Pdbe Api Tools

Configuration File: pdbe_api_tools.json Tool Type: Local Tools Count: 10

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

Available Tools

pdbe_get_entry_assemblies (Type: PDBeAPIRESTTool)

Get biological assembly information for a PDB entry including assembly IDs, symmetry operations, …

pdbe_get_entry_assemblies tool specification

Tool Information:

  • Name: pdbe_get_entry_assemblies

  • Type: PDBeAPIRESTTool

  • Description: Get biological assembly information for a PDB entry including assembly IDs, symmetry operations, and assembly composition. Note: The assemblies endpoint may return 404 for some entries. This tool automatically falls back to extracting assembly information from the summary endpoint. If both methods fail, use pdbe_get_entry_summary for comprehensive structure information.

Parameters:

  • pdb_id (string) (required) PDB entry ID (e.g., ‘1A2B’, ‘1CRN’). Will be converted to lowercase automatically.

Example Usage:

query = {
    "name": "pdbe_get_entry_assemblies",
    "arguments": {
        "pdb_id": "example_value"
    }
}
result = tu.run(query)

pdbe_get_entry_experiment (Type: PDBeAPIRESTTool)

Get experimental details for a PDB entry including experimental method, resolution, R-factors, co…

pdbe_get_entry_experiment tool specification

Tool Information:

  • Name: pdbe_get_entry_experiment

  • Type: PDBeAPIRESTTool

  • Description: Get experimental details for a PDB entry including experimental method, resolution, R-factors, completeness, refinement software, space group, and unit cell parameters. This provides detailed experimental metadata for structure determination.

Parameters:

  • pdb_id (string) (required) PDB entry ID (e.g., ‘1A2B’, ‘1CRN’). Will be converted to lowercase automatically.

Example Usage:

query = {
    "name": "pdbe_get_entry_experiment",
    "arguments": {
        "pdb_id": "example_value"
    }
}
result = tu.run(query)

pdbe_get_entry_molecules (Type: PDBeAPIRESTTool)

Get molecule information for a PDB entry including molecule type, entity ID, length, chains, muta…

pdbe_get_entry_molecules tool specification

Tool Information:

  • Name: pdbe_get_entry_molecules

  • Type: PDBeAPIRESTTool

  • Description: Get molecule information for a PDB entry including molecule type, entity ID, length, chains, mutations, molecular weight, and gene names. Use this to understand the composition and properties of molecules in the structure.

Parameters:

  • pdb_id (string) (required) PDB entry ID (e.g., ‘1A2B’, ‘1CRN’). Will be converted to lowercase automatically.

Example Usage:

query = {
    "name": "pdbe_get_entry_molecules",
    "arguments": {
        "pdb_id": "example_value"
    }
}
result = tu.run(query)

pdbe_get_entry_observed_residues_ratio (Type: PDBeAPIRESTTool)

Get observed residues ratio for chains in a PDB entry, indicating what fraction of residues are o…

pdbe_get_entry_observed_residues_ratio tool specification

Tool Information:

  • Name: pdbe_get_entry_observed_residues_ratio

  • Type: PDBeAPIRESTTool

  • Description: Get observed residues ratio for chains in a PDB entry, indicating what fraction of residues are observed in the structure. This helps assess structure completeness and quality. Returns information per chain including struct_asym_id, chain_id, number of residues, observed ratio, and partial ratio.

Parameters:

  • pdb_id (string) (required) PDB entry ID (e.g., ‘1A2B’, ‘1CRN’). Will be converted to lowercase automatically.

Example Usage:

query = {
    "name": "pdbe_get_entry_observed_residues_ratio",
    "arguments": {
        "pdb_id": "example_value"
    }
}
result = tu.run(query)

pdbe_get_entry_publications (Type: PDBeAPIRESTTool)

Get publication information associated with a PDB entry including authors, journal, DOI, and cita…

pdbe_get_entry_publications tool specification

Tool Information:

  • Name: pdbe_get_entry_publications

  • Type: PDBeAPIRESTTool

  • Description: Get publication information associated with a PDB entry including authors, journal, DOI, and citation details.

Parameters:

  • pdb_id (string) (required) PDB entry ID (e.g., ‘1A2B’, ‘1CRN’). Will be converted to lowercase automatically.

Example Usage:

query = {
    "name": "pdbe_get_entry_publications",
    "arguments": {
        "pdb_id": "example_value"
    }
}
result = tu.run(query)

pdbe_get_entry_quality (Type: PDBeAPIRESTTool)

Get quality metrics and validation information for a PDB entry including resolution, R-free, Rama…

pdbe_get_entry_quality tool specification

Tool Information:

  • Name: pdbe_get_entry_quality

  • Type: PDBeAPIRESTTool

  • Description: Get quality metrics and validation information for a PDB entry including resolution, R-free, Ramachandran statistics, and validation scores. Note: Quality endpoint may not be available for all PDB entries. If this returns 404, try pdbe_get_entry_summary which includes basic quality information.

Parameters:

  • pdb_id (string) (required) PDB entry ID (e.g., ‘1A2B’, ‘1CRN’). Will be converted to lowercase automatically.

Example Usage:

query = {
    "name": "pdbe_get_entry_quality",
    "arguments": {
        "pdb_id": "example_value"
    }
}
result = tu.run(query)

pdbe_get_entry_related_publications (Type: PDBeAPIRESTTool)

Get publications related to a PDB entry that appear without citation, including PubMed IDs, title…

pdbe_get_entry_related_publications tool specification

Tool Information:

  • Name: pdbe_get_entry_related_publications

  • Type: PDBeAPIRESTTool

  • Description: Get publications related to a PDB entry that appear without citation, including PubMed IDs, titles, journals, authors, and citation counts. This complements pdbe_get_entry_publications by showing additional related publications.

Parameters:

  • pdb_id (string) (required) PDB entry ID (e.g., ‘1A2B’, ‘1CRN’). Will be converted to lowercase automatically.

Example Usage:

query = {
    "name": "pdbe_get_entry_related_publications",
    "arguments": {
        "pdb_id": "example_value"
    }
}
result = tu.run(query)

pdbe_get_entry_secondary_structure (Type: PDBeAPIRESTTool)

Get secondary structure information for a PDB entry including helix, sheet, and turn assignments.

pdbe_get_entry_secondary_structure tool specification

Tool Information:

  • Name: pdbe_get_entry_secondary_structure

  • Type: PDBeAPIRESTTool

  • Description: Get secondary structure information for a PDB entry including helix, sheet, and turn assignments.

Parameters:

  • pdb_id (string) (required) PDB entry ID (e.g., ‘1A2B’, ‘1CRN’). Will be converted to lowercase automatically.

Example Usage:

query = {
    "name": "pdbe_get_entry_secondary_structure",
    "arguments": {
        "pdb_id": "example_value"
    }
}
result = tu.run(query)

pdbe_get_entry_status (Type: PDBeAPIRESTTool)

Get status information for a PDB entry including release date, status code, authors, experimental…

pdbe_get_entry_status tool specification

Tool Information:

  • Name: pdbe_get_entry_status

  • Type: PDBeAPIRESTTool

  • Description: Get status information for a PDB entry including release date, status code, authors, experimental method, and whether the entry has been superseded or obsoleted. Use this to check the current status and availability of a PDB entry.

Parameters:

  • pdb_id (string) (required) PDB entry ID (e.g., ‘1A2B’, ‘1CRN’). Will be converted to lowercase automatically.

Example Usage:

query = {
    "name": "pdbe_get_entry_status",
    "arguments": {
        "pdb_id": "example_value"
    }
}
result = tu.run(query)

pdbe_get_entry_summary (Type: PDBeAPIRESTTool)

Get summary information for a PDB entry including title, authors, release date, and basic structu…

pdbe_get_entry_summary tool specification

Tool Information:

  • Name: pdbe_get_entry_summary

  • Type: PDBeAPIRESTTool

  • Description: Get summary information for a PDB entry including title, authors, release date, and basic structure metadata.

Parameters:

  • pdb_id (string) (required) PDB entry ID (e.g., ‘1A2B’, ‘1CRN’). Will be converted to lowercase automatically.

Example Usage:

query = {
    "name": "pdbe_get_entry_summary",
    "arguments": {
        "pdb_id": "example_value"
    }
}
result = tu.run(query)