stko

Molecular optimisers and property calculators for use with stk.

Module attributes

`MoleculeT`	Type parameter matching any `stk.Molecule` or subclasses.
`ConstructedMoleculeT`	Type parameter matching `stk.ConstructedMolecule` or subclasses.

Functions

`calculate_angle`	Calculate the angle between three points in degrees.
`calculate_dihedral`	Calculate the dihedral between four points in degrees.
`cap_absolute_value`	Returns value with absolute value capped at max_absolute_value.
`get_approximate_cell_size`	Cell size determined from projection of atoms on cell vectors.
`get_atom_distance`	Return the distance between two atoms.
`get_from_parameters`	Create a Lattice using unit cell lengths and angles (in degrees).
`get_torsion_info_angles`	Get the angles for torsion_info in mol.
`is_valid_xtb_solvent`	Check if solvent is valid [#]_ for the given GFN version.
`unit_vector`	Returns the unit vector of the vector.
`vector_angle`	Returns the angle between two vectors in radians.

Classes

`Aligner`	Use SpinDry to align two molecules.
`AlignmentPotential`
`Collapser`	Collapse stk.ConstructedMolecule to decrease enlarged bonds.
`CollapserMC`	Collapse molecule to decrease enlarged bonds using MC algorithm.
`ConstructedMoleculeTorsionCalculator`	Uses rdkit to extract all torsions in a molecule.
`ConstructedMoleculeTorsionResults`	Results class containing molecule torsions.
`Du`	Dummy of an stk.Atom.
`ETKDG`	Uses ETKDG v2 algorithm in `rdkit` to optimize a structure.
`EnergyResults`	Results class containing molecule energy.
`GulpUFFMDOptimizer`	Applies forcefield MD that can handle metal centres.
`GulpUFFOptimizer`	Applies forcefield optimizers that can handle metal centres.
`MAEExtractor`	Extracts the lowest energy conformer from a .maegz file.
`MDAnalysis`	Converter for `stk.Molecule` to and from MDAnalysis.
`MMFF`	Use the MMFF force field in `rdkit` to optimize molecules.
`MMFFEnergy`	Uses the MMFF force field to calculate energies.
`MacroModelForceField`	Uses MacroModel force fields to optimize molecules.
`MacroModelMD`	Runs a molecular dynamics conformer search using MacroModel.
`MatchedTorsionCalculator`	Matches rdkit generated torsions with building block torsions.
`MetalOptimizer`	Applies forcefield optimizers in `rdkit` that can handle metals.
`MoleculeSplitter`	Split an stk.molecule into many with dummy atoms.
`MoleculeTransformer`	Split an stk.molecule into many with new functional groups.
`Network`	Definition of a `networkx` graph of an `stk.Molecule`.
`OpenBabel`	Use OpenBabel to optimize molecules with forcefields.
`OpenBabelEnergy`	Uses OpenBabel to calculate forcefield energies.
`Optimizer`	A base class for optimizers.
`OptimizerSequence`	Applies optimizers in sequence.
`OrcaEnergy`	Uses Orca to calculate energy and other properties.
`OrcaExtractor`	Extracts properties from Orca 4.2 output files.
`OrcaResults`	Results class containing molecule Orca properties.
`PlanarityCalculator`	Calculates measures of planarity of a molecule.
`PlanarityResults`	Results class containing molecule planarity measures.
`PositionedAtom`	A container for stk.Atom and a coordinate.
`RmsdCalculator`	Calculates the root mean square distance between molecules.
`RmsdMappedCalculator`	Calculates the root mean square distance between molecules.
`RmsdResults`	Results class containing RMSD measures.
`ShapeCalculator`	Calculates shape measures of a molecule.
`ShapeResults`	Results class containing molecule shape measures.
`TopologyExtractor`	Extractor of topology definitions from a molecule.
`TopologyInfo`	Extracted information of a topology.
`Torsion`	Represents a torsion angle in a molecule.
`TorsionCalculator`	Uses rdkit to extract all torsions in a molecule.
`TorsionInfo`	Holds additional info about ConstructedMoleculeTorsioned torsions.
`TorsionResults`	Results class containing molecule torsions.
`TryCatchOptimizer`	Try to optimize with a Optimizer, use another on failure.
`UFF`	Use the UFF force field in `rdkit` to optimize molecules.
`UFFEnergy`	Uses the UFF force field to calculate energies.
`UnitCell`	Unit cell information for periodic systems.
`XTB`	Uses GFN-xTB to optimize molecules.
`XTBCREST`	Uses GFN-n to run CREST on molecules.
`XTBEnergy`	Uses GFN-xTB to calculate energy and other properties.
`XTBExtractor`	Extracts properties from xTB output files.
`XTBFF`	Uses GFN-FF to optimize molecules.
`XTBFFCREST`	Uses GFN-FF to run CREST on molecules.
`XTBResults`	Results class containing molecule xTB properties.
`ZMatrix`	Converter for `stk.Molecule` to Z-Matrix.

Exceptions

`CalculatorError`
`ConvergenceError`
`ConversionError`
`DifferentAtomError`
`DifferentMoleculeError`
`ExpectedMetalError`
`ForceFieldError`
`ForceFieldSetupError`
`InputError`
`InvalidSolventError`
`LewisStructureError`
`NotCompletedError`
`NotStartedError`
`OptimizerError`
`PathError`
`SettingConflictError`
`WrapperNotInstalledError`

Modules

`stko.functional_groups`	Tools for functional_groups.
`stko.molecule_analysis`	Tools for molecular analysis.