stko
====

.. automodule:: stko

   
   
   .. rubric:: Modules

   .. autosummary::
      :toctree:
      :template: module.rst
      :recursive:
   
      functional_groups
      molecular_utilities
      molecule_analysis
      topology_functions
   
   

   
   
   .. rubric:: Module attributes

   .. autosummary::
      :toctree:
   
      MoleculeT
      ConstructedMoleculeT
   
   

   
   
   .. rubric:: Functions

   .. autosummary::
      :toctree:
      :nosignatures:
   
      calculate_angle
      calculate_dihedral
      cap_absolute_value
      get_approximate_cell_size
      get_atom_distance
      get_from_parameters
      get_metal_atoms
      get_torsion_info_angles
      is_valid_xtb_solvent
      mol_from_mae_file
      move_generated_macromodel_files
      unit_vector
      vector_angle
   
   

   
   
   .. rubric:: Classes

   .. autosummary::
      :toctree:
      :template: class.rst
      :nosignatures:
   
      Aligner
      AlignmentPotential
      Collapser
      CollapserMC
      ConstructedMoleculeTorsionCalculator
      ConstructedMoleculeTorsionResults
      Du
      ETKDG
      EnergyResults
      GulpUFFMDOptimizer
      GulpUFFOptimizer
      KabschRmsdCalculator
      MAEExtractor
      MDAnalysis
      MMFF
      MMFFEnergy
      MacroModelForceField
      MacroModelMD
      MatchedTorsionCalculator
      MetalOptimizer
      MoleculeSplitter
      MoleculeTransformer
      Network
      NullOptimizer
      OpenBabel
      OpenBabelEnergy
      OpenMMEnergy
      OpenMMForceField
      OpenMMMD
      OptWriterSequence
      Optimizer
      OptimizerSequence
      OrcaEnergy
      OrcaExtractor
      OrcaResults
      PlanarityCalculator
      PlanarityResults
      PositionedAtom
      RmsdCalculator
      RmsdMappedCalculator
      RmsdResults
      ShapeCalculator
      ShapeResults
      TopologyExtractor
      TopologyInfo
      Torsion
      TorsionCalculator
      TorsionInfo
      TorsionResults
      TryCatchOptimizer
      UFF
      UFFEnergy
      UnitCell
      XTB
      XTBCREST
      XTBEnergy
      XTBExtractor
      XTBFF
      XTBFFCREST
      XTBResults
      ZMatrix
   
   

   
   
   .. rubric:: Exceptions

   .. autosummary::
      :toctree:
   
      CalculatorError
      ConvergenceError
      ConversionError
      DifferentAtomError
      DifferentMoleculeError
      ExpectedMetalError
      ForceFieldError
      ForceFieldSetupError
      InputError
      InvalidSolventError
      LewisStructureError
      NotCompletedError
      NotStartedError
      OptimizerError
      PathError
      SettingConflictError
      WrapperNotInstalledError