interfaces

class isicle.interfaces.FileParserInterface[source]

Abstract base class for file parser interface. All file parsers conform to this definition.

_abc_impl = <_abc._abc_data object>

abstract load(path: str)[source]: Load in the data file

abstract parse()[source]: Extract relevant information from data

class isicle.interfaces.GeometryInterface[source]

_abc_impl = <_abc._abc_data object>

abstract get_total_partial_charge()[source]: Determine total partial charge of molecule

abstract to_inchi(path: str)[source]: Return InChI representation

abstract to_mol(path: str)[source]: Returns RDKit Mol object for this Geometry.

abstract to_smarts(path: str)[source]: Return SMARTS representation

abstract to_smiles(path: str)[source]: Return SMILES representation

class isicle.interfaces.WrapperInterface[source]

Abstract base class for wrapper interfaces.

_abc_impl = <_abc._abc_data object>

abstract configure()[source]: Configure the run.

abstract finish(path: str)[source]: Finalize, parse, return result object.

abstract run()[source]: Execute/submit the run.

abstract set_geometry()[source]: Assign the input geometry.

abstract submit()[source]: Configure the run.

class isicle.interfaces.XYZGeometryInterface[source]

_abc_impl = <_abc._abc_data object>

abstract dft()[source]: Optimize geometry using density function theory (DFT) methods.

abstract get___dict__()[source]: Return a copy of this object’s attributes dictionary

abstract get_atom_indices()[source]: Extract indices of each atom from the internal geometry.

abstract get_natoms()[source]: Count number of atoms

abstract md()[source]: Optimize geometry using molecule dynamics methods (MD).

abstract to_xyzblock()[source]: Get XYZ text for this structure.