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AI toolkits for prediction of structure-based protein interaction 0.0.3 documentation
AI toolkits for prediction of structure-based protein interaction 0.0.3 documentation

Table of Contents

  • Backbone Models
    • deepfold
      • deepfold.common
        • deepfold.common.protein
        • deepfold.common.residue_constants
      • deepfold.config
      • 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.multimer
          • deepfold.data.multimer.input_features
          • deepfold.data.multimer.msa_pairing
        • deepfold.data.pdbio
        • deepfold.data.pdbx_parsing
        • deepfold.data.search
          • deepfold.data.search.crfalign
          • deepfold.data.search.input_features
          • deepfold.data.search.mmcif
          • deepfold.data.search.msa_identifiers
          • deepfold.data.search.parsers
          • deepfold.data.search.templates
        • deepfold.data.tools
          • deepfold.data.tools.hhblits
          • deepfold.data.tools.hhsearch
          • deepfold.data.tools.hmmbuild
          • deepfold.data.tools.hmmsearch
          • deepfold.data.tools.jackhmmer
          • deepfold.data.tools.kalign
          • deepfold.data.tools.utils
      • deepfold.distributed
        • deepfold.distributed.model_parallel
        • deepfold.distributed.utils
      • deepfold.eval
        • deepfold.eval.cell_lists
        • deepfold.eval.contact
        • deepfold.eval.distogram
        • deepfold.eval.msa
        • deepfold.eval.plot
        • deepfold.eval.pseudo_3d
      • deepfold.loss
      • deepfold.losses
        • deepfold.losses.auxillary
        • deepfold.losses.confidence
        • deepfold.losses.geometry
        • deepfold.losses.masked_msa
        • deepfold.losses.procrustes
        • deepfold.losses.utils
        • deepfold.losses.violation
      • deepfold.modules
        • deepfold.modules.alphafold
        • deepfold.modules.angle_resnet
        • deepfold.modules.attention
        • deepfold.modules.auxiliary_heads
        • deepfold.modules.backbone_update
        • deepfold.modules.dropout
        • deepfold.modules.evoformer_block
        • deepfold.modules.evoformer_block_pair_core
        • deepfold.modules.evoformer_stack
        • deepfold.modules.extra_msa_block
        • deepfold.modules.extra_msa_embedder
        • deepfold.modules.extra_msa_stack
        • deepfold.modules.global_attention
        • deepfold.modules.inductor
        • deepfold.modules.input_embedder
        • deepfold.modules.invariant_point_attention
        • deepfold.modules.layer_norm
        • deepfold.modules.linear
        • deepfold.modules.msa_column_attention
        • deepfold.modules.msa_column_global_attention
        • deepfold.modules.msa_row_attention_with_pair_bias
        • deepfold.modules.msa_transition
        • deepfold.modules.outer_product_mean
        • deepfold.modules.pair_transition
        • deepfold.modules.recycling_embedder
        • deepfold.modules.single_transition
        • deepfold.modules.structure_module
        • deepfold.modules.template_angle_embedder
        • deepfold.modules.template_pair_block
        • deepfold.modules.template_pair_embedder
        • deepfold.modules.template_pair_stack
        • deepfold.modules.template_pointwise_attention
        • deepfold.modules.template_projection
        • deepfold.modules.triangular_attention
        • deepfold.modules.triangular_multiplicative_update
        • deepfold.modules.tweaks
          • deepfold.modules.tweaks.evo_attn
      • deepfold.ops
        • deepfold.ops.evoformer_attention
      • deepfold.package_info
      • deepfold.relax
        • deepfold.relax.amber_minimize
        • deepfold.relax.cleanup
        • deepfold.relax.relax
        • deepfold.relax.utils
      • deepfold.runner
        • deepfold.runner.config_utils
        • deepfold.runner.parser
        • deepfold.runner.utils
      • deepfold.testing
        • deepfold.testing.common
        • deepfold.testing.utils
      • deepfold.train
        • deepfold.train.gradient_clipping
        • deepfold.train.lr_scheduler
        • deepfold.train.validation_metrics
      • deepfold.utils
        • deepfold.utils.checkpoint_utils
        • deepfold.utils.chunk_utils
        • deepfold.utils.crop_utils
        • deepfold.utils.datetime_utils
        • deepfold.utils.dist_utils
        • deepfold.utils.feats_utils
        • deepfold.utils.file_utils
        • deepfold.utils.geometry
          • deepfold.utils.geometry.quat_rigid
          • deepfold.utils.geometry.rigid_matrix_vector
          • deepfold.utils.geometry.rotation_matrix
          • deepfold.utils.geometry.utils
          • deepfold.utils.geometry.vector
        • deepfold.utils.hash_utils
        • deepfold.utils.import_utils
        • deepfold.utils.iter_utils
        • deepfold.utils.log_utils
        • deepfold.utils.precision
        • deepfold.utils.random
        • deepfold.utils.rigid_utils
        • deepfold.utils.script_utils
        • deepfold.utils.swa_utils
        • deepfold.utils.tensor_utils
    • miniworld
      • miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction
      • miniworld.feature
        • miniworld.feature.MiniWorld_featuring_species
      • miniworld.models_MiniWorld_v1_5_use_interaction
        • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module
        • miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor
        • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings
        • miniworld.models_MiniWorld_v1_5_use_interaction.MiniWorld
        • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module
        • miniworld.models_MiniWorld_v1_5_use_interaction.value_network
      • miniworld.utils
        • miniworld.utils.DataClass
        • miniworld.utils.My_mistake
        • miniworld.utils.ProteinClass
        • miniworld.utils.arguments_MiniWorld
        • miniworld.utils.chemical
        • miniworld.utils.data_refactoring
        • miniworld.utils.ffindex
        • miniworld.utils.hhpred_parser
        • miniworld.utils.kalign_mapping
        • miniworld.utils.kinematics
        • miniworld.utils.output_visualize
        • miniworld.utils.parser_util
        • miniworld.utils.template_parser
        • miniworld.utils.util
        • miniworld.utils.util_module
  • Tools
    • bapred
      • bapred.data
        • bapred.data.atom_feature
        • bapred.data.data
        • bapred.data.utils
      • bapred.inference
      • bapred.model
        • bapred.model.GatedGCNLSPE
        • bapred.model.GraphGPS
        • bapred.model.MHA
        • bapred.model.model
    • bindingrmsd
      • bindingrmsd.data
        • bindingrmsd.data.data
        • bindingrmsd.data.data_bck
        • bindingrmsd.data.ligand_atom_feature
        • bindingrmsd.data.protein_atom_feature
        • bindingrmsd.data.utils
      • bindingrmsd.inference
      • bindingrmsd.model
        • bindingrmsd.model.GatedGCNLSPE
        • bindingrmsd.model.model
    • bis_protein_structure
      • bis_protein_structure.CROSSLINK
      • bis_protein_structure.DATAGEN
      • bis_protein_structure.DISULFIDE
      • bis_protein_structure.MMEVAL
      • bis_protein_structure.SOLVENTACC
      • bis_protein_structure.TORSION2
      • bis_protein_structure.residue_constants
      • bis_protein_structure.split_pdb
    • bsitep
      • bsitep.proteindata
      • bsitep.seresnet
      • bsitep.utils
        • bsitep.utils.data_utils
        • bsitep.utils.model_utils
        • bsitep.utils.pocket_utils
    • diffalign
      • diffalign.models
        • diffalign.models.common
        • diffalign.models.encoder
          • diffalign.models.encoder.edge
          • diffalign.models.encoder.egnn
        • diffalign.models.epsnet
          • diffalign.models.epsnet.diffusion
      • diffalign.train
      • diffalign.utils
        • diffalign.utils.chem
        • diffalign.utils.common
        • diffalign.utils.dataloader
        • diffalign.utils.datasets
        • diffalign.utils.evaluation
          • diffalign.utils.evaluation.covmat
        • diffalign.utils.misc
        • diffalign.utils.transforms
        • diffalign.utils.visualize
    • gd_dl
      • gd_dl.data
        • gd_dl.data.ML_inference
        • gd_dl.data.ML_rerank
        • gd_dl.data.all_ML_rerank
        • gd_dl.data.single_ML_rerank
      • gd_dl.lib_pdb_mol2
      • gd_dl.models
      • gd_dl.path_setting
      • gd_dl.rerank_model
      • gd_dl.utils
    • promptbind
      • promptbind.data
        • promptbind.data.data
        • promptbind.data.inference_preprocess_mol_confs
        • promptbind.data.inference_preprocess_protein
      • promptbind.models
        • promptbind.models.att_model
        • promptbind.models.cross_att
        • promptbind.models.egnn
        • promptbind.models.model
        • promptbind.models.model_utils
      • promptbind.test_promptbind
      • promptbind.train_promptbind
      • promptbind.utils
        • promptbind.utils.fabind_inference_dataset
        • promptbind.utils.feature_utils
        • promptbind.utils.generation_utils
        • promptbind.utils.inference_mol_utils
        • promptbind.utils.inference_pdb_utils
        • promptbind.utils.logging_utils
        • promptbind.utils.metrics
        • promptbind.utils.metrics_to_tsb
        • promptbind.utils.post_optim_utils
        • promptbind.utils.utils
      • promptbind.visualize_prompt_components
  • Examples
    • EGFR-antibody interaction analysis
      • Section 2: Finding binding pockets for EGFR KD using “BsiteP”
    • EGFR-ligand interaction analysis
      • Tips and Instructions
    • EGFR-ligand interaction analysis
      • Section 2: Finding binding pockets for a given protein (EGFR) using “BsiteP”
      • 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
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deepfold.utils.feats_utils¶

Functions

crop_a3m_string(a3m_string, start, end)

crop_features(feats, start, end)

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