CondensedReactionGraph

class stereomolgraph.CondensedReactionGraph(mol_graph: MolGraph | None = None, frozen: bool = False)

Bases: MolGraph

Graph representing a reaction. Atoms are nodes and (potentially changing) bonds are edges. Every node has to have an attribute “atom_type” of type Element. Edges can have an attribute “reaction” of type Change. This is used to represent the change in connectivity during the reaction.

Two graphs are equal, iff. they are isomporhic and of the same type.

add_bond(atom1: int, atom2: int, **attr: Any)

Adds a bond between atom1 and atom2.

Parameters:

• atom1 (int) – id of atom1

• atom2 (int) – id of atom2

set_bond_attribute(atom1: int, atom2: int, attr: str, value: Any)

sets the Attribute of the bond between Atom1 and Atom2.

Parameters:

• atom1 (int) – Atom1

• atom2 (int) – Atom2

• attr (str) – Attribute

• value (Any) – Value

add_formed_bond(atom1: int, atom2: int, **attr: Any)

Adds a bond between atom1 and atom2 with reaction attribute set to FORMED.

Parameters:

• atom1 (int) – Atom1

• atom2 (int) – Atom2

add_broken_bond(atom1: int, atom2: int, **attr: Any)

Adds a bond between atom1 and atom2 with reaction attribute set to BROKEN.

Parameters:

• atom1 (int) – Atom1

• atom2 (int) – Atom2

add_fleeting_bond(atom1: int, atom2: int, **attr: Any)

Adds a bond between atom1 and atom2 with reaction attribute set to FLEETING.

Parameters:

• atom1 (int) – Atom1

• atom2 (int) – Atom2

get_formed_bonds() → set[frozenset[int]]

Returns all bonds that are formed during the reaction

Return type:

set[frozenset[int]]

Returns:

formed bonds

get_broken_bonds() → set[frozenset[int]]

Returns all bonds that are broken during the reaction

Return type:

set[frozenset[int]]

Returns:

broken bonds

get_fleeting_bonds() → set[frozenset[int]]

Returns all bonds that are fleeting during the reaction.

Return type:

set[frozenset[int]]

Returns:

fleeting bonds

active_atoms(additional_layer: int = 0) → set[int]

Atoms involved in the reaction with additional layers of atoms in the neighborhood.

Parameters:

additional_layer (int) – Number of additional layers of atoms to include, defaults to 0 (default: 0)

Return type:

set[int]

Returns:

Atoms involved in the reaction

reactant(keep_attributes: bool = True) → MolGraph

Reactant of the reaction

Creates the reactant of the reaction. Formed bonds are not present in the reactant.

Parameters:

keep_attributes (bool) – attributes on atoms and bonds to be kept, defaults to True (default: True)

Return type:

MolGraph

Returns:

Reactant of the reaction

product(keep_attributes: bool = True) → MolGraph

Product of the reaction

Creates the product of the reaction. Broken bonds are not present in the product.

Parameters:

keep_attributes (bool) – attributes on atoms and bonds to be kept, defaults to True (default: True)

Return type:

MolGraph

Returns:

Product of the reaction

reverse_reaction() → Self

Creates the reaction in the opposite direction.

Broken bonds are turned into formed bonds and the other way around.

Return type:

Self

Returns:

Reversed reaction

classmethod from_graphs(reactant_graph: MolGraph, product_graph: MolGraph, ts_graph: MolGraph | None = None) → Self

Creates a CondensedReactionGraph from reactant and product MolGraphs

CondensedReactionGraph is constructed from bond changes from reactant to the product. The atoms order and atom types of the reactant and product have to be the same.

Parameters:

• reactant_graph (MolGraph) – reactant of the reaction

• product_graph (MolGraph) – product of the reaction

Return type:

Self

Returns:

CondensedReactionGraph

classmethod from_geometries(reactant_geo: ~stereomolgraph.coords.Geometry, product_geo: ~stereomolgraph.coords.Geometry, ts_geo: ~stereomolgraph.coords.Geometry | None = None, switching_function: ~stereomolgraph.coords.BondsFromDistance = <stereomolgraph.coords.BondsFromDistance object>) → Self

Creates a CondensedReactionGraph from reactant and product Geometries.

CondensedReactionGraph is constructed from bond changes from reactant to the product. The atoms order and atom types of the reactant and product have to be the same. The switching function is used to determine the connectivity of the atoms.

Parameters:

• reactant_geo (Geometry) – geometry of the reactant

• product_geo (Geometry) – geometry of the product

• switching_function (BondsFromDistance) – function to define the connectivity from geometry, defaults to StepSwitchingFunction() (default: <stereomolgraph.coords.BondsFromDistance object at 0x7c19f33787d0>)

Return type:

Self

Returns:

CondensedReactionGraph

add_atom(atom: int, atom_type: int | str, **attr: Any)

Adds atom to the MolGraph

Parameters:

• atom (int) – Atom ID

• atom_type (int | str) – Atom Type

property atom_types: tuple[int, ...]

Returns:

Returns all atom types in the MolGraph

property atoms: Collection[int]

Returns:

Returns all atoms of the molecule

property atoms_with_attributes: Mapping[int, dict[str, Any]]

Returns:

Returns all atoms in the MolGraph with their attributes

bonded_to(atom: int) → frozenset[int]

Returns the atoms connected to the atom.

Parameters:

atom (int) – Id of the atom.

Return type:

frozenset[int]

Returns:

tuple of atoms connected to the atom.

property bonds: Collection[frozenset[int]]

Returns:

Returns all bonds in the MolGraph

bonds_from_bond_order_matrix(matrix: ndarray, threshold: float = 0.5, include_bond_order: bool = False)

Adds bonds the the graph based on bond orders from a matrix

Parameters:

• matrix (ndarray) – Bond order Matrix

• threshold (float) – Threshold for bonds to be included as edges, defaults to 0.5 (default: 0.5)

• include_bond_order (bool) – If bond orders should be included as edge attributes, defaults to False (default: False)

property bonds_with_attributes: Mapping[frozenset[int], dict[str, Any]]

Returns:

Returns all bonds in the MolGraph with their attributes

classmethod compose(mol_graphs: Iterable[MolGraph]) → Self

Combines all graphs in the iterable into one. Duplicate nodes or edges are overwritten, such that the resulting graph only contains one node or edge with that name. Duplicate attributes of duplicate nodes or edges are also overwritten in order of iteration.

Parameters:

molgraphs – Iterable of MolGraph that will be composed into a single MolGraph

Return type:

Self

connected_components() → list[set[int]]

Return type:

list[set[int]]

Returns:

Returns the connected components of the graph

connectivity_matrix() → ndarray[tuple[int, int], dtype[int8]]

Returns a connectivity matrix of the graph as a list of lists. Order is the same as in self.atoms() 1 if nodes are connected, 0 if not.

Return type:

ndarray[tuple[int, int], dtype[int8]]

Returns:

Connectivity matrix as list of lists

copy(frozen: bool = False) → Self

Return type:

Self

Returns:

returns a copy of self

delete_atom_attribute(atom: int, attr: str)

Deletes the Attribute of the Atom Raises KeyError if attribute is not present. Raises KeyError if atom is not in graph.

Parameters:

• atom (int) – Atom ID

• attr (str) – Attribute

Raises:

ValueError – The attribute “atom_type” can not be deleted

delete_bond_attribute(atom1: int, atom2: int, attr: str)

Deletes the Attribute of the bond between Atom1 and Atom2

Parameters:

• atom1 (int)

• atom2 (int) – Atom1

• attr (str) – Attribute

freeze() → Self

Freeze the graph, making it immutable and hashable.

A frozen graph can be used in sets and as dict keys. Mutation methods will raise TypeError. Use copy() to get a mutable copy.

Return type:

Self

Returns:

self (for chaining)

classmethod from_atom_types_and_bond_order_matrix(atom_types: Sequence[int | str], matrix: ndarray, threshold: float = 0.5, include_bond_order: bool = False)

Parameters:

• atom_types (Sequence[int | str]) – list of atom types as integers or symbols, must correspond to the matrix

• matrix (ndarray) – np.matrix of bond orders or connectivities ([0..1])

• threshold (float) – Threshold for bonds to be included as edges, defaults to 0.5 (default: 0.5)

• include_bond_order (bool) – If bond orders should be included as edge attributes, defaults to False (default: False)

Returns:

Returns MolGraph

classmethod from_geometry_and_bond_order_matrix(geo: Geometry, matrix: ndarray, threshold: float = 0.5, include_bond_order: bool = False) → Self

Creates a graph of a molecule from a Geometry and a bond order matrix.

Parameters:

• geo (Geometry) – Geometry

• matrix (ndarray) – Bond order matrix

• threshold (float) – Threshold for bonds to be included as edges, defaults to 0.5 (default: 0.5)

• include_bond_order (bool) – If bond orders should be included as edge attributes, defaults to False (default: False)

Return type:

Self

Returns:

Graph of Molecule

classmethod from_rdmol(rdmol: Mol, use_atom_map_number: bool = False) → Self

Creates a StereoMolGraph from an RDKit Mol object. Implicit Hydrogens are added to the graph. Stereo information is conserved. Double bonds, aromatic bonds and conjugated bonds are interpreted as planar. Atoms with 5 bonding partners are assumed to be TrigonalBipyramidal and allow interchange of the substituents (berry pseudorotation). Atoms with 6 bonding partners are assumed to be octahedral and do not allow interchange of the substituents.

Parameters:

• rdmol (Mol) – RDKit Mol object

• use_atom_map_number (bool) – If the atom map number should be used instead of the atom index (default: False)

Return type:

Self

Returns:

StereoMolGraph

property frozen: bool

Whether the graph is currently frozen (immutable).

get_atom_attribute(atom: int, attr: str) → Any | None

Returns the value of the attribute of the atom or None if the atom does not have this attribute. Raises KeyError if atom is not in graph.

Parameters:

• atom (int) – Atom

• attr (str) – Attribute

Raises:

KeyError – Atom not in graph

Return type:

Optional[Any]

Returns:

Returns the value of the attribute of the atom

get_atom_attributes(atom: int, attributes: Iterable[str] | None = None) → Mapping[str, Any]

Returns the attributes of the atom. If no attributes are given, all attributes are returned. Raises KeyError if atom is not in graph.

Parameters:

• atom (int) – Atom

• attributes (Optional[Iterable[str]]) – Specific attributes to return (default: None)

Return type:

Mapping[str, Any]

Returns:

Returns all or just the chosen attributes of the atom

get_atom_type(atom: int) → int

Returns the atom type of the atom. Raises KeyError if atom is not in graph.

Parameters:

atom (int) – Atom

Raises:

KeyError – Atom not in graph

Return type:

int

Returns:

Returns the atom type of the atom

get_bond_attribute(atom1: int, atom2: int, attr: str) → Any

Returns the value of the attribute of the bond between Atom1 and Atom2. Raises KeyError if bond is not in graph.

Parameters:

• atom1 (int) – Atom1

• atom2 (int) – Atom2

• attr (str) – Attribute

Return type:

Any

Returns:

Returns the value of the attribute of the bond between Atom1 and Atom2

get_bond_attributes(atom1: int, atom2: int, attributes: Iterable[str] | None = None) → Mapping[str, Any]

Parameters:

• atom1 (int) – Atom1

• atom2 (int) – Atom2

• attributes (Optional[Iterable[str]]) – Specific attributes to return (default: None)

Return type:

Mapping[str, Any]

Returns:

Returns chosen attributes of the bond between Atom1 and Atom2

has_atom(atom: int) → bool

Returns True if the molecules contains an atom with this id.

Parameters:

atom (int) – Atom

Return type:

bool

Returns:

value

has_bond(atom1: int, atom2: int) → bool

Returns True if bond is in MolGraph.

Parameters:

• atom1 (int) – Atom1

• atom2 (int) – Atom2

Return type:

bool

Returns:

If the bond is in MolGraph

property n_atoms: int

Returns:

Returns number of atoms in the MolGraph

property neighbors: Mapping[int, set[int]]

Returns:

Returns all neighbors of the atoms in the MolGraph

node_connected_component(atom: int) → set[int]

Parameters:

atom (int) – atom id

Return type:

set[int]

Returns:

Returns the connected component that includes atom_id

relabel_atoms(mapping: dict[int, int], copy: bool = True) → Self

Changes the atom labels according to mapping.

Parameters:

• mapping (dict[int, int]) – dict used for map old atom labels to new atom labels

• copy (bool) – defines if the relabeling is done inplace or a new object should be created (default: True)

Return type:

Self

Returns:

this object (self) or a new instance of self.__class__

remove_atom(atom: int)

Removes atom from graph.

Parameters:

atom (int) – Atom ID

Raises:

KeyError if atom is not in graph.

remove_bond(atom1: int, atom2: int)

Removes bond between Atom1 and Atom2.

Parameters:

• atom1 (int) – Atom1

• atom2 (int) – Atom2

set_atom_attribute(atom: int, attr: str, value: Any)

sets the Value of the Attribute on Atom. Raises KeyError if atom is not in graph.

Parameters:

• atom (int) – Atom

• attr (str) – Attribute

• value (Any) – Value

Raises:

• KeyError – Atom not in graph

• ValueError – The attribute “atom_type” can only have values of type Element

subgraph(atoms: Iterable[int]) → Self

Returns a subgraph copy only containing the given atoms

Parameters:

atoms (Iterable[int]) – Iterable of atom ids to be

Return type:

Self

Returns:

Subgraph