opi.input.structures¶

Modules that hold Python objects representing chemical structures (i.e. atom types and coordinates) and structure files supported by ORCA.

Submodules¶

Classes¶

`Atom`	Class to model singular atom in a structure.
`DummyAtom`	Class to model dummy atom.
`EmbeddingPotential`	Class to model embedding potential
`GhostAtom`	Class to model ghost atom.
`PointCharge`	Class to model point charge.
`Coordinates`	Coordinates of an atom in Cartesian space.
`Structure`	Class to model internal structure for ORCA calculations.
`BaseStructureFile`	Class to model structure file.
`GzmtFile`	Class to model .gzmt structure file.
`PdbFile`	Class to model .pdb structure file.
`XyzFile`	Class to model .xyz structure file.

Package Contents¶

class opi.input.structures.Atom(element, *args, **kwargs)¶

Bases: _CoordLineWithElementBase

Class to model singular atom in a structure.

Parameters:

element (opi.utils.element.Element | str)
args (Any)
kwargs (Any)

element¶

Specify what element the atom is

Type:: Element
Return type:: opi.utils.element.Element

coordinates¶

Define coordinates in Cartesian space

Type:: Coordinates
Return type:: opi.input.structures.coordinates.Coordinates

fragment_id¶

Define id of fragment

Type:: int
Return type:: int | None

nuclear_charge¶

Define nuclear charge of atom

Type:: float | int
Return type:: float | None

mass¶

Define mass of atom

Type:: float | int
Return type:: float | None

append_str¶

Append an arbitrary string to coordinate line if needed

Type:: str

_element: opi.utils.element.Element¶

property element: opi.utils.element.Element¶

Return type:: opi.utils.element.Element

class opi.input.structures.DummyAtom(*args, **kwargs)¶

Bases: _CoordLineWithElementBase

Class to model dummy atom.

Parameters:

args (Any)
kwargs (Any)

_element: Any | None = 'DA'¶

class opi.input.structures.EmbeddingPotential(charge, *args, **kwargs)¶

Bases: _CoordLineWithSymbolAndChargeBase

Class to model embedding potential

Parameters:

charge (float | int)
args (Any)
kwargs (Any)

_fmt_element()¶

Return type:: str

class opi.input.structures.GhostAtom(element, *args, **kwargs)¶

Bases: Atom

Class to model ghost atom.

Parameters:

element (opi.utils.element.Element | str)
args (Any)
kwargs (Any)

_fmt_element()¶

Return type:: str

class opi.input.structures.PointCharge(*args, **kwargs)¶

Bases: _CoordLineWithSymbolAndChargeBase

Class to model point charge.

Parameters:

args (Any)
kwargs (Any)

_element = 'Q'¶

class opi.input.structures.Coordinates(coordinates)¶

Coordinates of an atom in Cartesian space.

Can be initialized using a tuple, numpy arrays or another instance of Coordinates.

Parameters:: coordinates (Coordinates | tuple[int | float, int | float, int | float] | npt.NDArray[np.float64])

coordinates¶

Type:: Column vector with three rows.
Return type:: numpy.typing.NDArray[numpy.float64]

_coordinates: numpy.typing.NDArray[numpy.float64]¶

property coordinates: numpy.typing.NDArray[numpy.float64]¶

Return type:: numpy.typing.NDArray[numpy.float64]

to_list()¶

Returns coordinates as list

Return type:: list[float] | tuple[]

property x: numpy.float64¶

x-coordinate

Return type:: numpy.float64

property y: numpy.float64¶

y-coordinate

Return type:: numpy.float64

property z: numpy.float64¶

z-coordinate

Return type:: numpy.float64

class opi.input.structures.Structure(atoms, charge=0, multiplicity=1, origin=None)¶

Class to model internal structure for ORCA calculations.

Parameters:

atoms (opi.input.structures.atom.Atom | opi.input.structures.atom.DummyAtom | opi.input.structures.atom.EmbeddingPotential | opi.input.structures.atom.GhostAtom | opi.input.structures.atom.PointCharge | Sequence[opi.input.structures.atom.Atom | opi.input.structures.atom.DummyAtom | opi.input.structures.atom.EmbeddingPotential | opi.input.structures.atom.GhostAtom | opi.input.structures.atom.PointCharge] | Iterable[opi.input.structures.atom.Atom | opi.input.structures.atom.DummyAtom | opi.input.structures.atom.EmbeddingPotential | opi.input.structures.atom.GhostAtom | opi.input.structures.atom.PointCharge])
charge (int)
multiplicity (int)
origin (pathlib.Path | str | None)

atoms¶

Atoms in the molecule

Type:: list[Atom | DummyAtom | EmbeddingPotential | GhostAtom | PointCharge]
Return type:: list[opi.input.structures.atom.Atom | opi.input.structures.atom.DummyAtom | opi.input.structures.atom.EmbeddingPotential | opi.input.structures.atom.GhostAtom | opi.input.structures.atom.PointCharge]

charge¶

Charge of structure

Type:: int
Return type:: int

multiplicity¶

Multiplicity of structure

Type:: int
Return type:: int

origin¶

Origin of the molecule, usually path to a file or some identifier

Type:: Path | str

_atoms: list[opi.input.structures.atom.Atom | opi.input.structures.atom.DummyAtom | opi.input.structures.atom.EmbeddingPotential | opi.input.structures.atom.GhostAtom | opi.input.structures.atom.PointCharge] = []¶

property atoms: list[opi.input.structures.atom.Atom | opi.input.structures.atom.DummyAtom | opi.input.structures.atom.EmbeddingPotential | opi.input.structures.atom.GhostAtom | opi.input.structures.atom.PointCharge]¶

Return type:: list[opi.input.structures.atom.Atom | opi.input.structures.atom.DummyAtom | opi.input.structures.atom.EmbeddingPotential | opi.input.structures.atom.GhostAtom | opi.input.structures.atom.PointCharge]

_charge: int¶

property charge: int¶

Return type:: int

_multiplicity: int¶

property multiplicity: int¶

Return type:: int

origin: Any | None = None¶

classmethod combine_molecules(structure1, structure2)¶

function to combine two objects of Molecule class

Parameters:

structure1 (Structure) -- Define first structure to be combined
structure2 (Structure) -- Define second structure to be combined

Returns:

Structure

Return type:

Combined structure

format_orca()¶

Returns string representation of Molecule Iteratively calls Atom.format_orca() and compiles it all together to create string representation of Molecule

Returns:: String representation of Molecule
Return type:: str

add_atom(new_atom, position=None)¶

Adds Atom object at specified index. If index is None, Atom object appended to end of list

Parameters:

new_atom (Atom) -- Atom model to be added to self.atoms
position (int | None, default = None) -- position at which Atom is supposed to be added , default value None

Raises:

ValueError -- if index is an invalid value

Return type:

None

delete_atom(index)¶

Deletes Atom at specified index

Parameters:: index (int) -- specifies index of Atom to be deleted
Raises:: ValueError -- if index is invalid value
Return type:: None

replace_atom(new_atom, index)¶

replaces Atom at index with a new Atom object

Parameters:

new_atom (Atom | DummyAtom | EmbeddingPotential | GhostAtom | PointCharge) -- new Atom object to replace the old Atom object
index (int) -- index of Atom to be replaced

Raises:

ValueError -- if index is invalid value

Return type:

None

extract_substructure(indexes)¶

returns Molecule object that is a sub-molecule specified by indexes.

Parameters:: indexes (list[int]) -- specifies indexes of Atom objects to be extracted
Returns:: Molecule
Return type:: new Molecule object

update_coordinates(array)¶

Validates dimensions of array first replace all coordinates of all atoms in Molecule object. Calls Atom.update_coordinates() iteratively , replacing the Atom.coordinates with rows from array argument

Parameters:: array (npt.NDArray[np.float64]) -- new coordinates
Raises:: ValueError -- in the case of wrong dimensions
Return type:: None

to_xyz_block()¶

Function to generate XYZ block

Return type:: str

classmethod from_xyz(xyzfile, /, *, charge=0, multiplicity=1)¶

Function for reading a xyz file and converting it to a molecular Structure

Parameters:

xyzfile (Path | str | PathLike[str]) -- Name or path to xyz file
charge (int, default: 0) -- Charge of the molecule
multiplicity (int, default: 1) -- Electron spin multiplicity of the molecule

Returns:

`Structure`

Return type:

`Structure object extracted from file

classmethod from_smiles(smiles, /, *, charge=None, multiplicity=None)¶

Function to read SMILES string and convert string to 3D coordinate structure and create Molecule object with it to store in self.molecule.

Parameters:

smiles (str) -- SMILES string to be converted
charge (int | None) -- Charge of the molecule, will overwrite charge obtained from SMILES string
multiplicity (int | None) -- Electron spin multiplicity of the molecule, will overwrite multiplicity obtained from SMILES (which is always 1 by default)

Returns:

`Structure`

Return type:

`Structure object extracted from file

Raises:

RuntimeError -- If EmbedMolecule() is unsuccessful

classmethod from_rdkitmol(mol, /, *, charge=None, multiplicity=None)¶

Function to convert a RDKit Mol object to Structure object

Parameters:

mol (RdkitMol) -- RDKit Mol object to be converted
charge (int | None) -- Charge of the molecule, will overwrite charge obtained from RDKit Mol
multiplicity (int | None) -- Electron spin multiplicity of the molecule, will overwrite multiplicity obtained from RDKit Mol

Returns:

`Structure`

Return type:

Structure object created from information given by RDKit Mol object

to_rdkitmol(structure, /)¶

Function to convert Molecule object to RDKit Mol object The Structure is converted into XYZ file format, which is then read by RDKit.

Parameters:: structure (Structure) -- Molecule object to be converted
Returns:: RdkitMol
Return type:: RDKit Mol object generated from Structure object

__len__()¶

Return type:: int

class opi.input.structures.BaseStructureFile(file, /, *, charge=0, multiplicity=1)¶

Bases: abc.ABC

Class to model structure file. The structure file is directly passed to ORCA. This interface not read or modify the contents of the file.

Parameters:

file (pathlib.Path | str | os.PathLike[str])
charge (int)
multiplicity (int)

_type¶

Type of the structure file. Use as prefix for ORCA input: *<_type>file

Type:: str

_type: str¶

_file: pathlib.Path¶

property file: pathlib.Path¶

Return type:: pathlib.Path

charge = 0¶

multiplicity = 1¶

format_orca(*, full_path=False)¶

Format respectively line in ORCA input.

Parameters:: full_path (bool, default: False) -- True: Print full path to the structure in the ORCA input file. False: Print only the filename. This is usually the preferred way!
Return type:: str

copy_to(dest, /)¶

Copy the structure file to the destination.

Parameters:: dest (Path) -- Copy the self.file to dest. dest can point to a file or a folder. For details see documentation of shutil.copy().
Raises:: OSError -- If structure file cannot be copied.
Returns:: True if the file was copied, False otherwise.
Return type:: bool

class opi.input.structures.GzmtFile(file, /, *, charge=0, multiplicity=1)¶

Bases: BaseStructureFile

Class to model .gzmt structure file.

Parameters:

file (pathlib.Path | str | os.PathLike[str])
charge (int)
multiplicity (int)

_type = 'gzmt'¶

class opi.input.structures.PdbFile(file, /, *, charge=0, multiplicity=1)¶

Bases: BaseStructureFile

Class to model .pdb structure file.

Parameters:

file (pathlib.Path | str | os.PathLike[str])
charge (int)
multiplicity (int)

_type = 'pdb'¶

class opi.input.structures.XyzFile(file, /, *, charge=0, multiplicity=1)¶

Bases: BaseStructureFile

Class to model .xyz structure file.

Parameters:

file (pathlib.Path | str | os.PathLike[str])
charge (int)
multiplicity (int)

_type = 'xyz'¶