Bond¶

This is the pydoc code for the bond module.

# molli.chem.bond

This submodule defines classes Bond, Connectivity and others.

class molli.chem.bond.BondType(value)¶

Bases: IntEnum

The BondType class is an Enumeration class for assigning bond types

Parameters:: IntEnum – Accepts integer enumerations for different bond types

Examples

>>> ml.BondType(20) == ml.BondType.Aromatic
True

class molli.chem.bond.BondStereo(value)¶

Bases: IntEnum

The BondStereo class is an Enumeration class for assigning bond geometry

Parameters:: IntEnum – Accepts integer enumerations for different bond geometry

Examples

>>> ml.BondStereo(10) == ml.BondStereo.E
True

class molli.chem.bond.Bond(a1: Atom, a2: Atom, label: str = None, btype: BondType = BondType.Single, stereo: BondStereo = BondStereo.Unknown, f_order=1.0, attrib: dict = NOTHING, parent=None)¶

Bases: object

The class for bonds in the MOLLI package. a1 and a2 are the atoms that the bond connects and are interchangeable. The atoms are ordered upon initialization.

evolve(**changes) → Bond¶

Evolves the bond into a new bond with the changes specified

Returns:: A new Bond instance with the changes specified
Return type:: Bond

Examples

>>> benzene = ml.Molecule.load_mol2(ml.files.benzene_mol2)
>>> bond = benzene.get_bond(0)
>>> bond.btype
<BondType.Aromatic: 20>
>>> new_bond = bond.evolve(btype = ml.BondType.Double)
>>> new_bond.btype
<BondType.Double: 2>

property order: float¶

returns: Returns the bond order as a float :rtype: float

Examples

Bonds default to 1.0 when not specified

>>> bond = ml.Bond(a1 = ml.Atom("C"), a2= ml.Atom("C"))
>>> bond.order
1.0

Aromatic Bonds default to 1.5

>>> benzene = ml.Molecule.load_mol2(ml.files.benzene_mol2)
>>> bond = benzene.get_bond(0)
>>> bond.order
1.5

as_dict(schema: List[str] = None) → dict¶

Returns the bond as a dictionary

Parameters:: schema (List[str], optional) – Can be used to specify if only certain properties are desired, by default None
Returns:: This dictionary contains properties of the associated bond
Return type:: dict

Examples

>>> ml.Bond(a1 = ml.Atom("C"), a2= ml.Atom("C")).as_dict()
{'a1':{'element': C...}, 'a2': {'element': C ...}, 'label': None, ...}
>>> bond = ml.Bond(a1 = ml.Atom("C"), a2= ml.Atom("C")).as_dict(
    ['a1','stereo','attrib']
    )
{'a1':{'element': C...}, 'stereo': <BondStereo.Unknown: 0>,
'attrib': {}}}

as_tuple(schema: List[str] = None) → tuple¶

Returns the bond as a tuple

Parameters:: schema (List[str], optional) – Can be used to specify if only certain properties are desired, by default None
Returns:: This tuple contains properties of the associated bond, also returning a1 and a2 as tuples
Return type:: tuple

Examples

>>> ml.Bond(a1 = ml.Atom("C"), a2= ml.Atom("C")).as_tuple()
((C,...),(C,...), None, <BondType.Single: 1>, ...)
>>> bond = ml.Bond(a1 = ml.Atom("C"), a2= ml.Atom("C")).as_tuple(
    ['a1','stereo','attrib']
    )
((C,...),<BondStereo.Unknown: 0>, {})

property expected_length: float¶

returns: Returns an estimated value of a bond connection between two atoms: based on the covalent radius of a single bond

Return type:: float

Examples

>>> a1, a2 = ml.Atom("Pb", label='a1'), ml.Atom("H", label="a2")
>>> bond = ml.Bond(a1, a2)
>>> bond.expected_length
1.76 # (Pb = 1.44, H = 0.32)

get_mol2_type() → str¶

Used to return the Sybyl Mol2 Type of a bond

Returns:: Returns the Sybyl Mol2 type of a bond
Return type:: str

Examples

>>> unknown_molli_bond.get_mol2_type()
'am' # Indicates it was an amide bond

class molli.chem.bond.Connectivity(other: Promolecule = None, /, *, n_atoms: int = 0, name: str = None, copy_atoms: bool = False, charge: int = None, mult: int = None, **kwds)¶

Bases: Promolecule

This is a parent class that employs methods that work on Promolecule (i.e. a list of disconnected atoms with no structure or geometry assigned to them) and connections between these disconnected atoms. This can be thought of as an undirected graph of nodes (atoms) and edges (bonds) without explicit coordinates.

property bonds: List[Bond]¶

returns: Returns an ordered list of the Bonds in the Connectivity instance :rtype: List[Bond]

Examples

The Molecule class inherits bonds

>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> dendrobine.bonds
[Bond(a1=42, a2=22, ...), Bond(a1=41,a2=22, ...), ...]

If desired, one can work directly with Connectivity class instead

>>> connect = ml.Connectivity(dendrobine)
>>> connect.bonds
[Bond(a1=42, a2=22, ...), Bond(a1=41,a2=22, ...), ...]

property n_bonds: int¶

returns: Returns the total number of bonds in the Connectivity instance :rtype: int

Examples

The Molecule class inherits n_bonds

>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> dendrobine.n_bonds
47

If desired, one can work directly with Connectivity class instead

>>> connect = ml.Connectivity(dendrobine)
>>> connect.n_bonds
47

lookup_bond(a1: Atom | int | str | Element, a2: Atom | int | str | Element) → Bond | None¶

Retrieves the bond that connects two atoms

Parameters:

a1 (AtomLike) – The first Atom instance
a2 (AtomLike) – the second Atom instance

Returns:

Returns the bond found or None if the bond doesn’t exist

Return type:

Bond | None

Examples

The Molecule class inherits lookup_bond()

>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> a1, a2 = dendrobine.get_atoms(0,1)
>>> dendrobine.lookup_bond(a1, a2)
Bond(a1=0, a2=1, label=None, ...)

If desired, one can work directly with Connectivity class instead

>>> connect = ml.Connectivity(dendrobine)
>>> connect.lookup_bond(a1, a2)
Bond(a1=0, a2=1, label=None, ...)

index_bond(b: Bond) → int¶

Fetches the atom index from the Connectivity instance

Parameters:: b (Bond) – Must be a bond in the Connectivity instance list
Returns:: Returns the index of the bond
Return type:: int

Examples

The Molecule class inherits index_bond()

>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> bond = dendrobine.lookup_bond(3,4)
>>> dendrobine.index_bond(bond)
31

If desired, one can work directly with Connectivity class instead

>>> connect = ml.Connectivity(dendrobine)
>>> bond = connect.lookup_bond(3,4)
>>> connect.index_bond(bond)
31

get_bond(b: Bond | int) → Bond¶

Fetches a bond from the Connectivity instance

Parameters:: b (Bond | int) – A bond or index
Returns:: Returns the Bond instance
Return type:: Bond

Examples

The Molecule class inherits get_bond()

>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> dendrobine.get_bond(10)
Bond(a1=21, a2=39, label=None, btype=Single, stereo=Unknown, f_order=1.0)

If desired, one can work directly with Connectivity class instead

>>> connect = ml.Connectivity(dendrobine)
>>> connect.get_bond(10)
Bond(a1=21, a2=39, label=None, btype=Single, stereo=Unknown, f_order=1.0)

append_bond(bond: Bond) → None¶

Appends a bond to the Connectivity instance

Parameters:: bond (Bond) – A bond instance to be added

Examples

The Molecule class inherits append_bond()

>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> a1, a2 = dendrobine.get_atoms(0,35)
>>> new_bond = ml.Bond(a1,a2)
>>> dendrobine.append_bond(new_bond)
>>> dendrobine.lookup_bond(new_bond)
Bond(a1=0, a2=35, label=None, btype=Single, stereo=Unknown, f_order=1.0)

If desired, one can work directly with Connectivity class instead

>>> connect = ml.Connectivity(dendrobine)
>>> a1, a2 = connect.get_atoms(0,35)
>>> new_bond = ml.Bond(a1,a2)
>>> connect.append_bond(new_bond)
>>> connect.lookup_bond(new_bond)
Bond(a1=0, a2=35, label=None, btype=Single, stereo=Unknown, f_order=1.0)

append_bonds(*bonds: Bond) → None¶

Appends multiple bonds to the Connectivity instance

Examples

The Molecule class inherits append_bonds()

>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> a1, a2, a3 = dendrobine.get_atoms(0,35, 39)
>>> b1 = ml.Bond(a1,a2)
>>> b2 = ml.Bond(a1,a3)
>>> dendrobine.append_bonds(b1,b2)
>>> dendrobine.lookup_bond(a1,a2)
Bond(a1=0, a2=35, label=None, btype=Single, stereo=Unknown, f_order=1.0)
>>> dendrobine.lookup_bond(a1,a3)
Bond(a1=0, a2=39, label=None, btype=Single, stereo=Unknown, f_order=1.0)

If desired, one can work directly with Connectivity class instead

>>> connect = ml.Connectivity(dendrobine)
>>> a1, a2, a3 = connect.get_atoms(0,35, 39)
>>> b1 = ml.Bond(a1,a2)
>>> b2 = ml.Bond(a1,a3)
>>> connect.append_bonds(b1,b2)
>>> connect.lookup_bond(a1,a2)
Bond(a1=0, a2=35, label=None, btype=Single, stereo=Unknown, f_order=1.0)
>>> connect.lookup_bond(a1,a3)
Bond(a1=0, a2=39, label=None, btype=Single, stereo=Unknown, f_order=1.0)

extend_bonds(bonds: Iterable[Bond]) → None¶

Extends the list of bonds to the Connectivity instance

Examples

The Molecule class inherits extend_bonds()

>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> a1, a2, a3 = dendrobine.get_atoms(0,35, 39)
>>> b1 = ml.Bond(a1,a2)
>>> b2 = ml.Bond(a1,a3)
>>> dendrobine.extend_bonds([b1,b2])
>>> dendrobine.lookup_bond(a1,a2)
Bond(a1=0, a2=35, label=None, btype=Single, stereo=Unknown, f_order=1.0)
>>> dendrobine.lookup_bond(a1,a3)
Bond(a1=0, a2=39, label=None, btype=Single, stereo=Unknown, f_order=1.0)

If desired, one can work directly with Connectivity class instead

>>> connect = ml.Connectivity(dendrobine)
>>> a1, a2, a3 = connect.get_atoms(0,35, 39)
>>> b1 = ml.Bond(a1,a2)
>>> b2 = ml.Bond(a1,a3)
>>> connect.extend_bonds([b1,b2])
>>> connect.lookup_bond(a1,a2)
Bond(a1=0, a2=35, label=None, btype=Single, stereo=Unknown, f_order=1.0)
>>> connect.lookup_bond(a1,a3)
Bond(a1=0, a2=39, label=None, btype=Single, stereo=Unknown, f_order=1.0)

connect_like(other: Connectivity)¶

Connect the atoms in current instance like they are connected in other

This function assumes that the equivalent atom indices are the same in both sequences.

Parameters:: other (Connectivity) – Instance to copy the connectivity from

del_bond(b: Bond) → None¶

Deletes a bond from the Connectivity instance

Parameters:: b (Bond) – Bond to delete

Examples

The Molecule class inherits del_bond()

>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> dendrobine.get_bond(0)
Bond(a1=42, a2=22, label=None, btype=Single, stereo=Unknown, f_order=1.0)
>>> dendrobine.del_bond(dendrobine.get_bond(0))
>>> dendrobine.get_bond(0)
Bond(a1=41, a2=22, label=None, btype=Single, stereo=Unknown, f_order=1.0)

If desired, one can work directly with Connectivity class instead

>>> connect = ml.Connectivity(dendrobine)
>>> connect.get_bond(0)
Bond(a1=42, a2=22, label=None, btype=Single, stereo=Unknown, f_order=1.0)
>>> connect.del_bond(connect.get_bond(0))
>>> connect.get_bond(0)
Bond(a1=41, a2=22, label=None, btype=Single, stereo=Unknown, f_order=1.0)

del_atom(_a: Atom | int | str | Element)¶

Deletes an atom and its respective bonds from the Connectivity instance

Parameters:: _a (AtomLike) – An atom, index, label, or Element. This will only delete the first instance of the label or Element found

Examples

The Molecule class inherits del_atom()

>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> print(dendrobine.n_atoms, dendrobine.n_bonds)
44, 47
>>> dendrobine.del_atom(0)
>>> print(dendrobine.n_atoms, dendrobine.n_bonds)
43, 44

If desired, one can work directly with Connectivity class instead

>>> connect = ml.Connectivity(dendrobine)
>>> print(connect.n_atoms, connect.n_bonds)
44, 47
>>> connect.del_bond(connect.get_bond(0))
>>> print(connect.n_atoms, connect.n_bonds)
44, 47

bonds_with_atom(a: Atom | int | str | Element) → Generator[Bond, None, None]¶

Yields bonds attached to an atom in a Connectivity instance

Parameters:: a (AtomLike) – An atom, index, label, or Element. This will only delete the first instance of the label or Element found
Yields:: Generator[Bond, None, None] – Yields generator of Bond instances

Examples

The Molecule class inherits bonds_with_atom()

>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> dendrobine.bonds_with_atom(0)
<generator object Connectivity.bonds_with_atom at ...>

If desired, one can work directly with Connectivity class instead

>>> connect = ml.Connectivity(dendrobine)
>>> connect.bonds_with_atom(0)
<generator object Connectivity.bonds_with_atom at ...>

connected_atoms(a: Atom | int | str | Element) → Generator[Atom, None, None]¶

Yields atoms attached to an atom in a Connectivity instance

Parameters:: a (AtomLike) – An atom, index, label, or Element. This will only delete the first instance of the label or Element found
Yields:: Generator[Atom, None, None] – Yields generator of Atom instances

Examples

The Molecule class inherits connected_atoms()

>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> dendrobine.connected_atoms(0)
<generator object Connectivity.connected_atoms at ...>

If desired, one can work directly with Connectivity class instead

>>> connect = ml.Connectivity(dendrobine)
>>> connect.connected_atoms(0)
<generator object Connectivity.connected_atoms at ...>

bonded_valence(a: Atom | int | str | Element) → float¶

Sum of valences of the atoms bonded in a Connectivity instance

Parameters:: a (AtomLike) – An atom, index, label, or Element. This will only delete the first instance of the label or Element found
Returns:: Returns sum of valences of atoms connected
Return type:: float

Examples

The Molecule class inherits bonded_valence()

>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> dendrobine.bonded_valence(0)
3.0

If desired, one can work directly with Connectivity class instead

>>> connect = ml.Connectivity(dendrobine)
>>> connect.bonded_valence(0)
3.0

n_bonds_with_atom(a: Atom | int | str | Element) → int¶

Total number of bonds to an atom in a Connectivity instance

Parameters:: a (AtomLike) – An atom, index, label, or Element. This will only delete the first instance of the label or Element found
Returns:: Returns the total number of bonds to an atom
Return type:: int

Examples

The Molecule class inherits n_bonds_with_atom()

>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> dendrobine.n_bonds_with_atom(0)
3

If desired, one can work directly with Connectivity class instead

>>> connect = ml.Connectivity(dendrobine)
>>> connect.n_bonds_with_atom(0)
3

yield_bfsd(_start: Atom | int | str | Element, _direction: Atom | int | str | Element = None) → Generator[Tuple[Atom, int], None, None]¶

Yields atoms in breadth-first search, in traversal order, Distance from the start atom is also yielded

Parameters:

_start (AtomLike) – An atom, index, label, or Element. This will only delete the first instance of the label or Element found
_direction (AtomLike, optional) – An atom, index, label, or Element. This will only delete the first instance of the label or Element found, by default None

Yields:

Generator[Tuple[Atom, int], None, None] – the atoms in breadth-first search, in traversal order, Distance from the start atom is also yielded

Examples

The Molecule class inherits yield_bfsd()

>>> dmf = ml.Molecule.load_mol2(ml.files.dmf_mol2)
>>> dmf.yield_bfsd(0)
<generator object Connectivity.yield_bfsd at ...>

If desired, one can work directly with Connectivity class instead

>>> connect = ml.Connectivity(dmf)
>>> connect.yield_bfsd(0)
<generator object Connectivity.yield_bfsd at ...>

yield_bfs(_start: Atom | int | str | Element, _direction: Atom | int | str | Element = None) → Generator[Atom, None, None]¶

Yields atoms in breadth-first search, in traversal order, Distance is not yielded

Parameters:

_start (AtomLike) – An atom, index, label, or Element. This will only delete the first instance of the label or Element found
_direction (AtomLike, optional) – An atom, index, label, or Element. This will only delete the first instance of the label or Element found, by default None

Yields:

Generator[Atom, None, None] – The Atoms in a breadth-first search, in traversal order

Examples

The Molecule class inherits yield_bfsd()

>>> dmf = ml.Molecule.load_mol2(ml.files.dmf_mol2)
>>> dmf.yield_bfsd(0)
<generator object Connectivity.yield_bfs at ...>

If desired, one can work directly with Connectivity class instead

>>> connect = ml.Connectivity(dmf)
>>> connect.yield_bfsd(0)
<generator object Connectivity.yield_bfs at ...>

to_nxgraph() → Graph¶

Converts an insantce of Connectivity class into networkx object

Returns:¶

nx_mol: nx.Graph(): instance of Networkx Graph object

Notes:¶

In latest version, all the atom and bond attributes are added to Networkx Graph.

find_cycle_containing_atom(start: Atom | int | str | Element) → list¶

Finds the first cycle containing “start” atom Parameters: ———– start: ml.chem.AtomLike

atom or its atomic index or a unique identifier for starting searching for cycles (loops)

Returns:¶

cycle: list: the first found cycle that countains “start” atom

Current implementation using networkx grpah. Should be rewritten w/o any extra dependencies.

match(pattern: Connectivity, /, *, node_match: Callable[[dict, dict], bool] | None = None, edge_match: Callable[[dict, dict], bool] | None = None) → Generator[dict | Any, None, None]¶

Checks two molli connectivities for isomorphism. Yields generator over subgraph isomorphism mappings.

```python for mapping in connectivity.match(pattern):

…

``` Parameters: ———– pattern: Connectivity

query-Connectivity (Molecule) to match with given Connectivity

get_substr_indices(pattern: Connectivity) → Generator[list[int], None, None]¶

Yields all possible combinations of substructure indices that matched with the given pattern.

Parameters:¶

pattern: Connectivity

Returns:¶

Generator over list of all possible mappings to pattern

If only one variation of substructure indices is needed, use next(ens.get_substr_indices(pattern))

``python for ens in tqdm(library):

for mapping in ens.get_substr_indices(pattern):
…

```