LibBase API index

class UnifiedChemicalSystem

A class representing a chemical system in the Amsterdam Modeling Suite

__init__(*args, **kwargs)

Overloaded function.

  1. __init__(self: scm_libbase_internal.UnifiedChemicalSystem) -> None

Creates a new, empty ChemicalSystem.

  1. __init__(self: scm_libbase_internal.UnifiedChemicalSystem, system_block: str) -> None

Creates a new ChemicalSystem from a System block string.

__len__(self: UnifiedChemicalSystem) → int
__str__(self: UnifiedChemicalSystem) → str
add_all_atoms_to_region(self: UnifiedChemicalSystem, region: str) → None

Adds all of the system’s atoms to a region.

add_atom(*args, **kwargs)

Overloaded function.

  1. add_atom(self: scm_libbase_internal.UnifiedChemicalSystem, atom: scm_libbase_internal.UnifiedAtom) -> None

Adds a copy of an Atom to a ChemicalSystem.

  1. add_atom(self: scm_libbase_internal.UnifiedChemicalSystem, atom: scm_libbase_internal.UnifiedAtom, coords: numpy.ndarray[numpy.float64[3, 1]], unit: str = ‘angstrom’) -> None

Adds a copy of an Atom to a ChemicalSystem.

  1. add_atom(self: scm_libbase_internal.UnifiedChemicalSystem, Z: int, coords: numpy.ndarray[numpy.float64[3, 1]], unit: str = ‘angstrom’) -> None

Adds a new Atom of a given atomic number to the ChemicalSystem.

  1. add_atom(self: scm_libbase_internal.UnifiedChemicalSystem, element: scm_libbase_internal.UnifiedElement, coords: numpy.ndarray[numpy.float64[3, 1]], unit: str = ‘angstrom’) -> None

Adds a new Atom of a given Element to the ChemicalSystem.

  1. add_atom(self: scm_libbase_internal.UnifiedChemicalSystem, symbol: str, coords: numpy.ndarray[numpy.float64[3, 1]], unit: str = ‘angstrom’) -> None

Adds a new Atom to the ChemicalSystem given its symbol.

add_atom_to_region(*args, **kwargs)

Overloaded function.

  1. add_atom_to_region(self: scm_libbase_internal.UnifiedChemicalSystem, atom: int, region: str) -> None

Adds an atom to a region.

  1. add_atom_to_region(self: scm_libbase_internal.UnifiedChemicalSystem, atom: scm_libbase_internal.UnifiedAtom, region: str) -> None

Adds an atom to a region.

add_atoms_to_region(self: UnifiedChemicalSystem, atom_indices: numpy.ndarray[numpy.int32[m, 1]], region: str) → None

Adds multiple atoms to a region, given their atom indices.

add_hydrogen_atoms(*args, **kwargs)

Overloaded function.

  1. add_hydrogen_atoms(self: scm_libbase_internal.UnifiedChemicalSystem, atom_indices: List[int]) -> None

Add missing hydrogen atoms to organic compounds.

  1. add_hydrogen_atoms(self: scm_libbase_internal.UnifiedChemicalSystem) -> None

Add missing hydrogen atoms to organic compounds.

add_other(self: UnifiedChemicalSystem, other: UnifiedChemicalSystem) → None

Merges another ChemicalSystem into this one.

align_to(self: UnifiedChemicalSystem, other: UnifiedChemicalSystem) → None

Translate and rotate the system to maximally align it with ‘other’.

static all_from_input(input_file: scm_libbase_internal.InputFile) → Dict[str, UnifiedChemicalSystem]

Constructs and returns ChemicalSystems for all System (and LoadSystem) blocks in an InputFile.

apply_strain(self: UnifiedChemicalSystem, strain_matrix: numpy.ndarray[numpy.float64[m, n]]) → None

Apply a strain deformation to a periodic system.

apply_strain_voigt(self: UnifiedChemicalSystem, strain_voigt: List[float]) → None

Apply a strain deformation to a periodic system.

atom_index(self: UnifiedChemicalSystem, atom: scm_libbase_internal.UnifiedAtom) → int

Given an Atom instance, returns its index in ChemicalSystem.atoms.

atom_is_in_ring(*args, **kwargs)

Overloaded function.

  1. atom_is_in_ring(self: scm_libbase_internal.UnifiedChemicalSystem, atom: int) -> bool

Checks if an atom is part of any ring.

  1. atom_is_in_ring(self: scm_libbase_internal.UnifiedChemicalSystem, atom: scm_libbase_internal.UnifiedAtom) -> bool

Checks if an atom is part of any ring.

atomic_properties_enabled(self: UnifiedChemicalSystem, group_prefix: str) → bool

Checks if a group of atomic properties is enabled or not.

bond_cuts_molecule(*args, **kwargs)

Overloaded function.

  1. bond_cuts_molecule(self: scm_libbase_internal.UnifiedChemicalSystem, from_atom: int, to_atom: int) -> bool

Checks if removing the bonds between two atoms would cut the graph into two disjoint subgraphs.

  1. bond_cuts_molecule(self: scm_libbase_internal.UnifiedChemicalSystem, from_atom: scm_libbase_internal.UnifiedAtom, to_atom: scm_libbase_internal.UnifiedAtom) -> bool

Checks if removing the bonds between two atoms would cut the graph into two disjoint subgraphs.

bounding_box_volume(self: UnifiedChemicalSystem, unit: str = 'angstrom3') → float

Volume of the bounding box.

center_of_mass(self: UnifiedChemicalSystem, unit: str = 'angstrom') → numpy.ndarray[numpy.float64[3, 1]]

Position of the center of mass.

check_molecule_symmetry(self: UnifiedChemicalSystem, label: str, tolerance: float = 1e-07) → bool

Checks if a molecule has a particular symmetry given by a Schoenflies symbol.

contains_atom(self: UnifiedChemicalSystem, atom: scm_libbase_internal.UnifiedAtom) → bool

Checks if an Atom instance is part of a ChemicalSystem.

copy(self: UnifiedChemicalSystem) → UnifiedChemicalSystem

Creates a deep copy of the ChemicalSystem.

density(self: UnifiedChemicalSystem, unit: str = 'dalton/angstrom3') → float

Returns the density of the system in the specified unit. Only valid for 3D periodic systems.

deselect_all(self: UnifiedChemicalSystem) → None

Deselects all atoms, or in other words: clears the current selection.

deselect_atom(*args, **kwargs)

Overloaded function.

  1. deselect_atom(self: scm_libbase_internal.UnifiedChemicalSystem, arg0: int) -> None

Selects an atom given its index.

  1. deselect_atom(self: scm_libbase_internal.UnifiedChemicalSystem, arg0: scm_libbase_internal.UnifiedAtom) -> None

Selects an instance of an atom.

deselect_atoms(self: UnifiedChemicalSystem, atom_indices: numpy.ndarray[numpy.int32[m, 1]]) → None

Deselects multiple atoms at once, given their atom indices.

deselect_atoms_if(self: UnifiedChemicalSystem, pred: Callable[[scm_libbase_internal.UnifiedAtom], bool]) → None

Deselects atoms based on a predicate function.

determine_species(self: UnifiedChemicalSystem, comp: Callable[[scm_libbase_internal.UnifiedAtom, scm_libbase_internal.UnifiedAtom], bool]) → Tuple[int, List[int], List[int]]

Determines the present atomic species, based on a user defined comparator function.

disable_atomic_properties(self: UnifiedChemicalSystem, group_prefix: str) → None

Disables the use of a group of atomic properties. Any set properties within the group will be discarded.

do_regions_intersect(self: UnifiedChemicalSystem, regionA: str, regionB: str) → bool

Checks if two regions or region expressions intersect, i.e. have at least one atom in common.

enable_atomic_properties(self: UnifiedChemicalSystem, group_prefix: str) → None

Enables the use of a group of atomic properties.

extract_atoms(self: UnifiedChemicalSystem, atom_indices: List[int]) → UnifiedChemicalSystem

Returns a new system build from a subset of atoms.

formula(self: UnifiedChemicalSystem) → str

Chemical formula in Hill notation, e.g. H2O or CH4.

static from_in(filename: str, name: str = '') → UnifiedChemicalSystem

Constructs and returns a new ChemicalSystem from a (possibly named) System block in an AMS input file.

static from_input(input_file: scm_libbase_internal.InputFile, prefix: str) → UnifiedChemicalSystem

Constructs and returns a new ChemicalSystem from an InputFile instance, given a prefix, e.g. ‘System[1]%’.

static from_kf(*args, **kwargs)

Overloaded function.

  1. from_kf(filename: str, section: str = ‘Molecule’) -> scm_libbase_internal.UnifiedChemicalSystem

Constructs and returns a new ChemicalSystem from a section on a KF file.

  1. from_kf(kf: scm_libbase_internal.KFFile, section: str = ‘Molecule’) -> scm_libbase_internal.UnifiedChemicalSystem

Constructs and returns a new ChemicalSystem from a section on a KF file.

static from_xyz(filename: str) → UnifiedChemicalSystem

Constructs and returns a new ChemicalSystem from an extended XYZ file.

geometric_center(self: UnifiedChemicalSystem, unit: str = 'angstrom') → numpy.ndarray[numpy.float64[3, 1]]

Position of the geometric center.

get_atoms_in_region(self: UnifiedChemicalSystem, region: str) → numpy.ndarray[numpy.int32[m, 1]]

Returns a sorted array of atom indices of all atoms in a region or region expression.

get_atoms_outside_region(self: UnifiedChemicalSystem, region: str) → numpy.ndarray[numpy.int32[m, 1]]

Returns a sorted array of atom indices of all atoms outside of a region or region expression.

get_distance(*args, **kwargs)

Overloaded function.

  1. get_distance(self: scm_libbase_internal.UnifiedChemicalSystem, a: int, b: int, unit: str = ‘angstrom’) -> float

Measures the distance between two atoms.

  1. get_distance(self: scm_libbase_internal.UnifiedChemicalSystem, a: scm_libbase_internal.UnifiedAtom, b: scm_libbase_internal.UnifiedAtom, unit: str = ‘angstrom’) -> float

Measures the distance between two atoms.

get_fractional_coordinate(self: UnifiedChemicalSystem, atom: scm_libbase_internal.UnifiedAtom, unit: str = 'angstrom') → numpy.ndarray[numpy.float64[3, 1]]

Returns the fractional coordinate of a single atom with respect to the cell. In non-periodic directions the plain coordinates are returned in the specified unit.

get_fractional_coordinates(self: UnifiedChemicalSystem, unit: str = 'angstrom') → numpy.ndarray[numpy.float64[m, 3]]

Returns the fractional coordinates of all atoms with respect to the cell. In non-periodic directions the plain coordinates are returned in the specified unit.

static get_operands_in_region_expression(region_expression: str) → List[str]

Returns a sorted list of all unique operands used in a region expression.

get_regions_of_atom(*args, **kwargs)

Overloaded function.

  1. get_regions_of_atom(self: scm_libbase_internal.UnifiedChemicalSystem, atom: int) -> List[str]

Returns an alphabetically sorted list of the names of all regions an atom is part of.

  1. get_regions_of_atom(self: scm_libbase_internal.UnifiedChemicalSystem, atom: scm_libbase_internal.UnifiedAtom) -> List[str]

Returns an alphabetically sorted list of the names of all regions an atom is part of.

get_selected_atoms(self: UnifiedChemicalSystem) → numpy.ndarray[numpy.int32[m, 1]]

Returns an array of indices of all selected atoms.

get_species(self: UnifiedChemicalSystem, comp: Callable[[scm_libbase_internal.UnifiedAtom, scm_libbase_internal.UnifiedAtom], bool]) → List[List[int]]

Determines the present atomic species, based on a user defined comparator function.

guess_bonds(self: UnifiedChemicalSystem) → None

Guesses bonds based on the atomic elements and the geometry. Keeps existing bonds.

has_bonds(self: UnifiedChemicalSystem) → bool

Checks if the system has any bonding information.

has_ghost_atoms(self: UnifiedChemicalSystem) → bool

Checks whether the ChemicalSystem contains any Ghost atoms.

has_lattice(self: UnifiedChemicalSystem) → bool

Checks if the system has a lattice.

has_region(self: UnifiedChemicalSystem, region: str) → bool

Checks if a region exists in the system, given its region name.

has_same_atoms(*args, **kwargs)

Overloaded function.

  1. has_same_atoms(self: scm_libbase_internal.UnifiedChemicalSystem, other: scm_libbase_internal.UnifiedChemicalSystem, properties: List[str] = []) -> bool

Checks if two systems have identical atoms in the same order.

  1. has_same_atoms(self: scm_libbase_internal.UnifiedChemicalSystem, other: scm_libbase_internal.UnifiedChemicalSystem, comp: Callable[[scm_libbase_internal.UnifiedAtom, scm_libbase_internal.UnifiedAtom], bool]) -> bool

Checks if two systems have identical atoms in the same order given a user defined comparator.

has_same_coords(self: UnifiedChemicalSystem, other: UnifiedChemicalSystem, tol: float = 0.001, unit: str = 'angstrom') → bool

Checks if the atomic coordinates of two systems are within a threshold of each other.

has_same_geometry(self: UnifiedChemicalSystem, other: UnifiedChemicalSystem, tol: float = 0.001, unit: str = 'angstrom') → bool

Checks if the atomic coordinates and lattice vectors of two systems are within a threshold of each other.

has_same_regions(self: UnifiedChemicalSystem, other: UnifiedChemicalSystem) → bool

Checks if two systems have identical regions, meaning region names and included atom indices.

has_same_selection(self: UnifiedChemicalSystem, other: UnifiedChemicalSystem, consider_selection_order: bool = False) → bool

Checks if two systems have the same atom selection.

inertia_tensor(self: UnifiedChemicalSystem) → numpy.ndarray[numpy.float64[3, 3]]

Returns the system’s inertia tensor as a 3x3 matrix (units amu*angstrom^2).

invert_selection(self: UnifiedChemicalSystem) → None

Inverts the set of selected atoms.

is_atom_in_region(*args, **kwargs)

Overloaded function.

  1. is_atom_in_region(self: scm_libbase_internal.UnifiedChemicalSystem, atom: int, region: str) -> bool

Checks if an atom is in a region or region expression.

  1. is_atom_in_region(self: scm_libbase_internal.UnifiedChemicalSystem, atom: scm_libbase_internal.UnifiedAtom, region: str) -> bool

Checks if an atom is in a region or region expression.

is_atom_outside_region(*args, **kwargs)

Overloaded function.

  1. is_atom_outside_region(self: scm_libbase_internal.UnifiedChemicalSystem, atom: int, region: str) -> bool

Checks if an atom is outside of a region or region expression.

  1. is_atom_outside_region(self: scm_libbase_internal.UnifiedChemicalSystem, atom: scm_libbase_internal.UnifiedAtom, region: str) -> bool

Checks if an atom is outside of a region or region expression.

is_atom_selected(*args, **kwargs)

Overloaded function.

  1. is_atom_selected(self: scm_libbase_internal.UnifiedChemicalSystem, arg0: int) -> bool

Checks if an atom is currently selected, given its index.

  1. is_atom_selected(self: scm_libbase_internal.UnifiedChemicalSystem, arg0: scm_libbase_internal.UnifiedAtom) -> None

Checks if an instance of an atom is currently selected.

is_linear(self: UnifiedChemicalSystem) → bool

Checks is a ChemicalSystem is linear.

static is_valid_region_name(name: str) → bool

Checks if a string is a valid region name.

make_selection_cappable(self: UnifiedChemicalSystem) → None

Extends the current selection but does not cross single bonds, unless they are to hydrogen atoms.

map_atoms(*args, **kwargs)

Overloaded function.

  1. map_atoms(self: scm_libbase_internal.UnifiedChemicalSystem, start_range: float) -> Tuple[bool, numpy.ndarray[numpy.int32[m, 3]]]

Maps all atoms into a unit cell from [start_range:start_range+1] in fractional coordinates.

  1. map_atoms(self: scm_libbase_internal.UnifiedChemicalSystem, start_range: numpy.ndarray[numpy.float64[m, 1]]) -> Tuple[bool, numpy.ndarray[numpy.int32[m, 3]]]

Maps all atoms into a unit cell from [start_range:start_range+1] in fractional coordinates.

map_atoms_around_atom(*args, **kwargs)

Overloaded function.

  1. map_atoms_around_atom(self: scm_libbase_internal.UnifiedChemicalSystem, atom: scm_libbase_internal.UnifiedAtom) -> Tuple[bool, numpy.ndarray[numpy.int32[m, 3]]]

Map all atoms around the chosen atom that will be in the center of the new unit cell.

  1. map_atoms_around_atom(self: scm_libbase_internal.UnifiedChemicalSystem, atom: int) -> Tuple[bool, numpy.ndarray[numpy.int32[m, 3]]]

Map all atoms around the chosen atom that will be in the center of the new unit cell.

map_atoms_continuous(self: UnifiedChemicalSystem) → bool

Map all atoms that are bonded across the periodic boundary back.

molecule_indices(self: UnifiedChemicalSystem) → numpy.ndarray[numpy.int32[m, 1]]

Returns a num_atoms sized array mapping the atoms to connected molecules of the system.

molgraph_dijkstra(self: UnifiedChemicalSystem, from_atidx: int, dist_func: Callable[[int, int, scm_libbase_internal.UnifiedBond], float], to_atidx: int = -1) → Tuple[List[float], List[int], List[bool]]

General method implementing the Dijkstra algorithm on the molecular graph.

moments_of_inertia(self: UnifiedChemicalSystem) → Tuple[numpy.ndarray[numpy.float64[3, 1]], numpy.ndarray[numpy.float64[3, 3]]]

Calculates the system’s moments of inertia and the corresponding principal axes (units amu*angstrom^2).

moving_atoms_for_angle_change(self: scm_libbase_internal.UnifiedChemicalSystem, a: int, b: int, c: int, policy: scm_libbase_internal.UnifiedChemicalSystem.InternalCoordinateManipulationPolicy = <InternalCoordinateManipulationPolicy.SecondPartMoves: 1>) → numpy.ndarray[numpy.int32[m, 1]]

Determines which atoms will move when changing the angle between three atoms.

moving_atoms_for_dihedral_change(self: scm_libbase_internal.UnifiedChemicalSystem, a: int, b: int, c: int, d: int, policy: scm_libbase_internal.UnifiedChemicalSystem.InternalCoordinateManipulationPolicy = <InternalCoordinateManipulationPolicy.SecondPartMoves: 1>) → numpy.ndarray[numpy.int32[m, 1]]

Determines which atoms will move when changing the dihedral between four atoms.

moving_atoms_for_distance_change(self: scm_libbase_internal.UnifiedChemicalSystem, a: int, b: int, policy: scm_libbase_internal.UnifiedChemicalSystem.InternalCoordinateManipulationPolicy = <InternalCoordinateManipulationPolicy.LighterPartMoves: 2>) → numpy.ndarray[numpy.int32[m, 1]]

Determines which atoms will move when changing the distance between two atoms.

num_atoms_in_region(self: UnifiedChemicalSystem, region: str) → int

Returns the number of atoms in a region or region expression.

num_atoms_outside_region(self: UnifiedChemicalSystem, region: str) → int

Returns the number of atoms outside of a region or region expression.

num_molecules(self: UnifiedChemicalSystem) → int

Counts the number of connected molecules that are part of this system.

num_selected_atoms(self: UnifiedChemicalSystem) → int

The number of currently selected atoms.

perturb_coordinates(self: UnifiedChemicalSystem, noise_level: float, unit: str = 'angstrom') → None

Perturb the atomic coordinates by adding random numbers between to each Cartesian component.

perturb_lattice(self: UnifiedChemicalSystem, noise_level: float) → None

Perturb the lattice vectors by applying a random strain.

remove_all_regions(self: UnifiedChemicalSystem) → None

Removes all regions. All atoms will keep existing, but will not longer be part of any region.

remove_atom(self: UnifiedChemicalSystem, atom_index: int) → None

Removes a single atom from the system, given its index.

remove_atom_from_all_regions(*args, **kwargs)

Overloaded function.

  1. remove_atom_from_all_regions(self: scm_libbase_internal.UnifiedChemicalSystem, atom: int) -> None

Removes an atom from all regions.

  1. remove_atom_from_all_regions(self: scm_libbase_internal.UnifiedChemicalSystem, atom: scm_libbase_internal.UnifiedAtom) -> None

Removes an atom from all regions.

remove_atom_from_region(*args, **kwargs)

Overloaded function.

  1. remove_atom_from_region(self: scm_libbase_internal.UnifiedChemicalSystem, atom: int, region: str) -> None

Removes an atom from a region.

  1. remove_atom_from_region(self: scm_libbase_internal.UnifiedChemicalSystem, atom: scm_libbase_internal.UnifiedAtom, region: str) -> None

Removes an atom from a region.

remove_atoms(self: UnifiedChemicalSystem, atom_indices: numpy.ndarray[numpy.int32[m, 1]]) → None

Removes multiple atoms from the system, given their atom indices.

remove_atoms_from_region(self: UnifiedChemicalSystem, atom_indices: numpy.ndarray[numpy.int32[m, 1]], region: str) → None

Adds multiple atoms to a region, given their atom indices.

remove_region(self: UnifiedChemicalSystem, region: str) → None

Removes a region. Atoms in that region will keep existing, but will not longer be part of that region.

reorder_atoms(self: UnifiedChemicalSystem, atom_order: List[int]) → None

Reorders the system’s atoms given a list of atom indices in the desired order.

static rmsd(a: UnifiedChemicalSystem, b: UnifiedChemicalSystem, align: bool, unit: str = 'angstrom') → float

Computes the RMSD between two systems. ‘align’: whether or not the systems should be roto-translated as to maximize the RMSD.

rotate(self: UnifiedChemicalSystem, rot_mat: numpy.ndarray[numpy.float64[3, 3]]) → None

Rotate the system according to the rotation matrix.

rotation_axis_for_angle_change(self: UnifiedChemicalSystem, arg0: int, arg1: int, arg2: int) → numpy.ndarray[numpy.float64[3, 1]]

Determines the rotation axis for changing the angle between three atoms.

static rotation_matrix_minimizing_rmsd(a: UnifiedChemicalSystem, b: UnifiedChemicalSystem) → numpy.ndarray[numpy.float64[3, 3]]

Given two chemical systems, returns the rotation matrix that minimizes the RMSD.

select_all(self: UnifiedChemicalSystem) → None

Selects all atoms.

select_atom(*args, **kwargs)

Overloaded function.

  1. select_atom(self: scm_libbase_internal.UnifiedChemicalSystem, arg0: int) -> None

Selects an atom given its index.

  1. select_atom(self: scm_libbase_internal.UnifiedChemicalSystem, arg0: scm_libbase_internal.UnifiedAtom) -> None

Selects an instance of an atom.

select_atom_close_to_origin(self: UnifiedChemicalSystem) → None

Selects the atom that is closest to the origin of the coordinate system.

select_atoms(self: UnifiedChemicalSystem, atom_indices: numpy.ndarray[numpy.int32[m, 1]]) → None

Selects multiple atoms at once, given their atom indices.

select_atoms_if(self: UnifiedChemicalSystem, pred: Callable[[scm_libbase_internal.UnifiedAtom], bool]) → None

Selects atoms based on a predicate function.

select_atoms_of_same_type(self: UnifiedChemicalSystem) → None

Selects all atoms whose element is the same as of a currently selected atom.

select_connected(self: UnifiedChemicalSystem) → None

Selects all atoms bonded to the currently selected atoms.

select_connected_if(self: UnifiedChemicalSystem, pred: Callable[[scm_libbase_internal.UnifiedAtom, scm_libbase_internal.UnifiedAtom, scm_libbase_internal.UnifiedBond], bool]) → None

Selects atoms bonded to the currently selected atoms based on a predicate function.

select_molecule(self: UnifiedChemicalSystem) → None

Using the bonds, selects entire molecules that include any currently selected atom.

select_molecule_if(self: UnifiedChemicalSystem, pred: Callable[[scm_libbase_internal.UnifiedAtom, scm_libbase_internal.UnifiedAtom, scm_libbase_internal.UnifiedBond], bool]) → None

Using the bonds and a predicate function, selects all molecules that include a currently selected atom.

select_region(self: UnifiedChemicalSystem, region: str) → None

Selects atoms in a region or region expression.

select_within_radius(self: UnifiedChemicalSystem, radius: float, unit: str = 'angstrom') → None

Selects all atoms within a given radius of any of the currently selected atoms.

set_angle(*args, **kwargs)

Overloaded function.

  1. set_angle(self: scm_libbase_internal.UnifiedChemicalSystem, a: int, b: int, c: int, angle: float, policy: scm_libbase_internal.UnifiedChemicalSystem.InternalCoordinateManipulationPolicy = <InternalCoordinateManipulationPolicy.SecondPartMoves: 1>) -> None

Sets the angle between three atoms by moving atoms according to a policy.

  1. set_angle(self: scm_libbase_internal.UnifiedChemicalSystem, a: int, b: int, c: int, angle: float, unit: str, policy: scm_libbase_internal.UnifiedChemicalSystem.InternalCoordinateManipulationPolicy = <InternalCoordinateManipulationPolicy.SecondPartMoves: 1>) -> None

Sets the angle between three atoms by moving atoms according to a policy.

  1. set_angle(self: scm_libbase_internal.UnifiedChemicalSystem, a: int, b: int, c: int, angle: float, rotation_axis: numpy.ndarray[numpy.float64[3, 1]], moving_atoms: numpy.ndarray[numpy.int32[m, 1]]) -> None

Sets the angle between three atoms by moving a specified set of atoms.

  1. set_angle(self: scm_libbase_internal.UnifiedChemicalSystem, a: int, b: int, c: int, angle: float, unit: str, rotation_axis: numpy.ndarray[numpy.float64[3, 1]], moving_atoms: numpy.ndarray[numpy.int32[m, 1]]) -> None

Sets the angle between three atoms by moving a specified set of atoms.

set_atom(self: UnifiedChemicalSystem, atom_index: int, atom: scm_libbase_internal.UnifiedAtom) → None

Safe assignment of an Atom instance to atoms[atom_index].

set_atoms_in_region(self: UnifiedChemicalSystem, atom_indices: numpy.ndarray[numpy.int32[m, 1]], region: str) → None

Creates or sets an entire region given the indices of the atoms to be part of the region.

set_density(self: UnifiedChemicalSystem, target_density: float, unit: str = 'dalton/angstrom3') → None

Applies a uniform strain to match the specified target density. Only valid for 3D periodic systems.

set_dihedral(*args, **kwargs)

Overloaded function.

  1. set_dihedral(self: scm_libbase_internal.UnifiedChemicalSystem, a: int, b: int, c: int, d: int, angle: float, policy: scm_libbase_internal.UnifiedChemicalSystem.InternalCoordinateManipulationPolicy = <InternalCoordinateManipulationPolicy.SecondPartMoves: 1>) -> None

Sets the dihedral between four atoms by moving atoms according to a policy.

  1. set_dihedral(self: scm_libbase_internal.UnifiedChemicalSystem, a: int, b: int, c: int, d: int, angle: float, unit: str, policy: scm_libbase_internal.UnifiedChemicalSystem.InternalCoordinateManipulationPolicy = <InternalCoordinateManipulationPolicy.SecondPartMoves: 1>) -> None

Sets the dihedral between four atoms by moving atoms according to a policy.

  1. set_dihedral(self: scm_libbase_internal.UnifiedChemicalSystem, a: int, b: int, c: int, d: int, angle: float, moving_atoms: numpy.ndarray[numpy.int32[m, 1]]) -> None

Sets the dihedral between four atoms by moving a specified set of atoms.

  1. set_dihedral(self: scm_libbase_internal.UnifiedChemicalSystem, a: int, b: int, c: int, d: int, angle: float, unit: str, moving_atoms: numpy.ndarray[numpy.int32[m, 1]]) -> None

Sets the dihedral between four atoms by moving a specified set of atoms.

set_distance(*args, **kwargs)

Overloaded function.

  1. set_distance(self: scm_libbase_internal.UnifiedChemicalSystem, a: int, b: int, dist: float, policy: scm_libbase_internal.UnifiedChemicalSystem.InternalCoordinateManipulationPolicy = <InternalCoordinateManipulationPolicy.LighterPartMoves: 2>) -> None

Sets the distance between two atoms by moving atoms according to a policy.

  1. set_distance(self: scm_libbase_internal.UnifiedChemicalSystem, a: int, b: int, dist: float, unit: str, policy: scm_libbase_internal.UnifiedChemicalSystem.InternalCoordinateManipulationPolicy = <InternalCoordinateManipulationPolicy.LighterPartMoves: 2>) -> None

Sets the distance between two atoms by moving atoms according to a policy.

  1. set_distance(self: scm_libbase_internal.UnifiedChemicalSystem, a: int, b: int, dist: float, moving_atoms: numpy.ndarray[numpy.int32[m, 1]]) -> None

Sets the distance between two atoms by moving a specified set of atoms.

  1. set_distance(self: scm_libbase_internal.UnifiedChemicalSystem, a: int, b: int, dist: float, unit: str, moving_atoms: numpy.ndarray[numpy.int32[m, 1]]) -> None

Sets the distance between two atoms by moving a specified set of atoms.

set_fractional_coordinates(self: UnifiedChemicalSystem, frac_coords: numpy.ndarray[numpy.float64[m, 3]], unit: str = 'angstrom') → None

Sets the fractional coordinates of all atoms. In non-periodic directions the plain coordinates should be passed in the specified unit.

set_lattice_displacements_from_minimum_image_convention(self: UnifiedChemicalSystem) → None

Applies the minimum image convention which sets the lattice_displacements for all bonds to be the shortest possible.

set_num_lattice_vectors(self: UnifiedChemicalSystem, nvec: int) → None

Sets the number of lattice vectors.

set_selected_atoms(self: UnifiedChemicalSystem, atom_indices: numpy.ndarray[numpy.int32[m, 1]]) → None

Sets the selection to the given atom indices. Any previous selection is cleared.

shortest_path_between(*args, **kwargs)

Overloaded function.

  1. shortest_path_between(self: scm_libbase_internal.UnifiedChemicalSystem, from_atom: int, to_atom: int, dist_func: Callable[[int, int, scm_libbase_internal.UnifiedBond], float]) -> Optional[List[int]]

Returns the shortest path between two atoms (using a custom distance function).

  1. shortest_path_between(self: scm_libbase_internal.UnifiedChemicalSystem, from_atom: int, to_atom: int) -> Optional[List[int]]

Returns the shortest path between two atoms (measured in number of hops).

  1. shortest_path_between(self: scm_libbase_internal.UnifiedChemicalSystem, from_atom: scm_libbase_internal.UnifiedAtom, to_atom: scm_libbase_internal.UnifiedAtom, dist_func: Callable[[int, int, scm_libbase_internal.UnifiedBond], float]) -> Optional[List[int]]

Returns the shortest path between two atoms (using a custom distance function).

  1. shortest_path_between(self: scm_libbase_internal.UnifiedChemicalSystem, from_atom: scm_libbase_internal.UnifiedAtom, to_atom: scm_libbase_internal.UnifiedAtom) -> Optional[List[int]]

Returns the shortest path between two atoms (measured in number of hops).

shortest_path_length_between(*args, **kwargs)

Overloaded function.

  1. shortest_path_length_between(self: scm_libbase_internal.UnifiedChemicalSystem, from_atom: int, to_atom: int, dist_func: Callable[[int, int, scm_libbase_internal.UnifiedBond], float]) -> float

Returns the lengths of the shortest path between two atoms (measured using a custom distance function).

  1. shortest_path_length_between(self: scm_libbase_internal.UnifiedChemicalSystem, from_atom: int, to_atom: int) -> float

Returns the length of the shortest path between two atoms (measured in number of hops).

  1. shortest_path_length_between(self: scm_libbase_internal.UnifiedChemicalSystem, from_atom: scm_libbase_internal.UnifiedAtom, to_atom: scm_libbase_internal.UnifiedAtom, dist_func: Callable[[int, int, scm_libbase_internal.UnifiedBond], float]) -> float

Returns the lengths of the shortest path between two atoms (measured using a custom distance function).

  1. shortest_path_length_between(self: scm_libbase_internal.UnifiedChemicalSystem, from_atom: scm_libbase_internal.UnifiedAtom, to_atom: scm_libbase_internal.UnifiedAtom) -> float

Returns the length of the shortest path between two atoms (measured in number of hops).

shortest_path_lengths_from(*args, **kwargs)

Overloaded function.

  1. shortest_path_lengths_from(self: scm_libbase_internal.UnifiedChemicalSystem, from_atom: int, dist_func: Callable[[int, int, scm_libbase_internal.UnifiedBond], float]) -> List[float]

Returns the lengths of all shortest paths from a source atom using a custom distance function.

  1. shortest_path_lengths_from(self: scm_libbase_internal.UnifiedChemicalSystem, from_atom: int) -> List[float]

Returns the lengths (in number of hops) of all shortest paths from a source atom.

  1. shortest_path_lengths_from(self: scm_libbase_internal.UnifiedChemicalSystem, from_atom: scm_libbase_internal.UnifiedAtom, dist_func: Callable[[int, int, scm_libbase_internal.UnifiedBond], float]) -> List[float]

Returns the lengths of all shortest paths from a source atom using a custom distance function.

  1. shortest_path_lengths_from(self: scm_libbase_internal.UnifiedChemicalSystem, from_atom: scm_libbase_internal.UnifiedAtom) -> List[float]

Returns the lengths (in number of hops) of all shortest paths from a source atom.

slice_layers(self: UnifiedChemicalSystem, ref_atom: int, num_layers: int, miller: numpy.ndarray[numpy.int32[3, 1]], translate: float = 0.0, unit: str = 'angstrom') → None

Slice a 3D cell to create a 2D slab by specifying the amount of layers in the resulting slab.

slice_thickness(self: UnifiedChemicalSystem, ref_atom: int, top: float, bottom: float, miller: numpy.ndarray[numpy.int32[3, 1]], translate: float = 0.0, unit: str = 'angstrom') → None

Slice a 3D cell to create a 2D slab by specifying the upper and lower bound of the resulting slab.

sort_atoms(self: UnifiedChemicalSystem, comp: Callable[[scm_libbase_internal.UnifiedAtom, scm_libbase_internal.UnifiedAtom], bool]) → None

Sorts the system’s atoms according to a user defined comparator function.

sorted_atom_order(self: UnifiedChemicalSystem, comp: Callable[[scm_libbase_internal.UnifiedAtom, scm_libbase_internal.UnifiedAtom], bool]) → List[int]

Returns the atom order based on a user defined comparator function as a list of atom indices.

split(self: UnifiedChemicalSystem, part_indices: numpy.ndarray[numpy.int32[m, 1]]) → List[UnifiedChemicalSystem]

Splits the system into parts and returns a list of these parts as separate systems.

split_into_molecules(self: UnifiedChemicalSystem) → List[UnifiedChemicalSystem]

Splits the system into individual molecules based on the connectivity between atoms.

supercell(self: UnifiedChemicalSystem, supercell: numpy.ndarray[numpy.int32[m, 1]]) → None

Create a supercell by scaling the lattice vectors.

supercell_trafo(self: UnifiedChemicalSystem, supercell: numpy.ndarray[numpy.int32[m, n]]) → None

Create a supercell by creating the matrix product of the lattice vectors and the supercell.

symmetrize(self: UnifiedChemicalSystem) → str

Symmetrizes a system, using either symmetrize_molecule or symmetrize_cell, depending on periodicity.

symmetrize_cell(self: UnifiedChemicalSystem, precision: float = 0.1) → Tuple[int, str, str]

Symmetrize a 3D cell and return the symmetry symbols (number, international symbol, schoenflies symbol).

symmetrize_molecule(self: UnifiedChemicalSystem, tolerance: float = 0.05) → str

Symmetrizes and reorients a molecule.

to_conventional_cell(self: UnifiedChemicalSystem, precision: float = 0.1) → None

Convert a 2D or 3D cell to its conventional representation.

to_primitive_cell(self: UnifiedChemicalSystem, precision: float = 0.1) → None

Convert a 2D or 3D cell to its primitive representation.

total_mass(self: UnifiedChemicalSystem) → float

Total mass in atomic mass units (dalton).

translate(self: UnifiedChemicalSystem, shift: numpy.ndarray[numpy.float64[3, 1]], unit: str = 'angstrom') → None

Translates all atoms in the ChemicalSystem by a vector.

write_in(self: UnifiedChemicalSystem, filename: str) → None

Writes a ChemicalSystem to file as an AMS System block.

write_kf(*args, **kwargs)

Overloaded function.

  1. write_kf(self: scm_libbase_internal.UnifiedChemicalSystem, filename: str, section: str = ‘Molecule’, omode: scm_libbase_internal.KFFile.OpenMode = <OpenMode.Any: 0>) -> None

Writes a ChemicalSystem to a section on a KF file.

  1. write_kf(self: scm_libbase_internal.UnifiedChemicalSystem, kf: scm_libbase_internal.KFFile, section: str = ‘Molecule’) -> None

Writes a ChemicalSystem to a section on a KF file.

write_xyz(self: UnifiedChemicalSystem, filename: str, extended_xyz_format: bool = True) → None

Writes a ChemicalSystem to an extended XYZ file.

property adfprops

An optional list of all ADFProperties for all atoms.

property atoms

A list of all Atom instances that are part of this ChemicalSystem.

property bandprops

An optional list of all BANDProperties for all atoms.

property bonds

The bonds of the system.

property charge

The total charge of the system in in atomic units.

property coords: AngstromCoordsArray

The coordinates of the atoms in Angstrom

property dftbprops

An optional list of all DFTBProperties for all atoms.

property electrostatic_embedding

The electrostatic embedding of the system.

property forcefieldprops

An optional list of all ForcefieldProperties for all atoms.

property guiprops

An optional list of all GUIProperties for all atoms.

property lattice

The lattice of the system.

property num_atoms

The number of Atoms in the ChemicalSystem.

property num_regions

Returns the number of regions used in the system.

property qeprops

An optional list of all QEProperties for all atoms.

property reaxffprops

An optional list of all ReaxFFProperties for all atoms.

property region_names

Returns a list of the names of all regions in the system.

class InternalCoordinateManipulationPolicy

Members:

FirstPartMoves

SecondPartMoves

LighterPartMoves

HeavierPartMoves

__init__(self: InternalCoordinateManipulationPolicy, value: int) → None
property name
class UnifiedElement
property Z

The atomic number of the element.

property bond_guess_connectors

Number of connectors of an atom as used by the AMS bond guessing algorithm.

property bond_guess_electro_negative

Whether or not an element is considered electronegative by the AMS bond guessing algorithm.

property bond_guess_metallic

Whether or not an element is considered metallic by the AMS bond guessing algorithm.

property color

The color of the element used in the AMS graphical user interface.

property lone_pairs

The element’s number of lone pairs as used by the AMS bond guessing algorithm.

property mass

The atomic mass (in Dalton) of the most abundant naturally occurring isotope of the element.

property radius

The covalent radius of the element in angstrom.

property symbol

The symbol of the element, e.g C for carbon.

class UnifiedElements
static from_atomic_number(Z: int) → UnifiedElement

Returns an Element given its atomic number.

static from_symbol(symbol: str) → UnifiedElement

Returns an Element given the element symbol as a string.