Rcsb Pdb Tools

Configuration File: rcsb_pdb_tools.json Tool Type: Local Tools Count: 39

This page contains all tools defined in the rcsb_pdb_tools.json configuration file.

Available Tools

get_assembly_info_by_pdb_id (Type: RCSBTool)

Retrieve all associated biological assembly details for a given PDB structure.

get_assembly_info_by_pdb_id tool specification

Tool Information:

  • Name: get_assembly_info_by_pdb_id

  • Type: RCSBTool

  • Description: Retrieve all associated biological assembly details for a given PDB structure.

Parameters:

  • pdb_id (string) (optional) 4-character RCSB PDB ID

Example Usage:

query = {
    "name": "get_assembly_info_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_assembly_summary (Type: RCSBTool)

Get key assembly composition and symmetry summary for an assembly associated with a PDB entry.

get_assembly_summary tool specification

Tool Information:

  • Name: get_assembly_summary

  • Type: RCSBTool

  • Description: Get key assembly composition and symmetry summary for an assembly associated with a PDB entry.

Parameters:

  • assembly_id (string) (optional) Assembly ID in format ‘PDBID-assemblyNumber’ (e.g., ‘1A8M-1’)

Example Usage:

query = {
    "name": "get_assembly_summary",
    "arguments": {
    }
}
result = tu.run(query)

get_binding_affinity_by_pdb_id (Type: RCSBTool)

Retrieve binding affinity constants (Kd, Ki, IC50) associated with ligands in a PDB entry.

get_binding_affinity_by_pdb_id tool specification

Tool Information:

  • Name: get_binding_affinity_by_pdb_id

  • Type: RCSBTool

  • Description: Retrieve binding affinity constants (Kd, Ki, IC50) associated with ligands in a PDB entry.

Parameters:

  • pdb_id (string) (optional) RCSB PDB ID (e.g., 1A8M)

Example Usage:

query = {
    "name": "get_binding_affinity_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_chem_comp_audit_info (Type: RCSBTool)

Fetch audit history for a chemical component: action type, date, details, ordinal, and processing…

get_chem_comp_audit_info tool specification

Tool Information:

  • Name: get_chem_comp_audit_info

  • Type: RCSBTool

  • Description: Fetch audit history for a chemical component: action type, date, details, ordinal, and processing site.

Parameters:

  • pdb_id (string) (optional) Chemical component ID to retrieve audit info for

Example Usage:

query = {
    "name": "get_chem_comp_audit_info",
    "arguments": {
    }
}
result = tu.run(query)

get_chem_comp_charge_and_ambiguity (Type: RCSBTool)

Retrieve the formal charge and ambiguity flag of a chemical component.

get_chem_comp_charge_and_ambiguity tool specification

Tool Information:

  • Name: get_chem_comp_charge_and_ambiguity

  • Type: RCSBTool

  • Description: Retrieve the formal charge and ambiguity flag of a chemical component.

Parameters:

  • pdb_id (string) (optional) Chemical component ID to query charge and ambiguity

Example Usage:

query = {
    "name": "get_chem_comp_charge_and_ambiguity",
    "arguments": {
    }
}
result = tu.run(query)

get_citation_info_by_pdb_id (Type: RCSBTool)

Retrieve citation information (authors, journal, year) for a given PDB structure.

get_citation_info_by_pdb_id tool specification

Tool Information:

  • Name: get_citation_info_by_pdb_id

  • Type: RCSBTool

  • Description: Retrieve citation information (authors, journal, year) for a given PDB structure.

Parameters:

  • pdb_id (string) (optional) 4-character RCSB PDB ID

Example Usage:

query = {
    "name": "get_citation_info_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_core_refinement_statistics (Type: RCSBTool)

Retrieve essential refinement statistics for a given PDB structure including R-factors, occupancy…

get_core_refinement_statistics tool specification

Tool Information:

  • Name: get_core_refinement_statistics

  • Type: RCSBTool

  • Description: Retrieve essential refinement statistics for a given PDB structure including R-factors, occupancy, phase errors, and solvent model parameters.

Parameters:

  • pdb_id (string) (optional) PDB entry ID (e.g., ‘1ABC’)

Example Usage:

query = {
    "name": "get_core_refinement_statistics",
    "arguments": {
    }
}
result = tu.run(query)

get_crystal_growth_conditions_by_pdb_id (Type: RCSBTool)

Get information about the crystallization method and conditions for a structure.

get_crystal_growth_conditions_by_pdb_id tool specification

Tool Information:

  • Name: get_crystal_growth_conditions_by_pdb_id

  • Type: RCSBTool

  • Description: Get information about the crystallization method and conditions for a structure.

Parameters:

  • pdb_id (string) (optional) PDB ID of the structure

Example Usage:

query = {
    "name": "get_crystal_growth_conditions_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_crystallization_ph_by_pdb_id (Type: RCSBTool)

Fetch the pH used during crystallization of the sample.

get_crystallization_ph_by_pdb_id tool specification

Tool Information:

  • Name: get_crystallization_ph_by_pdb_id

  • Type: RCSBTool

  • Description: Fetch the pH used during crystallization of the sample.

Parameters:

  • pdb_id (string) (optional) RCSB PDB ID of the structure

Example Usage:

query = {
    "name": "get_crystallization_ph_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_crystallographic_properties_by_pdb_id (Type: RCSBTool)

Retrieve crystallographic properties such as unit cell dimensions and space group for a PDB entry.

get_crystallographic_properties_by_pdb_id tool specification

Tool Information:

  • Name: get_crystallographic_properties_by_pdb_id

  • Type: RCSBTool

  • Description: Retrieve crystallographic properties such as unit cell dimensions and space group for a PDB entry.

Parameters:

  • pdb_id (string) (optional) PDB ID of the structure

Example Usage:

query = {
    "name": "get_crystallographic_properties_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_ec_number_by_entity_id (Type: RCSBTool)

Retrieve the Enzyme Commission (EC) number(s) for an entity.

get_ec_number_by_entity_id tool specification

Tool Information:

  • Name: get_ec_number_by_entity_id

  • Type: RCSBTool

  • Description: Retrieve the Enzyme Commission (EC) number(s) for an entity.

Parameters:

  • entity_id (string) (optional) Polymer entity ID (e.g., ‘1A8M_1’)

Example Usage:

query = {
    "name": "get_ec_number_by_entity_id",
    "arguments": {
    }
}
result = tu.run(query)

get_em_3d_fitting_and_reconstruction_details (Type: RCSBTool)

Retrieve EM 3D fitting model details and associated 3D reconstruction info for a given PDB entry.

get_em_3d_fitting_and_reconstruction_details tool specification

Tool Information:

  • Name: get_em_3d_fitting_and_reconstruction_details

  • Type: RCSBTool

  • Description: Retrieve EM 3D fitting model details and associated 3D reconstruction info for a given PDB entry.

Parameters:

  • pdb_id (string) (optional) 4-character RCSB PDB ID

Example Usage:

query = {
    "name": "get_em_3d_fitting_and_reconstruction_details",
    "arguments": {
    }
}
result = tu.run(query)

get_emdb_ids_by_pdb_id (Type: RCSBTool)

Retrieve Electron Microscopy Data Bank (EMDB) identifiers linked to a PDB entry.

get_emdb_ids_by_pdb_id tool specification

Tool Information:

  • Name: get_emdb_ids_by_pdb_id

  • Type: RCSBTool

  • Description: Retrieve Electron Microscopy Data Bank (EMDB) identifiers linked to a PDB entry.

Parameters:

  • pdb_id (string) (optional) 4-character PDB ID

Example Usage:

query = {
    "name": "get_emdb_ids_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_gene_name_by_entity_id (Type: RCSBTool)

Retrieve gene name(s) associated with a polymer entity.

get_gene_name_by_entity_id tool specification

Tool Information:

  • Name: get_gene_name_by_entity_id

  • Type: RCSBTool

  • Description: Retrieve gene name(s) associated with a polymer entity.

Parameters:

  • entity_id (string) (optional) Entity ID like ‘1A8M_1’

Example Usage:

query = {
    "name": "get_gene_name_by_entity_id",
    "arguments": {
    }
}
result = tu.run(query)

get_host_organism_by_pdb_id (Type: RCSBTool)

Get the host organism used for protein expression in a PDB entry.

get_host_organism_by_pdb_id tool specification

Tool Information:

  • Name: get_host_organism_by_pdb_id

  • Type: RCSBTool

  • Description: Get the host organism used for protein expression in a PDB entry.

Parameters:

  • pdb_id (string) (optional) 4-character PDB ID

Example Usage:

query = {
    "name": "get_host_organism_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_ligand_bond_count_by_pdb_id (Type: RCSBTool)

Get the number of bonds for each ligand in a given PDB structure.

get_ligand_bond_count_by_pdb_id tool specification

Tool Information:

  • Name: get_ligand_bond_count_by_pdb_id

  • Type: RCSBTool

  • Description: Get the number of bonds for each ligand in a given PDB structure.

Parameters:

  • pdb_id (string) (optional) PDB ID of the entry

Example Usage:

query = {
    "name": "get_ligand_bond_count_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_ligand_smiles_by_chem_comp_id (Type: RCSBTool)

Retrieve the SMILES chemical structure string for a given chemical component (ligand) ID.

get_ligand_smiles_by_chem_comp_id tool specification

Tool Information:

  • Name: get_ligand_smiles_by_chem_comp_id

  • Type: RCSBTool

  • Description: Retrieve the SMILES chemical structure string for a given chemical component (ligand) ID.

Parameters:

  • chem_comp_id (string) (optional) Chemical component ID (e.g., ‘ATP’)

Example Usage:

query = {
    "name": "get_ligand_smiles_by_chem_comp_id",
    "arguments": {
    }
}
result = tu.run(query)

get_mutation_annotations_by_pdb_id (Type: RCSBTool)

Retrieve mutation annotations for a given PDB structure.

get_mutation_annotations_by_pdb_id tool specification

Tool Information:

  • Name: get_mutation_annotations_by_pdb_id

  • Type: RCSBTool

  • Description: Retrieve mutation annotations for a given PDB structure.

Parameters:

  • pdb_id (string) (optional) 4-character RCSB PDB ID

Example Usage:

query = {
    "name": "get_mutation_annotations_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_oligosaccharide_descriptors_by_entity_id (Type: RCSBTool)

Retrieve structural descriptors for branched entities (e.g., oligosaccharides) in a PDB entry.

get_oligosaccharide_descriptors_by_entity_id tool specification

Tool Information:

  • Name: get_oligosaccharide_descriptors_by_entity_id

  • Type: RCSBTool

  • Description: Retrieve structural descriptors for branched entities (e.g., oligosaccharides) in a PDB entry.

Parameters:

  • entity_id (string) (optional) Branched entity ID like ‘5FMB_2’

Example Usage:

query = {
    "name": "get_oligosaccharide_descriptors_by_entity_id",
    "arguments": {
    }
}
result = tu.run(query)

get_polymer_entity_annotations (Type: RCSBTool)

Retrieve functional annotations (Pfam domains, GO terms) and associated UniProt accession IDs for…

get_polymer_entity_annotations tool specification

Tool Information:

  • Name: get_polymer_entity_annotations

  • Type: RCSBTool

  • Description: Retrieve functional annotations (Pfam domains, GO terms) and associated UniProt accession IDs for a polymer entity.

Parameters:

  • entity_id (string) (optional) Polymer entity ID like ‘1A8M_1’

Example Usage:

query = {
    "name": "get_polymer_entity_annotations",
    "arguments": {
    }
}
result = tu.run(query)

get_polymer_entity_count_by_pdb_id (Type: RCSBTool)

Get the number of distinct polymer entities (chains) in a structure.

get_polymer_entity_count_by_pdb_id tool specification

Tool Information:

  • Name: get_polymer_entity_count_by_pdb_id

  • Type: RCSBTool

  • Description: Get the number of distinct polymer entities (chains) in a structure.

Parameters:

  • pdb_id (string) (optional) 4-character PDB ID

Example Usage:

query = {
    "name": "get_polymer_entity_count_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_polymer_entity_ids_by_pdb_id (Type: RCSBTool)

List polymer entity IDs for a given PDB ID. Useful for building further queries on individual pol…

get_polymer_entity_ids_by_pdb_id tool specification

Tool Information:

  • Name: get_polymer_entity_ids_by_pdb_id

  • Type: RCSBTool

  • Description: List polymer entity IDs for a given PDB ID. Useful for building further queries on individual polymer entities.

Parameters:

  • pdb_id (string) (optional) 4-character RCSB PDB ID of the protein

Example Usage:

query = {
    "name": "get_polymer_entity_ids_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_polymer_entity_type_by_entity_id (Type: RCSBTool)

Get the polymer entity type (e.g., Protein, DNA) using the polymer entity ID.

get_polymer_entity_type_by_entity_id tool specification

Tool Information:

  • Name: get_polymer_entity_type_by_entity_id

  • Type: RCSBTool

  • Description: Get the polymer entity type (e.g., Protein, DNA) using the polymer entity ID.

Parameters:

  • entity_id (string) (optional) Polymer entity ID like ‘1A8M_1’

Example Usage:

query = {
    "name": "get_polymer_entity_type_by_entity_id",
    "arguments": {
    }
}
result = tu.run(query)

get_polymer_molecular_weight_by_entity_id (Type: RCSBTool)

Retrieve the molecular weight of a polymer entity.

get_polymer_molecular_weight_by_entity_id tool specification

Tool Information:

  • Name: get_polymer_molecular_weight_by_entity_id

  • Type: RCSBTool

  • Description: Retrieve the molecular weight of a polymer entity.

Parameters:

  • entity_id (string) (optional) Polymer entity ID like ‘1A8M_1’

Example Usage:

query = {
    "name": "get_polymer_molecular_weight_by_entity_id",
    "arguments": {
    }
}
result = tu.run(query)

get_protein_classification_by_pdb_id (Type: RCSBTool)

Get the classification of the protein structure (e.g., transferase, oxidoreductase).

get_protein_classification_by_pdb_id tool specification

Tool Information:

  • Name: get_protein_classification_by_pdb_id

  • Type: RCSBTool

  • Description: Get the classification of the protein structure (e.g., transferase, oxidoreductase).

Parameters:

  • pdb_id (string) (optional) PDB ID of the entry

Example Usage:

query = {
    "name": "get_protein_classification_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_protein_metadata_by_pdb_id (Type: RCSBTool)

Retrieve basic protein structure metadata, including structure title, experimental method, resolu…

get_protein_metadata_by_pdb_id tool specification

Tool Information:

  • Name: get_protein_metadata_by_pdb_id

  • Type: RCSBTool

  • Description: Retrieve basic protein structure metadata, including structure title, experimental method, resolution, and initial release date.

Parameters:

  • pdb_id (string) (optional) 4-character RCSB PDB ID of the protein

Example Usage:

query = {
    "name": "get_protein_metadata_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_refinement_resolution_by_pdb_id (Type: RCSBTool)

Retrieve the reported resolution from refinement data for X-ray structures.

get_refinement_resolution_by_pdb_id tool specification

Tool Information:

  • Name: get_refinement_resolution_by_pdb_id

  • Type: RCSBTool

  • Description: Retrieve the reported resolution from refinement data for X-ray structures.

Parameters:

  • pdb_id (string) (optional) PDB entry ID

Example Usage:

query = {
    "name": "get_refinement_resolution_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_release_deposit_dates_by_pdb_id (Type: RCSBTool)

Get the release and deposition dates for a PDB entry.

get_release_deposit_dates_by_pdb_id tool specification

Tool Information:

  • Name: get_release_deposit_dates_by_pdb_id

  • Type: RCSBTool

  • Description: Get the release and deposition dates for a PDB entry.

Parameters:

  • pdb_id (string) (optional) 4-character RCSB PDB ID

Example Usage:

query = {
    "name": "get_release_deposit_dates_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_sequence_by_pdb_id (Type: RCSBTool)

Retrieve amino acid or nucleotide sequence of polymer entities for a given PDB structure.

get_sequence_by_pdb_id tool specification

Tool Information:

  • Name: get_sequence_by_pdb_id

  • Type: RCSBTool

  • Description: Retrieve amino acid or nucleotide sequence of polymer entities for a given PDB structure.

Parameters:

  • pdb_id (string) (optional) 4-character RCSB PDB ID

Example Usage:

query = {
    "name": "get_sequence_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_sequence_lengths_by_pdb_id (Type: RCSBTool)

Retrieve the sequence lengths of polymer entities for a given PDB structure.

get_sequence_lengths_by_pdb_id tool specification

Tool Information:

  • Name: get_sequence_lengths_by_pdb_id

  • Type: RCSBTool

  • Description: Retrieve the sequence lengths of polymer entities for a given PDB structure.

Parameters:

  • pdb_id (string) (optional) 4-character RCSB PDB ID

Example Usage:

query = {
    "name": "get_sequence_lengths_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_sequence_positional_features_by_instance_id (Type: RCSBTool)

Retrieve sequence positional features (e.g., binding sites, motifs) for a polymer entity instance.

get_sequence_positional_features_by_instance_id tool specification

Tool Information:

  • Name: get_sequence_positional_features_by_instance_id

  • Type: RCSBTool

  • Description: Retrieve sequence positional features (e.g., binding sites, motifs) for a polymer entity instance.

Parameters:

  • instance_id (string) (optional) Polymer entity instance ID like ‘1NDO.A’

Example Usage:

query = {
    "name": "get_sequence_positional_features_by_instance_id",
    "arguments": {
    }
}
result = tu.run(query)

get_source_organism_by_pdb_id (Type: RCSBTool)

Retrieve the scientific name of the source organism for a given PDB structure.

get_source_organism_by_pdb_id tool specification

Tool Information:

  • Name: get_source_organism_by_pdb_id

  • Type: RCSBTool

  • Description: Retrieve the scientific name of the source organism for a given PDB structure.

Parameters:

  • pdb_id (string) (optional) 4-character RCSB PDB ID of the structure

Example Usage:

query = {
    "name": "get_source_organism_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_space_group_by_pdb_id (Type: RCSBTool)

Get the crystallographic space group of the structure.

get_space_group_by_pdb_id tool specification

Tool Information:

  • Name: get_space_group_by_pdb_id

  • Type: RCSBTool

  • Description: Get the crystallographic space group of the structure.

Parameters:

  • pdb_id (string) (optional) 4-character RCSB PDB ID

Example Usage:

query = {
    "name": "get_space_group_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_structure_determination_software_by_pdb_id (Type: RCSBTool)

Retrieve names of software used during structure determination.

get_structure_determination_software_by_pdb_id tool specification

Tool Information:

  • Name: get_structure_determination_software_by_pdb_id

  • Type: RCSBTool

  • Description: Retrieve names of software used during structure determination.

Parameters:

  • pdb_id (string) (optional) RCSB PDB entry ID

Example Usage:

query = {
    "name": "get_structure_determination_software_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_structure_title_by_pdb_id (Type: RCSBTool)

Retrieve the structure title for a given PDB entry.

get_structure_title_by_pdb_id tool specification

Tool Information:

  • Name: get_structure_title_by_pdb_id

  • Type: RCSBTool

  • Description: Retrieve the structure title for a given PDB entry.

Parameters:

  • pdb_id (string) (optional) 4-character PDB ID

Example Usage:

query = {
    "name": "get_structure_title_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_structure_validation_metrics_by_pdb_id (Type: RCSBTool)

Retrieve structure validation metrics such as R-free, R-work, and clashscore for a PDB entry.

get_structure_validation_metrics_by_pdb_id tool specification

Tool Information:

  • Name: get_structure_validation_metrics_by_pdb_id

  • Type: RCSBTool

  • Description: Retrieve structure validation metrics such as R-free, R-work, and clashscore for a PDB entry.

Parameters:

  • pdb_id (string) (optional) PDB ID of the structure

Example Usage:

query = {
    "name": "get_structure_validation_metrics_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_target_cofactor_info (Type: RCSBTool)

Retrieve essential cofactor information for a given target including cofactor IDs, mechanism of a…

get_target_cofactor_info tool specification

Tool Information:

  • Name: get_target_cofactor_info

  • Type: RCSBTool

  • Description: Retrieve essential cofactor information for a given target including cofactor IDs, mechanism of action, literature references, and resource metadata.

Parameters:

  • pdb_id (string) (optional) Target ID or entity identifier (e.g., UniProt ID or internal target id)

Example Usage:

query = {
    "name": "get_target_cofactor_info",
    "arguments": {
    }
}
result = tu.run(query)

get_taxonomy_by_pdb_id (Type: RCSBTool)

Get the scientific name and taxonomy of the organism(s) associated with a PDB entry.

get_taxonomy_by_pdb_id tool specification

Tool Information:

  • Name: get_taxonomy_by_pdb_id

  • Type: RCSBTool

  • Description: Get the scientific name and taxonomy of the organism(s) associated with a PDB entry.

Parameters:

  • pdb_id (string) (optional) 4-character RCSB PDB ID

Example Usage:

query = {
    "name": "get_taxonomy_by_pdb_id",
    "arguments": {
    }
}
result = tu.run(query)

get_uniprot_accession_by_entity_id (Type: RCSBTool)

Fetch UniProt accession numbers associated with a specific polymer entity.

get_uniprot_accession_by_entity_id tool specification

Tool Information:

  • Name: get_uniprot_accession_by_entity_id

  • Type: RCSBTool

  • Description: Fetch UniProt accession numbers associated with a specific polymer entity.

Parameters:

  • entity_id (string) (optional) Polymer entity ID (e.g., ‘1A8M_1’)

Example Usage:

query = {
    "name": "get_uniprot_accession_by_entity_id",
    "arguments": {
    }
}
result = tu.run(query)