Structural Biology Tools

Configuration File: packages/structural_biology_tools.json Tool Type: Local Tools Count: 12

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

Available Tools

get_ase_info (Type: PackageTool)

Get comprehensive information about ASE (Atomic Simulation Environment) – a toolkit for building,…

get_ase_info tool specification

Tool Information:

  • Name: get_ase_info

  • Type: PackageTool

  • Description: Get comprehensive information about ASE (Atomic Simulation Environment) – a toolkit for building, running and analysing atomistic simulations.

Parameters:

  • include_examples (boolean) (optional) Whether to include usage examples and quick start guide

Example Usage:

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

get_biopandas_info (Type: PackageTool)

Get comprehensive information about BioPandas – pandas-based molecular structure analysis

get_biopandas_info tool specification

Tool Information:

  • Name: get_biopandas_info

  • Type: PackageTool

  • Description: Get comprehensive information about BioPandas – pandas-based molecular structure analysis

Parameters:

  • include_examples (boolean) (optional) Whether to include usage examples and quick start guide

Example Usage:

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

get_descriptastorus_info (Type: PackageTool)

Get comprehensive information about Descriptastorus – molecular descriptor calculation

get_descriptastorus_info tool specification

Tool Information:

  • Name: get_descriptastorus_info

  • Type: PackageTool

  • Description: Get comprehensive information about Descriptastorus – molecular descriptor calculation

Parameters:

  • info_type (string) (required) Type of information to retrieve about Descriptastorus

Example Usage:

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

get_diffdock_info (Type: PackageTool)

Get comprehensive information about DiffDock – diffusion model for molecular docking

get_diffdock_info tool specification

Tool Information:

  • Name: get_diffdock_info

  • Type: PackageTool

  • Description: Get comprehensive information about DiffDock – diffusion model for molecular docking

Parameters:

  • info_type (string) (required) Type of information to retrieve about DiffDock

Example Usage:

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

get_freesasa_info (Type: PackageTool)

Get information about the freesasa package. Calculate solvent accessible surface areas of proteins

get_freesasa_info tool specification

Tool Information:

  • Name: get_freesasa_info

  • Type: PackageTool

  • Description: Get information about the freesasa package. Calculate solvent accessible surface areas of proteins

Parameters:

No parameters required.

Example Usage:

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

get_htmd_info (Type: PackageTool)

Get information about the htmd package. High throughput molecular dynamics platform

get_htmd_info tool specification

Tool Information:

  • Name: get_htmd_info

  • Type: PackageTool

  • Description: Get information about the htmd package. High throughput molecular dynamics platform

Parameters:

No parameters required.

Example Usage:

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

get_mdanalysis_info (Type: PackageTool)

Get comprehensive information about MDAnalysis – molecular dynamics trajectory analysis

get_mdanalysis_info tool specification

Tool Information:

  • Name: get_mdanalysis_info

  • Type: PackageTool

  • Description: Get comprehensive information about MDAnalysis – molecular dynamics trajectory analysis

Parameters:

  • info_type (string) (required) Type of information to retrieve about MDAnalysis

Example Usage:

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

get_mdtraj_info (Type: PackageTool)

Get information about the mdtraj package. Modern library for molecular dynamics trajectory analysis

get_mdtraj_info tool specification

Tool Information:

  • Name: get_mdtraj_info

  • Type: PackageTool

  • Description: Get information about the mdtraj package. Modern library for molecular dynamics trajectory analysis

Parameters:

No parameters required.

Example Usage:

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

get_nglview_info (Type: PackageTool)

Get information about the nglview package. Jupyter widget for molecular visualization

get_nglview_info tool specification

Tool Information:

  • Name: get_nglview_info

  • Type: PackageTool

  • Description: Get information about the nglview package. Jupyter widget for molecular visualization

Parameters:

No parameters required.

Example Usage:

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

get_openmm_info (Type: PackageTool)

Get comprehensive information about OpenMM – molecular dynamics simulation toolkit

get_openmm_info tool specification

Tool Information:

  • Name: get_openmm_info

  • Type: PackageTool

  • Description: Get comprehensive information about OpenMM – molecular dynamics simulation toolkit

Parameters:

  • include_examples (boolean) (optional) Whether to include usage examples and quick start guide

Example Usage:

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

get_pyrosetta_info (Type: PackageTool)

Get information about the pyrosetta package. Python interface to Rosetta macromolecular modeling …

get_pyrosetta_info tool specification

Tool Information:

  • Name: get_pyrosetta_info

  • Type: PackageTool

  • Description: Get information about the pyrosetta package. Python interface to Rosetta macromolecular modeling suite

Parameters:

No parameters required.

Example Usage:

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

get_pyscf_info (Type: PackageTool)

Get comprehensive information about PySCF – a versatile quantum-chemistry framework in Python.

get_pyscf_info tool specification

Tool Information:

  • Name: get_pyscf_info

  • Type: PackageTool

  • Description: Get comprehensive information about PySCF – a versatile quantum-chemistry framework in Python.

Parameters:

  • include_examples (boolean) (optional) Whether to include usage examples and quick start guide

Example Usage:

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