MolGraph#

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

Graph representing a molecular entity. Nodes represent atoms and edges represent bonds. All nodes have an atom_type attribute of type Element. The node ids should be integers. The graph is considered equal to another graph, iff. they are isomorphic and of the same type.

property atoms: Collection[int]#

Returns:: Returns all atoms of the molecule

property atom_types: tuple[int, ...]#

Returns:: Returns all atom types in the MolGraph

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

Returns:: Returns all atoms in the MolGraph with their attributes

property bonds: Collection[frozenset[int]]#

Returns:: Returns all bonds in the MolGraph

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

Returns:: Returns all bonds in the MolGraph with their attributes

property neighbors: Mapping[int, frozenset[int]]#

Returns:: Returns all neighbors of the atoms in the MolGraph

property n_atoms: int#

Returns:: Returns number of atoms in the MolGraph

property frozen: bool#: Whether the graph is currently frozen (immutable).

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)

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

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

remove_atom(atom: int)#

Removes atom from graph.

Parameters:: atom (int) – Atom ID
Raises:: KeyError if atom is not in graph.

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_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

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

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

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

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

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

Adds bond between Atom1 and Atom2.

Parameters:

atom1 (int) – Atom1
atom2 (int) – Atom2

remove_bond(atom1: int, atom2: int)#

Removes bond between Atom1 and Atom2.

Parameters:

atom1 (int) – Atom1
atom2 (int) – Atom2

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

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

sets the Attribute of the bond between Atom1 and Atom2. The Attribute “bond_order” can only have numerical values. Raises KeyError if bond is not in graph.

Parameters:

atom1 (int) – Atom1
atom2 (int) – Atom2
attr (str) – Attribute
value (Any) – Value

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

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

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.

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

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

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__

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

connected_components() → list[set[int]]#

Return type:: list[set[int]]
Returns:: Returns the connected components of the graph

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

copy(frozen: bool = False) → Self#

Return type:: Self
Returns:: returns a copy of self

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)

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

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