom_feature.load_obj
            • load_obj()
          • bindingrmsd.data.ligand_atom_feature.mol_to_graph
            • mol_to_graph()
          • bindingrmsd.data.ligand_atom_feature.one_hot
            • one_hot()
          • bindingrmsd.data.ligand_atom_feature.save_obj
            • save_obj()
        • bindingrmsd.data.protein_atom_feature
          • bindingrmsd.data.protein_atom_feature.get_all_graph
            • get_all_graph()
          • bindingrmsd.data.protein_atom_feature.pl_to_c_graph
            • pl_to_c_graph()
          • bindingrmsd.data.protein_atom_feature.prot_to_graph
            • prot_to_graph()
          • bindingrmsd.data.protein_atom_feature.scaler
            • scaler()
        • bindingrmsd.data.utils
          • bindingrmsd.data.utils.is_one
            • is_one()
          • bindingrmsd.data.utils.load_obj
            • load_obj()
          • bindingrmsd.data.utils.one_hot
            • one_hot()
          • bindingrmsd.data.utils.save_obj
            • save_obj()
      • bindingrmsd.inference
        • bindingrmsd.inference.inference
          • inference()
        • bindingrmsd.inference.main
          • main()
      • bindingrmsd.model
        • bindingrmsd.model.GatedGCNLSPE
          • bindingrmsd.model.GatedGCNLSPE.GatedGCNLSPELayer
            • GatedGCNLSPELayer
              • GatedGCNLSPELayer.__init__()
        • bindingrmsd.model.model
          • bindingrmsd.model.model.PredictionRMSD
            • PredictionRMSD
              • PredictionRMSD.__init__()
  • BIS Protein Structure
    • bis_protein_structure
      • bis_protein_structure.CROSSLINK
        • bis_protein_structure.CROSSLINK.calculate_calpha_distogram
          • calculate_calpha_distogram()
        • bis_protein_structure.CROSSLINK.calculate_lys_leu_map
          • calculate_lys_leu_map()
        • bis_protein_structure.CROSSLINK.calculate_sa_map
          • calculate_sa_map()
        • bis_protein_structure.CROSSLINK.calculate_tryptic_map
          • calculate_tryptic_map()
        • bis_protein_structure.CROSSLINK.load_list_from_file
          • load_list_from_file()
        • bis_protein_structure.CROSSLINK.plot_cross_link
          • plot_cross_link()
        • bis_protein_structure.CROSSLINK.readMMCIF
          • readMMCIF()
        • bis_protein_structure.CROSSLINK.readPDB
          • readPDB()
      • bis_protein_structure.DATAGEN
        • bis_protein_structure.DATAGEN.create_structure_from_feature
          • create_structure_from_feature()
        • bis_protein_structure.DATAGEN.generate_feature_dict
          • generate_feature_dict()
        • bis_protein_structure.DATAGEN.mmcif_to_pdbs
          • mmcif_to_pdbs()
        • bis_protein_structure.DATAGEN.parallel_processing
          • parallel_processing()
        • bis_protein_structure.DATAGEN.parse_fasta
          • parse_fasta()
        • bis_protein_structure.DATAGEN.parse_mmcif
          • parse_mmcif()
        • bis_protein_structure.DATAGEN.process_mmcif_to_pdbs
          • process_mmcif_to_pdbs()
        • bis_protein_structure.DATAGEN.read_fasta
          • read_fasta()
        • bis_protein_structure.DATAGEN.AllResiduesSelector
          • AllResiduesSelector
            • AllResiduesSelector.accept_residue()
            • AllResiduesSelector.__init__()
      • bis_protein_structure.DISULFIDE
        • bis_protein_structure.DISULFIDE.get_SS_ver5
          • get_SS_ver5()
        • bis_protein_structure.DISULFIDE.readMMCIF_label
          • readMMCIF_label()
      • bis_protein_structure.MMEVAL
        • bis_protein_structure.MMEVAL.convert_string
          • convert_string()
        • bis_protein_structure.MMEVAL.eval_interface
          • eval_interface()
        • bis_protein_structure.MMEVAL.get_ICS
          • get_ICS()
        • bis_protein_structure.MMEVAL.get_IPS
          • get_IPS()
        • bis_protein_structure.MMEVAL.get_contact
          • get_contact()
        • bis_protein_structure.MMEVAL.readPDB
          • readPDB()
        • bis_protein_structure.MMEVAL.restype_refer_atoms
          • restype_refer_atoms()
      • bis_protein_structure.SOLVENTACC
        • bis_protein_structure.SOLVENTACC.contains_non_numeric
          • contains_non_numeric()
        • bis_protein_structure.SOLVENTACC.convert_mmcif_to_dssp
          • convert_mmcif_to_dssp()
        • bis_protein_structure.SOLVENTACC.convert_mmcif_to_dssp_parallel
          • convert_mmcif_to_dssp_parallel()
        • bis_protein_structure.SOLVENTACC.convert_pdb_to_dssp
          • convert_pdb_to_dssp()
        • bis_protein_structure.SOLVENTACC.create_structure_from_feature
          • create_structure_from_feature()
        • bis_protein_structure.SOLVENTACC.extract_coords_from_pdb
          • extract_coords_from_pdb()
        • bis_protein_structure.SOLVENTACC.getTMscore
          • getTMscore()
        • bis_protein_structure.SOLVENTACC.load_pickle_file
          • load_pickle_file()
      • bis_protein_structure.TORSION2
        • bis_protein_structure.TORSION2.angles_to_sincos
          • angles_to_sincos()
        • bis_protein_structure.TORSION2.getDistogram
          • getDistogram()
        • bis_protein_structure.TORSION2.getTorsion_acc
          • getTorsion_acc()
        • bis_protein_structure.TORSION2.get_bondangle
          • get_bondangle()
        • bis_protein_structure.TORSION2.get_coordinates
          • get_coordinates()
        • bis_protein_structure.TORSION2.get_refer_atoms
          • get_refer_atoms()
        • bis_protein_structure.TORSION2.get_torsion
          • get_torsion()
        • bis_protein_structure.TORSION2.new_dihedral
          • new_dihedral()
        • bis_protein_structure.TORSION2.readPDB
          • readPDB()
        • bis_protein_structure.TORSION2.restype_refer_atoms
          • restype_refer_atoms()
        • bis_protein_structure.TORSION2.sidechain_sym_angle
          • sidechain_sym_angle()
        • bis_protein_structure.TORSION2.torsion_angle_loss
          • torsion_angle_loss()
      • bis_protein_structure.residue_constants
        • bis_protein_structure.residue_constants.chi_angle_atom
          • chi_angle_atom()
        • bis_protein_structure.residue_constants.load_stereo_chemical_props
          • load_stereo_chemical_props()
        • bis_protein_structure.residue_constants.make_atom14_dists_bounds
          • make_atom14_dists_bounds()
        • bis_protein_structure.residue_constants.sequence_to_onehot
          • sequence_to_onehot()
        • bis_protein_structure.residue_constants.Bond
          • Bond
            • Bond.__init__()
        • bis_protein_structure.residue_constants.BondAngle
          • BondAngle
            • BondAngle.__init__()
      • bis_protein_structure.split_pdb
        • bis_protein_structure.split_pdb.extract
          • extract()
        • bis_protein_structure.split_pdb.split_the_pdb
          • split_the_pdb()
  • SwinSite
  • DiffAlign
    • diffalign
      • diffalign.models
        • diffalign.models.common
          • diffalign.models.common.extend_graph_order_radius
            • extend_graph_order_radius()
          • diffalign.models.common.extend_to_cross_attention
            • extend_to_cross_attention()
          • diffalign.models.common.MultiLayerPerceptron
            • MultiLayerPerceptron
              • MultiLayerPerceptron.__init__()
        • diffalign.models.encoder
          • diffalign.models.encoder.cross_attention
            • diffalign.models.encoder.cross_attention.CrossAttention
              • CrossAttention
            • diffalign.models.encoder.cross_attention.CrossGraphAligner
              • CrossGraphAligner
          • diffalign.models.encoder.edge
            • diffalign.models.encoder.edge.MLPEdgeEncoder
              • MLPEdgeEncoder
          • diffalign.models.encoder.egnn
            • diffalign.models.encoder.egnn.unsorted_segment_sum
              • unsorted_segment_sum()
            • diffalign.models.encoder.egnn.EGNN
              • EGNN
            • diffalign.models.encoder.egnn.E_GCL
              • E_GCL
        • diffalign.models.epsnet
          • diffalign.models.epsnet.diffusion
            • diffalign.models.epsnet.diffusion.cosine_beta_schedule
              • cosine_beta_schedule()
            • diffalign.models.epsnet.diffusion.get_distance
              • get_distance()
            • diffalign.models.epsnet.diffusion.linear_beta_schedule
              • linear_beta_schedule()
            • diffalign.models.epsnet.diffusion.merge_graphs_in_batch
              • merge_graphs_in_batch()
            • diffalign.models.epsnet.diffusion.DDPMTimeEncoder
              • DDPMTimeEncoder
            • diffalign.models.epsnet.diffusion.DiffAlign
              • DiffAlign
            • diffalign.models.epsnet.diffusion.SinusoidalPosEmb
              • SinusoidalPosEmb
      • diffalign.utils
        • diffalign.utils.chem
          • diffalign.utils.chem.bond_type_to_int
            • bond_type_to_int()
          • diffalign.utils.chem.draw_mol_svg
            • draw_mol_svg()
          • diffalign.utils.chem.get_2D_mol
            • get_2D_mol()
          • diffalign.utils.chem.get_atom_symbol
            • get_atom_symbol()
          • diffalign.utils.chem.get_atoms_in_ring
            • get_atoms_in_ring()
          • diffalign.utils.chem.get_best_rmsd
            • get_best_rmsd()
          • diffalign.utils.chem.mol_to_graph_data_obj
            • mol_to_graph_data_obj()
          • diffalign.utils.chem.mol_to_smiles
            • mol_to_smiles()
          • diffalign.utils.chem.mol_to_smiles_without_Hs
            • mol_to_smiles_without_Hs()
          • diffalign.utils.chem.remove_duplicate_mols
            • remove_duplicate_mols()
          • diffalign.utils.chem.set_conformer_positions
            • set_conformer_positions()
          • diffalign.utils.chem.set_rdmol_positions
            • set_rdmol_positions()
          • diffalign.utils.chem.set_rdmol_positions_
            • set_rdmol_positions_()
          • diffalign.utils.chem.update_data_pos_from_rdmol
            • update_data_pos_from_rdmol()
          • diffalign.utils.chem.update_data_rdmol_positions
            • update_data_rdmol_positions()
  • GalaxyDock DL
    • gd_dl
      • gd_dl.data
        • gd_dl.data.ML_inference
          • gd_dl.data.ML_inference.calc_e
            • calc_e()
          • gd_dl.data.ML_inference.calculate_energy
            • calculate_energy()
          • gd_dl.data.ML_inference.get_ref_vec
            • get_ref_vec()
          • gd_dl.data.ML_inference.load_files
            • load_files()
          • gd_dl.data.ML_inference.main
            • main()
        • gd_dl.data.ML_rerank
          • gd_dl.data.ML_rerank.calc_e
            • calc_e()
          • gd_dl.data.ML_rerank.main
            • main()
        • gd_dl.data.all_ML_rerank
          • gd_dl.data.all_ML_rerank.calc_e
            • calc_e()
          • gd_dl.data.all_ML_rerank.main
            • main()
        • gd_dl.data.single_ML_rerank
          • gd_dl.data.single_ML_rerank.calc_e
            • calc_e()
          • gd_dl.data.single_ML_rerank.main
            • main()
      • gd_dl.lib_pdb_mol2
        • gd_dl.lib_pdb_mol2.Atom
          • Atom
            • Atom.__init__()
        • gd_dl.lib_pdb_mol2.MOL2
          • MOL2
            • MOL2.__init__()
        • gd_dl.lib_pdb_mol2.MOL2_UNIT
          • MOL2_UNIT
            • MOL2_UNIT.__init__()
        • gd_dl.lib_pdb_mol2.Model
          • Model
            • Model.__init__()
        • gd_dl.lib_pdb_mol2.PDB
          • PDB
            • PDB.__init__()
        • gd_dl.lib_pdb_mol2.PDBline
          • PDBline
            • PDBline.__init__()
        • gd_dl.lib_pdb_mol2.Residue
          • Residue
            • Residue.__init__()
      • gd_dl.models
        • gd_dl.models.Cgc_block
          • Cgc_block
            • Cgc_block.__init__()
        • gd_dl.models.Rerank_model
          • Rerank_model
            • Rerank_model.__init__()
        • gd_dl.models.Weight_CGConv
          • Weight_CGConv
            • Weight_CGConv.__init__()
      • gd_dl.path_setting
      • gd_dl.rerank_model
        • gd_dl.rerank_model.Cgc_block
          • Cgc_block
            • Cgc_block.__init__()
        • gd_dl.rerank_model.Rerank_model
          • Rerank_model
            • Rerank_model.__init__()
        • gd_dl.rerank_model.Weight_CGConv
          • Weight_CGConv
            • Weight_CGConv.__init__()
      • gd_dl.utils
        • gd_dl.utils.set_prep
          • set_prep()
        • gd_dl.utils.str2bool
          • str2bool()
  • PromptBind
    • promptbind
      • promptbind.data
        • promptbind.data.data
          • promptbind.data.data.get_data
            • get_data()
          • promptbind.data.data.FABindDataSet
            • FABindDataSet
              • FABindDataSet.__init__()
        • promptbind.data.inference_preprocess_mol_confs
          • promptbind.data.inference_preprocess_mol_confs.get_mol_info
            • get_mol_info()
        • promptbind.data.inference_preprocess_protein
      • promptbind.models
        • promptbind.models.att_model
          • promptbind.models.att_model.sequential_and
            • sequential_and()
          • promptbind.models.att_model.sequential_or
            • sequential_or()
          • promptbind.models.att_model.ComplexGraph
            • ComplexGraph
              • ComplexGraph.__init__()
          • promptbind.models.att_model.EfficientMCAttModel
            • EfficientMCAttModel
              • EfficientMCAttModel.__init__()
        • promptbind.models.cross_att
          • promptbind.models.cross_att.CrossAttentionModule
            • CrossAttentionModule
              • CrossAttentionModule.__init__()
          • promptbind.models.cross_att.RowAttentionBlock
            • RowAttentionBlock
              • RowAttentionBlock.__init__()
          • promptbind.models.cross_att.RowTriangleAttentionBlock
            • RowTriangleAttentionBlock
              • RowTriangleAttentionBlock.__init__()
        • promptbind.models.egnn
          • promptbind.models.egnn.coord2radial
            • coord2radial()
          • promptbind.models.egnn.get_edges
            • get_edges()
          • promptbind.models.egnn.get_edges_batch
            • get_edges_batch()
          • promptbind.models.egnn.unsorted_segment_mean
            • unsorted_segment_mean()
          • promptbind.models.egnn.unsorted_segment_sum
            • unsorted_segment_sum()
          • promptbind.models.egnn.MCAttEGNN
            • MCAttEGNN
              • MCAttEGNN.__init__()
          • promptbind.models.egnn.MC_Att_L
            • MC_Att_L
              • MC_Att_L.__init__()
          • promptbind.models.egnn.MC_E_GCL
            • MC_E_GCL
              • MC_E_GCL.__init__()
          • promptbind.models.egnn.MC_E_GCL_Prompt
            • MC_E_GCL_Prompt
              • MC_E_GCL_Prompt.__init__()
        • promptbind.models.model
          • promptbind.models.model.get_model
            • get_model()
          • promptbind.models.model.IaBNet_mean_and_pocket_prediction_cls_coords_dependent
            • IaBNet_mean_and_pocket_prediction_cls_coords_dependent
              • IaBNet_mean_and_pocket_prediction_cls_coords_dependent.__init__()
          • promptbind.models.model.Transition_diff_out_dim
            • Transition_diff_out_dim
              • Transition_diff_out_dim.__init__()
        • promptbind.models.model_utils
          • promptbind.models.model_utils.flatten_final_dims
            • flatten_final_dims()
          • promptbind.models.model_utils.permute_final_dims
            • permute_final_dims()
          • promptbind.models.model_utils.Attention
            • Attention
              • Attention.__init__()
          • promptbind.models.model_utils.GaussianSmearing
            • GaussianSmearing
              • GaussianSmearing.__init__()
          • promptbind.models.model_utils.InteractionModule
            • InteractionModule
              • InteractionModule.__init__()
          • promptbind.models.model_utils.RBFDistanceModule
            • RBFDistanceModule
              • RBFDistanceModule.__init__()
          • promptbind.models.model_utils.Transition
            • Transition
              • Transition.__init__()
      • promptbind.test_promptbind
        • promptbind.test_promptbind.PromptBindInference
          • PromptBindInference
            • PromptBindInference.__init__()
              • PromptBindInference.config_path
              • PromptBindInference.args
              • PromptBindInference.accelerator
              • PromptBindInference.logger
              • PromptBindInference.device
              • PromptBindInference.model
              • PromptBindInference.criterion
              • PromptBindInference.com_coord_criterion
              • PromptBindInference.pocket_cls_criterion
              • PromptBindInference.pocket_coord_criterion
              • PromptBindInference.test_loader
              • PromptBindInference.test_unseen_loader
      • promptbind.train_promptbind
        • promptbind.train_promptbind.Seed_everything
          • Seed_everything()
      • promptbind.utils
        • promptbind.utils.fabind_inference_dataset
          • promptbind.utils.fabind_inference_dataset.InferenceDataset
            • InferenceDataset
              • InferenceDataset.__init__()
        • promptbind.utils.feature_utils
          • promptbind.utils.feature_utils.Seed_everything
            • Seed_everything()
          • promptbind.utils.feature_utils.binarize
            • binarize()
          • promptbind.utils.feature_utils.extract_torchdrug_feature_from_mol
            • extract_torchdrug_feature_from_mol()
          • promptbind.utils.feature_utils.extract_torchdrug_feature_from_mol_E3Bind
            • extract_torchdrug_feature_from_mol_E3Bind()
          • promptbind.utils.feature_utils.generate_and_write_sdf_from_smiles_using_rdkit_E3Bind
            • generate_and_write_sdf_from_smiles_using_rdkit_E3Bind()
          • promptbind.utils.feature_utils.generate_conformation
            • generate_conformation()
          • promptbind.utils.feature_utils.generate_rdkit_conformation_v2
            • generate_rdkit_conformation_v2()
          • promptbind.utils.feature_utils.generate_sdf_from_smiles_using_rdkit
            • generate_sdf_from_smiles_using_rdkit()
          • promptbind.utils.feature_utils.generate_sdf_from_smiles_using_rdkit_E3Bind
            • generate_sdf_from_smiles_using_rdkit_E3Bind()
          • promptbind.utils.feature_utils.get_LAS_distance_constraint_mask
            • get_LAS_distance_constraint_mask()
          • promptbind.utils.feature_utils.get_canonical_smiles
            • get_canonical_smiles()
          • promptbind.utils.feature_utils.get_clean_res_list
            • get_clean_res_list()
          • promptbind.utils.feature_utils.get_compound_pair_dis_distribution
            • get_compound_pair_dis_distribution()
          • promptbind.utils.feature_utils.get_protein_feature
            • get_protein_feature()
          • promptbind.utils.feature_utils.get_res_unique_id
            • get_res_unique_id()
          • promptbind.utils.feature_utils.n_hops_adj
            • n_hops_adj()
          • promptbind.utils.feature_utils.read_mol
            • read_mol()
          • promptbind.utils.feature_utils.remove_hetero_and_extract_ligand
            • remove_hetero_and_extract_ligand()
          • promptbind.utils.feature_utils.save_cleaned_protein
            • save_cleaned_protein()
          • promptbind.utils.feature_utils.select_chain_within_cutoff_to_ligand_v2
            • select_chain_within_cutoff_to_ligand_v2()
          • promptbind.utils.feature_utils.split_protein_and_ligand
            • split_protein_and_ligand()
          • promptbind.utils.feature_utils.write_renumbered_sdf
            • write_renumbered_sdf()
          • promptbind.utils.feature_utils.write_with_new_coords
            • write_with_new_coords()
        • promptbind.utils.generation_utils
          • promptbind.utils.generation_utils.binarize
            • binarize()
          • promptbind.utils.generation_utils.compute_RMSD
            • compute_RMSD()
          • promptbind.utils.generation_utils.distance_loss_function
            • distance_loss_function()
          • promptbind.utils.generation_utils.distance_optimize_compound_coords
            • distance_optimize_compound_coords()
          • promptbind.utils.generation_utils.get_LAS_distance_constraint_mask
            • get_LAS_distance_constraint_mask()
          • promptbind.utils.generation_utils.get_info_pred_distance
            • get_info_pred_distance()
          • promptbind.utils.generation_utils.n_hops_adj
            • n_hops_adj()
          • promptbind.utils.generation_utils.read_mol
            • read_mol()
          • promptbind.utils.generation_utils.write_with_new_coords
            • write_with_new_coords()
        • promptbind.utils.inference_mol_utils
          • promptbind.utils.inference_mol_utils.binarize
            • binarize()
          • promptbind.utils.inference_mol_utils.extract_torchdrug_feature_from_mol
            • extract_torchdrug_feature_from_mol()
          • promptbind.utils.inference_mol_utils.generate_conformation
            • generate_conformation()
          • promptbind.utils.inference_mol_utils.get_LAS_distance_constraint_mask
            • get_LAS_distance_constraint_mask()
          • promptbind.utils.inference_mol_utils.get_compound_pair_dis_distribution
            • get_compound_pair_dis_distribution()
          • promptbind.utils.inference_mol_utils.n_hops_adj
            • n_hops_adj()
          • promptbind.utils.inference_mol_utils.read_mol_and_renumber
            • read_mol_and_renumber()
          • promptbind.utils.inference_mol_utils.read_smiles
            • read_smiles()
          • promptbind.utils.inference_mol_utils.write_mol
            • write_mol()
        • promptbind.utils.inference_pdb_utils
          • promptbind.utils.inference_pdb_utils.extract_esm_feature
            • extract_esm_feature()
          • promptbind.utils.inference_pdb_utils.extract_protein_structure
            • extract_protein_structure()
          • promptbind.utils.inference_pdb_utils.get_clean_res_list
            • get_clean_res_list()
          • promptbind.utils.inference_pdb_utils.get_protein_structure
            • get_protein_structure()
        • promptbind.utils.logging_utils
          • promptbind.utils.logging_utils.Logger
            • Logger
              • Logger.__init__()
        • promptbind.utils.metrics
          • promptbind.utils.metrics.affinity_metrics
            • affinity_metrics()
          • promptbind.utils.metrics.cls_metric
            • cls_metric()
          • promptbind.utils.metrics.compute_individual_metrics
            • compute_individual_metrics()
          • promptbind.utils.metrics.myMetric
            • myMetric()
          • promptbind.utils.metrics.pocket_direct_metrics
            • pocket_direct_metrics()
          • promptbind.utils.metrics.pocket_metrics
            • pocket_metrics()
          • promptbind.utils.metrics.print_metrics
            • print_metrics()
        • promptbind.utils.metrics_to_tsb
          • promptbind.utils.metrics_to_tsb.metrics_runtime_no_prefix
            • metrics_runtime_no_prefix()
        • promptbind.utils.post_optim_utils
          • promptbind.utils.post_optim_utils.compute_RMSD
            • compute_RMSD()
          • promptbind.utils.post_optim_utils.post_optimize_compound_coords
            • post_optimize_compound_coords()
          • promptbind.utils.post_optim_utils.post_optimize_compound_coords_lbfgs
            • post_optimize_compound_coords_lbfgs()
          • promptbind.utils.post_optim_utils.post_optimize_loss_function
            • post_optimize_loss_function()
          • promptbind.utils.post_optim_utils.read_molecule
            • read_molecule()
          • promptbind.utils.post_optim_utils.write_mol
            • write_mol()
        • promptbind.utils.utils
          • promptbind.utils.utils.SetDihedral
            • SetDihedral()
          • promptbind.utils.utils.compute_dis_between_two_vector
            • compute_dis_between_two_vector()
          • promptbind.utils.utils.compute_dis_between_two_vector_tensor
            • compute_dis_between_two_vector_tensor()
          • promptbind.utils.utils.construct_data_from_graph_gvp_mean
            • construct_data_from_graph_gvp_mean()
          • promptbind.utils.utils.evaluate_mean_pocket_cls_coord_multi_task
            • evaluate_mean_pocket_cls_coord_multi_task()
          • promptbind.utils.utils.evaluate_mean_pocket_cls_coord_pocket_pred
            • evaluate_mean_pocket_cls_coord_pocket_pred()
          • promptbind.utils.utils.get_keepNode
            • get_keepNode()
          • promptbind.utils.utils.get_keepNode_tensor
            • get_keepNode_tensor()
          • promptbind.utils.utils.get_protein_edge_features_and_index
            • get_protein_edge_features_and_index()
          • promptbind.utils.utils.get_torsions
            • get_torsions()
          • promptbind.utils.utils.gumbel_softmax_no_random
            • gumbel_softmax_no_random()
          • promptbind.utils.utils.post_optim_mol
            • post_optim_mol()
          • promptbind.utils.utils.read_mol
            • read_mol()
          • promptbind.utils.utils.read_pdbbind_data
            • read_pdbbind_data()
          • promptbind.utils.utils.uniform_random_rotation
            • uniform_random_rotation()
      • promptbind.visualize_prompt_components
        • promptbind.visualize_prompt_components.main
          • main()
• Examples
  • EGFR-antibody interaction analysis
    • Section 2: Finding binding pockets for EGFR KD using “BsiteP”
      • #Section 3: Conducting Protein-Ligand Complex Structure Prediction Using GDDL
  • EGFR-ligand interaction analysis
    • Tips and Instructions
  • EGFR-ligand interaction analysis
    • Section 2: Finding binding pockets for a given protein (EGFR) using “BsiteP”
      • ## Benchmarking results of binding site prediction method
      • #Section 3: Conducting Protein-ligand Docking Using GDDL
    • Section 4: Re-scoring GDDL docking results using BindingRMSD.
    • 4-1. Re-scoring for Docked Protein-Ligand Complex
    • 4-2. 3D Visualization: Crystal Structure vs Docked Poses
    • 4-3. Crystal Ligand Pose vs Docked Ligand Pose: RMSD and Prediction Comparison

Indices and tables

• Index

• Module Index

• Search Page