CGRtools.containers package

Data classes.

class CGRtools.containers.CGRContainer

add_atom(atom: Union[DynamicElement, Element, int, str], *args, p_charge: int = 0, p_is_radical: bool = False, **kwargs): new atom addition

add_bond(n, m, bond: Union[DynamicBond, Bond, int]): new bond addition

adjacency_matrix(set_bonds=False)

Adjacency matrix of Graph.

Parameters: set_bonds – if True set bond orders instead of 1.

aromatic_rings: existed or formed aromatic rings atoms numbers

atom(n: int) → Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, DynamicAnyElement, ListElement]

atoms() → Iterator[Tuple[int, Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, DynamicAnyElement, ListElement]]]: iterate over all atoms

atoms_count

atoms_numbers

atoms_order

Morgan like algorithm for graph nodes ordering

Returns: dict of atom-order pairs

atoms_rings: Dict of atoms rings which contains it.

atoms_rings_sizes: Sizes of rings containing atom.

augmented_substructure(atoms: Iterable[int], deep: int = 1, **kwargs) → Graph

create substructure containing atoms and their neighbors

Parameters

atoms – list of core atoms in graph
deep – number of bonds between atoms and neighbors
meta – copy metadata to each substructure
as_query – return Query object based on graph substructure. for Molecule and CGR only

augmented_substructures(atoms: Iterable[int], deep: int = 1, **kwargs) → List[Graph]

create list of substructures containing atoms and their neighbors

Parameters

atoms – list of core atoms in graph
deep – number of bonds between atoms and neighbors
meta – copy metadata to each substructure
as_query – return Query object based on graph substructure. for Molecule and CGR only

Returns

list of graphs containing atoms, atoms + first circle, atoms + 1st + 2nd, etc up to deep or while new nodes available

bond(n: int, m: int) → Union[Bond, DynamicBond]

bonds() → Iterator[Tuple[int, int, Union[Bond, DynamicBond]]]: iterate other all bonds

bonds_count

center_atoms: Get list of atoms of reaction center (atoms with dynamic: bonds, charges, radicals).

center_bonds: Get list of bonds of reaction center (bonds with dynamic orders).

centers_list: Get a list of lists of atoms of reaction centers

clean2d(): Calculate 2d layout of graph. https://pubs.acs.org/doi/10.1021/acs.jcim.7b00425 JS implementation used.

compose(other: Union[MoleculeContainer, CGRContainer]) → CGRContainer

compose 2 graphs to CGR

Parameters: other – Molecule or CGR Container
Returns: CGRContainer

connected_components: Isolated components of single graph. E.g. salts as ion pair.

property connected_components_count: int: Number of components in graph

connected_rings: Rings groups with common atoms. E.g. naphthalene has two connected rings. Rings not atom ordered like sssr.

copy(**kwargs) → CGRContainer

copy of graph

Parameters: meta – include metadata

decompose() → Tuple[MoleculeContainer, MoleculeContainer]

decompose CGR to pair of Molecules, which represents reactants and products state of reaction

Returns: tuple of two molecules

delete_atom(n): implementation of atom removing

delete_bond(n, m): implementation of bond removing

depict(*, embedding=False)

depict3d(index: int = 0) → str

Get X3DOM XML string.

Parameters: index – index of conformer

classmethod depict_settings(*, carbon: bool = False, bond_color: str = 'black', font_size: float = 0.5, aam: bool = True, aam_color: str = '#0305A7', bond_width: float = 0.04, dashes: Tuple[float, float] = (0.2, 0.1), query_color: str = '#5D8AA8', atoms_colors: tuple = ('#909090', '#D9FFFF', '#CC80FF', '#C2FF00', '#FFB5B5', '#101010', '#3050F8', '#FF0D0D', '#90E050', '#B3E3F5', '#AB5CF2', '#8AFF00', '#BFA6A6', '#F0C8A0', '#FF8000', '#C6C600', '#1FF01F', '#80D1E3', '#8F40D4', '#3DFF00', '#E6E6E6', '#BFC2C7', '#A6A6AB', '#8A99C7', '#9C7AC7', '#E06633', '#F090A0', '#50D050', '#C88033', '#7D80B0', '#C28F8F', '#668F8F', '#BD80E3', '#FFA100', '#A62929', '#5CB8D1', '#702EB0', '#00FF00', '#94FFFF', '#94E0E0', '#73C2C9', '#54B5B5', '#3B9E9E', '#248F8F', '#0A7D8C', '#006985', '#C0C0C0', '#FFD98F', '#A67573', '#668080', '#9E63B5', '#D47A00', '#940094', '#429EB0', '#57178F', '#00C900', '#70D4FF', '#FFFFC7', '#D9FFC7', '#C7FFC7', '#A3FFC7', '#8FFFC7', '#61FFC7', '#45FFC7', '#30FFC7', '#1FFFC7', '#00FF9C', '#00E675', '#00D452', '#00BF38', '#00AB24', '#4DC2FF', '#4DA6FF', '#2194D6', '#267DAB', '#266696', '#175487', '#D0D0E0', '#FFD123', '#B8B8D0', '#A6544D', '#575961', '#9E4FB5', '#AB5C00', '#754F45', '#428296', '#420066', '#007D00', '#70ABFA', '#00BAFF', '#00A1FF', '#008FFF', '#0080FF', '#006BFF', '#545CF2', '#785CE3', '#8A4FE3', '#A136D4', '#B31FD4', '#B31FBA', '#B30DA6', '#BD0D87', '#C70066', '#CC0059', '#D1004F', '#D90045', '#E00038', '#E6002E', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026'), dx_ci: float = 0.05, dy_ci: float = 0.2, triple_space: float = 0.13, aromatic_dashes: Tuple[float, float] = (0.15, 0.05), dy_nh: float = 0.15, formed_color: str = 'green', monochrome: bool = False, atom_radius: float = 0.2, dy_m: float = 0.2, symbols_font_style: str = 'sans-serif', other_size: float = 0.3, double_space: float = 0.06, dx_m: float = 0.05, span_dy: float = 0.15, span_size: float = 0.35, dx_nh: float = 0.075, other_font_style: str = 'monospace', cgr_aromatic_space: float = 0.18, aam_size: float = 0.25, other_color: str = 'black', broken_color: str = 'red', aromatic_space: float = 0.14, bond_radius=0.02)

Settings for depict of chemical structures

Parameters

carbon – if True, depict atom C
font_size – font size
aam_size – atom-to-atom mapping font size
span_size – font size for hydrogen count
other_size – isotope, radical, charges, neighbors and hybridization symbols size
bond_width – bond width
bond_color – color of bonds
aam_color – atom-to-atom mapping color
query_color – hybridization and neighbors color
atoms_colors – atom colors where key is atomic number - 1, value is atom color (str)
broken_color – only CGRContainer: color of broken bond
formed_color – only CGRContainer: color of formed bond
other_color – color for charges, radicals, isotopes
symbols_font_style – font style for atom symbols
other_font_style – font style for mapping, charges, radicals, isotopes, hybridization and neighbors
aam – if True, depict mapping
monochrome – if True, colors of items in molecule not used
dashes – first value is long of visible line, second is long of invisible line
aromatic_space – space between simple and aromatic bonds
triple_space – space between simple and triple bonds
double_space – space between simple and double bonds
cgr_aromatic_space – only CGRContainer: space between simple and aromatic bonds
aromatic_dashes – first value is long of visible line, second is long of invisible line
atom_radius – radius of atoms spheres in depict3d. if negative is multiplier to covalent radii
bond_radius – radius of bonds spheres in depict3d
dx_ci – x-axis offset relative to the center of the atom symbol for radical, charges, isotope
dy_ci – y-axis offset relative to the center of the atom symbol for radical, charges, isotope
dx_m – x-axis offset relative to the center of the atom symbol for atom-to-atom mapping
dy_m – y-axis offset relative to the center of the atom symbol for atom-to-atom mapping
dx_nh – x-axis offset relative to the center of the atom symbol for neighbors and hybridization
dy_nh – y-axis offset relative to the center of the atom symbol for neighbors and hybridization
span_dy – y-axis offset relative to the center of the atom symbol for hydrogen count

environment(atom: int, include_bond: bool = True, include_atom: bool = True) → Tuple[Union[Tuple[int, Union[Bond, DynamicBond], Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, DynamicAnyElement, ListElement]], Tuple[int, Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, DynamicAnyElement, ListElement]], Tuple[int, Union[Bond, DynamicBond]], int], ...]

groups of (atom_number, bond, atom) connected to atom or groups of (atom_number, bond) connected to atom or groups of (atom_number, atom) connected to atom or neighbors atoms connected to atom

Parameters

atom – number
include_atom – include atom object
include_bond – include bond object

flush_cache()

get_automorphism_mapping() → Iterator[Dict[int, int]]: Iterator of all possible automorphism mappings.

get_mapping(other: CGRContainer, **kwargs)

Get self to other substructure mapping generator.

Parameters

automorphism_filter – Skip matches to same atoms.
optimize – Morgan weights based automorphism preventing.
fallback – Try without optimization then nothing matched.

get_mcs_mapping(other: CGRContainer, **kwargs)

find maximum common substructure. based on clique searching in product graph.

Parameters: limit – limit tested cliques

has_atom(n: int) → bool

has_bond(n: int, m: int) → bool

is_automorphic(): Test for automorphism symmetry of graph.

is_equal(other) → bool: Test self is same structure as other

is_substructure(other) → bool: Test self is substructure of other

property meta: Dict

property name: str

neighbors(n: int) → Tuple[int, int]: number of neighbors atoms excluding any-bonded

classmethod pickle_save_cache(arg: bool): Store cache of Graph into pickle for speedup loading

remap(mapping, *, copy=False) → CGRContainer

ring_atoms: Atoms in rings

rings_count: SSSR rings count.

skin_atoms: Atoms of rings and rings linkers [without terminal atoms]

skin_graph: Graph without terminal atoms. Only rings and linkers

smiles_atoms_order: Atoms order in canonic SMILES.

split(meta: bool = False) → List[Graph]

split disconnected structure to connected substructures

Parameters: meta – copy metadata to each substructure
Returns: list of substructures

sssr

Smallest Set of Smallest Rings.

:return rings atoms numbers

substructure(atoms, *, as_query: bool = False, **kwargs) → Union[CGRContainer, QueryCGRContainer]

create substructure containing atoms from atoms list

Parameters

atoms – list of atoms numbers of substructure
meta – if True metadata will be copied to substructure
as_query – return Query object based on graph substructure

union(other, **kwargs) → CGRContainer

Merge Graphs into one.

Parameters: remap – if atoms has collisions then remap other graph atoms else raise exception.

view3d(index: int = 0, width='600px', height='400px')

Jupyter widget for 3D visualization.

Parameters

index – index of conformer
width – widget width
height – widget height

class CGRtools.containers.MoleculeContainer

add_atom(atom: Union[Element, int, str], *args, charge=0, is_radical=False, **kwargs): Add new atom.

add_atom_stereo(n: int, env: Tuple[int, ...], mark: bool, *, clean_cache=True)

Add stereo data for specified neighbors bypass. Use it for tetrahedrons of allenes.

Parameters

n – number of tetrahedron atom or central atom of allene.
env – numbers of atoms with specified bypass
mark – clockwise or anti bypass.

See <https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html> and <http://opensmiles.org/opensmiles.html>

add_bond(n, m, bond: Union[Bond, int])

Connect atoms with bonds.

For Thiele forms of molecule causes invalidation of internal state. Implicit hydrogens marks will not be set if atoms in aromatic rings. Call kekule() and thiele() in sequence to fix marks.

add_cis_trans_stereo(n: int, m: int, n1: int, n2: int, mark: bool, *, clean_cache=True)

Add stereo data to cis-trans double bonds (not allenes).

n1/n=m/n2

Parameters

n – number of starting atom of double bonds chain (alkenes of cumulenes)
m – number of ending atom of double bonds chain (alkenes of cumulenes)
n1 – number of neighboring atom of starting atom
n2 – number of neighboring atom of ending atom
mark – cis or trans

See <https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html> and <http://opensmiles.org/opensmiles.html

add_wedge(n: int, m: int, mark: bool, *, clean_cache=True)

Add stereo data by wedge notation of bonds. Use it for tetrahedrons of allenes.

Parameters

n – number of atom from which wedge bond started
m – number of atom to which wedge bond coming
mark – up bond is True, down is False

adjacency_matrix(set_bonds=False)

Adjacency matrix of Graph.

Parameters: set_bonds – if True set bond orders instead of 1.

aromatic_rings: Aromatic rings atoms numbers

atom(n: int) → Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, DynamicAnyElement, ListElement]

atoms() → Iterator[Tuple[int, Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, DynamicAnyElement, ListElement]]]: iterate over all atoms

atoms_count

atoms_numbers

atoms_order

Morgan like algorithm for graph nodes ordering

Returns: dict of atom-order pairs

atoms_rings: Dict of atoms rings which contains it.

atoms_rings_sizes: Sizes of rings containing atom.

augmented_substructure(atoms: Iterable[int], deep: int = 1, **kwargs) → Graph

create substructure containing atoms and their neighbors

Parameters

atoms – list of core atoms in graph
deep – number of bonds between atoms and neighbors
meta – copy metadata to each substructure
as_query – return Query object based on graph substructure. for Molecule and CGR only

augmented_substructures(atoms: Iterable[int], deep: int = 1, **kwargs) → List[Graph]

create list of substructures containing atoms and their neighbors

Parameters

atoms – list of core atoms in graph
deep – number of bonds between atoms and neighbors
meta – copy metadata to each substructure
as_query – return Query object based on graph substructure. for Molecule and CGR only

Returns

list of graphs containing atoms, atoms + first circle, atoms + 1st + 2nd, etc up to deep or while new nodes available

bond(n: int, m: int) → Union[Bond, DynamicBond]

bonds() → Iterator[Tuple[int, int, Union[Bond, DynamicBond]]]: iterate other all bonds

bonds_count

brutto: Counted atoms dict

calculate_cis_trans_from_2d(*, clean_cache=True): Calculate cis-trans stereo bonds from given 2d coordinates. Unusable for SMILES and INCHI.

canonicalize(*, logging=False) → Union[bool, List[Tuple[Tuple[int, ...], int, str]]]

Convert molecule to canonical forms of functional groups and aromatic rings without explicit hydrogens.

Parameters: logging – return log.

check_thiele(fast=True) → bool

Check basic aromaticity errors of molecule.

Parameters: fast – don’t try to solve kekule form

check_valence() → List[int]

Check valences of all atoms.

Works only on molecules with aromatic rings in Kekule form. :return: list of invalid atoms

clean2d(): Calculate 2d layout of graph. https://pubs.acs.org/doi/10.1021/acs.jcim.7b00425 JS implementation used.

clean_isotopes() → bool: Clean isotope marks from molecule. Return True if any isotope found.

clean_stereo(): Remove stereo data

compose(other: Union[MoleculeContainer, CGRContainer]) → CGRContainer: Compose 2 graphs to CGR.

connected_components: Isolated components of single graph. E.g. salts as ion pair.

property connected_components_count: int: Number of components in graph

connected_rings: Rings groups with common atoms. E.g. naphthalene has two connected rings. Rings not atom ordered like sssr.

connected_rings_cumulenes: Connected ring with attached cumulenes.

copy(**kwargs) → MoleculeContainer

copy of graph

Parameters: meta – include metadata

cumulenes: Alkenes, allenes and cumulenes atoms numbers

delete_atom(n)

Remove atom.

For Thiele forms of molecule causes invalidation of internal state. Implicit hydrogens marks will not be set if atoms in aromatic rings. Call kekule() and thiele() in sequence to fix marks.

delete_bond(n, m)

Disconnect atoms.

For Thiele forms of molecule causes invalidation of internal state. Implicit hydrogens marks will not be set if atoms in aromatic rings. Call kekule() and thiele() in sequence to fix marks.

depict(*, embedding=False)

depict3d(index: int = 0) → str

Get X3DOM XML string.

Parameters: index – index of conformer

classmethod depict_settings(*, carbon: bool = False, bond_color: str = 'black', font_size: float = 0.5, aam: bool = True, aam_color: str = '#0305A7', bond_width: float = 0.04, dashes: Tuple[float, float] = (0.2, 0.1), query_color: str = '#5D8AA8', atoms_colors: tuple = ('#909090', '#D9FFFF', '#CC80FF', '#C2FF00', '#FFB5B5', '#101010', '#3050F8', '#FF0D0D', '#90E050', '#B3E3F5', '#AB5CF2', '#8AFF00', '#BFA6A6', '#F0C8A0', '#FF8000', '#C6C600', '#1FF01F', '#80D1E3', '#8F40D4', '#3DFF00', '#E6E6E6', '#BFC2C7', '#A6A6AB', '#8A99C7', '#9C7AC7', '#E06633', '#F090A0', '#50D050', '#C88033', '#7D80B0', '#C28F8F', '#668F8F', '#BD80E3', '#FFA100', '#A62929', '#5CB8D1', '#702EB0', '#00FF00', '#94FFFF', '#94E0E0', '#73C2C9', '#54B5B5', '#3B9E9E', '#248F8F', '#0A7D8C', '#006985', '#C0C0C0', '#FFD98F', '#A67573', '#668080', '#9E63B5', '#D47A00', '#940094', '#429EB0', '#57178F', '#00C900', '#70D4FF', '#FFFFC7', '#D9FFC7', '#C7FFC7', '#A3FFC7', '#8FFFC7', '#61FFC7', '#45FFC7', '#30FFC7', '#1FFFC7', '#00FF9C', '#00E675', '#00D452', '#00BF38', '#00AB24', '#4DC2FF', '#4DA6FF', '#2194D6', '#267DAB', '#266696', '#175487', '#D0D0E0', '#FFD123', '#B8B8D0', '#A6544D', '#575961', '#9E4FB5', '#AB5C00', '#754F45', '#428296', '#420066', '#007D00', '#70ABFA', '#00BAFF', '#00A1FF', '#008FFF', '#0080FF', '#006BFF', '#545CF2', '#785CE3', '#8A4FE3', '#A136D4', '#B31FD4', '#B31FBA', '#B30DA6', '#BD0D87', '#C70066', '#CC0059', '#D1004F', '#D90045', '#E00038', '#E6002E', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026'), dx_ci: float = 0.05, dy_ci: float = 0.2, triple_space: float = 0.13, aromatic_dashes: Tuple[float, float] = (0.15, 0.05), dy_nh: float = 0.15, formed_color: str = 'green', monochrome: bool = False, atom_radius: float = 0.2, dy_m: float = 0.2, symbols_font_style: str = 'sans-serif', other_size: float = 0.3, double_space: float = 0.06, dx_m: float = 0.05, span_dy: float = 0.15, span_size: float = 0.35, dx_nh: float = 0.075, other_font_style: str = 'monospace', cgr_aromatic_space: float = 0.18, aam_size: float = 0.25, other_color: str = 'black', broken_color: str = 'red', aromatic_space: float = 0.14, bond_radius=0.02)

Settings for depict of chemical structures

Parameters

carbon – if True, depict atom C
font_size – font size
aam_size – atom-to-atom mapping font size
span_size – font size for hydrogen count
other_size – isotope, radical, charges, neighbors and hybridization symbols size
bond_width – bond width
bond_color – color of bonds
aam_color – atom-to-atom mapping color
query_color – hybridization and neighbors color
atoms_colors – atom colors where key is atomic number - 1, value is atom color (str)
broken_color – only CGRContainer: color of broken bond
formed_color – only CGRContainer: color of formed bond
other_color – color for charges, radicals, isotopes
symbols_font_style – font style for atom symbols
other_font_style – font style for mapping, charges, radicals, isotopes, hybridization and neighbors
aam – if True, depict mapping
monochrome – if True, colors of items in molecule not used
dashes – first value is long of visible line, second is long of invisible line
aromatic_space – space between simple and aromatic bonds
triple_space – space between simple and triple bonds
double_space – space between simple and double bonds
cgr_aromatic_space – only CGRContainer: space between simple and aromatic bonds
aromatic_dashes – first value is long of visible line, second is long of invisible line
atom_radius – radius of atoms spheres in depict3d. if negative is multiplier to covalent radii
bond_radius – radius of bonds spheres in depict3d
dx_ci – x-axis offset relative to the center of the atom symbol for radical, charges, isotope
dy_ci – y-axis offset relative to the center of the atom symbol for radical, charges, isotope
dx_m – x-axis offset relative to the center of the atom symbol for atom-to-atom mapping
dy_m – y-axis offset relative to the center of the atom symbol for atom-to-atom mapping
dx_nh – x-axis offset relative to the center of the atom symbol for neighbors and hybridization
dy_nh – y-axis offset relative to the center of the atom symbol for neighbors and hybridization
span_dy – y-axis offset relative to the center of the atom symbol for hydrogen count

enumerate_kekule(): Enumerate all possible kekule forms of molecule.

enumerate_tautomers(*, prepare_molecules=True, full=True, zwitter=True, ring_chain=True, keto_enol=True, limit: int = 1000) → Iterator[MoleculeContainer]

Enumerate all possible tautomeric forms of molecule.

Parameters

prepare_molecules – Standardize structures before. Aromatization and implicit hydrogens required.
full – Do full enumeration.
zwitter – Enable acid-base tautomerization
ring_chain – Enable ring-chain tautomerization
keto_enol – Enable keto-enol tautomerization
limit – Maximum amount of generated structures.

environment(atom: int, include_bond: bool = True, include_atom: bool = True) → Tuple[Union[Tuple[int, Union[Bond, DynamicBond], Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, DynamicAnyElement, ListElement]], Tuple[int, Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, DynamicAnyElement, ListElement]], Tuple[int, Union[Bond, DynamicBond]], int], ...]

groups of (atom_number, bond, atom) connected to atom or groups of (atom_number, bond) connected to atom or groups of (atom_number, atom) connected to atom or neighbors atoms connected to atom

Parameters

atom – number
include_atom – include atom object
include_bond – include bond object

explicify_hydrogens(*, fix_stereo=True, start_map=None, return_maps=False) → int

Add explicit hydrogens to atoms.

Returns: number of added atoms

flush_cache()

get_automorphism_mapping() → Iterator[Dict[int, int]]: Iterator of all possible automorphism mappings.

get_fast_mapping(other: MoleculeContainer) → Optional[Dict[int, int]]: Get self to other fast (suboptimal) structure mapping. Only one possible atoms mapping returned. Effective only for big molecules.

get_mapping(other: MoleculeContainer, **kwargs)

Get self to other substructure mapping generator.

Parameters

automorphism_filter – Skip matches to same atoms.
optimize – Morgan weights based automorphism preventing.
fallback – Try without optimization then nothing matched.

get_mcs_mapping(other: MoleculeContainer, **kwargs)

find maximum common substructure. based on clique searching in product graph.

Parameters: limit – limit tested cliques

has_atom(n: int) → bool

has_bond(n: int, m: int) → bool

heteroatoms(n: int) → int: Number of neighbored heteroatoms (not carbon or hydrogen)

huckel_pi_electrons_energy: Huckel method based Pi electrons energy calculator. Parametrized for B C N O S.

implicify_hydrogens(*, fix_stereo=True) → int

Remove explicit hydrogen if possible. Works only with Kekule forms of aromatic structures. Keeps isotopes of hydrogen.

Returns: number of removed hydrogens

is_automorphic(): Test for automorphism symmetry of graph.

is_equal(other) → bool: Test self is same structure as other

is_radical: True if at least one atom is radical

is_substructure(other) → bool: Test self is substructure of other

kekule() → bool

Convert structure to kekule form. Return True if found any aromatic ring. Set implicit hydrogen count and hybridization marks on atoms.

Only one of possible double/single bonds positions will be set. For enumerate bonds positions use enumerate_kekule.

property meta: Dict

molecular_charge: Total charge of molecule

molecular_mass

property name: str

neighbors(n: int) → int: number of neighbors atoms excluding any-bonded

neutralize(*, fix_stereo=True, logging=False) → Union[bool, List[int]]

Transform biradical or dipole resonance structures into neutral form. Return True if structure form changed.

Parameters: logging – return list of changed atoms.

pack() → bytes

Pack into compressed bytes. Note:

Less than 4096 atoms supported. Atoms mapping should be in range 1-4095.

Implicit hydrogens count should be in range 0-7

Isotope shift should be in range -15 - 15 relatively mdl.common_isotopes

Atoms neighbors should be in range 0-15

Format specification: Big endian bytes order 12 bit - number of atoms 12 bit - cis/trans stereo block size Atom block 9 bytes (repeated): 12 bit - atom number 4 bit - number of neighbors 2 bit tetrahedron sign (00 - not stereo, 10 or 11 - has stereo) 2 bit - allene sign 5 bit - isotope (00000 - not specified, over = isotope - common_isotope + 16) 7 bit - atomic number (<=118) 32 bit - XY float16 coordinates 3 bit - hydrogens (0-7) 4 bit - charge (charge + 4. possible range -4 - 4) 1 bit - radical state Connection table: flatten list of neighbors. neighbors count stored in atom block. For example CC(=O)O - {1: [2], 2: [1, 3, 4], 3: [2], 4: [2]} >> [2, 1, 3, 4, 2, 2]. Repeated block (equal to bonds count). 24 bit - paired 12 bit numbers. Bonds order block (repeated): 16 bit - 5 bonds grouped (3 bit each). 1 bit unused. Zero padding used than bonds count not proportional to 5. Cis/trans data block (repeated): 24 bit - atoms pair 7 bit - zero padding 1 bit - sign

classmethod pickle_save_cache(arg: bool): Store cache of Graph into pickle for speedup loading

classmethod pure_unpack(data: bytes) → MoleculeContainer: Unpack from compressed bytes. Python implementation.

remap(mapping, *, copy=False) → MoleculeContainer

remove_hydrogen_bonds(*, keep_to_terminal=True, fix_stereo=True) → int

Remove hydrogen bonds marked with 8 (any) bond

Parameters: keep_to_terminal – Keep any bonds to terminal hydrogens
Returns: removed bonds count

ring_atoms: Atoms in rings

rings_count: SSSR rings count.

skin_atoms: Atoms of rings and rings linkers [without terminal atoms]

skin_graph: Graph without terminal atoms. Only rings and linkers

smiles_atoms_order: Atoms order in canonic SMILES.

split(meta: bool = False) → List[MoleculeContainer]

split disconnected structure to connected substructures

Parameters: meta – copy metadata to each substructure
Returns: list of substructures

sssr

Smallest Set of Smallest Rings.

:return rings atoms numbers

standardize(*, fix_stereo=True, logging=False) → Union[bool, List[Tuple[Tuple[int, ...], int, str]]]

Standardize functional groups. Return True if any non-canonical group found.

Parameters: logging – return list of fixed atoms with matched rules.

substructure(atoms, *, as_query: bool = False, recalculate_hydrogens=True, **kwargs) → Union[MoleculeContainer, QueryContainer]

Create substructure containing atoms from atoms list.

For Thiele forms of molecule In Molecule substructure causes invalidation of internal state. Implicit hydrogens marks will not be set if atoms in aromatic rings. Call kekule() and thiele() in sequence to fix marks.

Parameters

atoms – list of atoms numbers of substructure
meta – if True metadata will be copied to substructure
as_query – return Query object based on graph substructure

tautomerize(*, prepare_molecules=True, zwitter=True, ring_chain=True, keto_enol=True, limit: int = 1000) → bool: Convert structure to canonical tautomeric form. Return True if structure changed.

tetrahedrons: Carbon sp3 atoms numbers

thiele(*, fix_tautomers=True) → bool

Convert structure to aromatic form (Huckel rule ignored). Return True if found any kekule ring. Also marks atoms as aromatic.

Parameters: fix_tautomers – try to fix condensed rings with pyroles. N1C=CC2=NC=CC2=C1>>N1C=CC2=CN=CC=C12

union(other, **kwargs)

Merge Graphs into one.

Parameters: remap – if atoms has collisions then remap other graph atoms else raise exception.

classmethod unpack(data: bytes) → MoleculeContainer: Unpack from compressed bytes.

view3d(index: int = 0, width='600px', height='400px')

Jupyter widget for 3D visualization.

Parameters

index – index of conformer
width – widget width
height – widget height

class CGRtools.containers.QueryCGRContainer

add_atom(atom: Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, DynamicAnyElement, ListElement, int, str], *args, p_charge: int = 0, p_is_radical: bool = False, neighbors: Optional[Union[int, List[int], Tuple[int, ...]]] = None, hybridization: Optional[Union[int, List[int], Tuple[int, ...]]] = None, p_neighbors: Optional[Union[int, List[int], Tuple[int, ...]]] = None, p_hybridization: Optional[Union[int, List[int], Tuple[int, ...]]] = None, **kwargs): new atom addition

add_bond(n, m, bond: Union[DynamicBond, Bond, int]): new bond addition

adjacency_matrix(set_bonds=False)

Adjacency matrix of Graph.

Parameters: set_bonds – if True set bond orders instead of 1.

atom(n: int) → Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, DynamicAnyElement, ListElement]

atoms() → Iterator[Tuple[int, Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, DynamicAnyElement, ListElement]]]: iterate over all atoms

atoms_count

atoms_numbers

atoms_order

Morgan like algorithm for graph nodes ordering

Returns: dict of atom-order pairs

atoms_rings: Dict of atoms rings which contains it.

atoms_rings_sizes: Sizes of rings containing atom.

augmented_substructure(atoms: Iterable[int], deep: int = 1, **kwargs) → Graph

create substructure containing atoms and their neighbors

Parameters

atoms – list of core atoms in graph
deep – number of bonds between atoms and neighbors
meta – copy metadata to each substructure
as_query – return Query object based on graph substructure. for Molecule and CGR only

augmented_substructures(atoms: Iterable[int], deep: int = 1, **kwargs) → List[Graph]

create list of substructures containing atoms and their neighbors

Parameters

atoms – list of core atoms in graph
deep – number of bonds between atoms and neighbors
meta – copy metadata to each substructure
as_query – return Query object based on graph substructure. for Molecule and CGR only

Returns

list of graphs containing atoms, atoms + first circle, atoms + 1st + 2nd, etc up to deep or while new nodes available

bond(n: int, m: int) → Union[Bond, DynamicBond]

bonds() → Iterator[Tuple[int, int, Union[Bond, DynamicBond]]]: iterate other all bonds

bonds_count

clean2d(): Calculate 2d layout of graph. https://pubs.acs.org/doi/10.1021/acs.jcim.7b00425 JS implementation used.

connected_components: Isolated components of single graph. E.g. salts as ion pair.

property connected_components_count: int: Number of components in graph

connected_rings: Rings groups with common atoms. E.g. naphthalene has two connected rings. Rings not atom ordered like sssr.

copy(**kwargs) → QueryCGRContainer

copy of graph

Parameters: meta – include metadata

delete_atom(n): implementation of atom removing

delete_bond(n: int, m: int): implementation of bond removing

depict(*, embedding=False)

classmethod depict_settings(*, carbon: bool = False, bond_color: str = 'black', font_size: float = 0.5, aam: bool = True, aam_color: str = '#0305A7', bond_width: float = 0.04, dashes: Tuple[float, float] = (0.2, 0.1), query_color: str = '#5D8AA8', atoms_colors: tuple = ('#909090', '#D9FFFF', '#CC80FF', '#C2FF00', '#FFB5B5', '#101010', '#3050F8', '#FF0D0D', '#90E050', '#B3E3F5', '#AB5CF2', '#8AFF00', '#BFA6A6', '#F0C8A0', '#FF8000', '#C6C600', '#1FF01F', '#80D1E3', '#8F40D4', '#3DFF00', '#E6E6E6', '#BFC2C7', '#A6A6AB', '#8A99C7', '#9C7AC7', '#E06633', '#F090A0', '#50D050', '#C88033', '#7D80B0', '#C28F8F', '#668F8F', '#BD80E3', '#FFA100', '#A62929', '#5CB8D1', '#702EB0', '#00FF00', '#94FFFF', '#94E0E0', '#73C2C9', '#54B5B5', '#3B9E9E', '#248F8F', '#0A7D8C', '#006985', '#C0C0C0', '#FFD98F', '#A67573', '#668080', '#9E63B5', '#D47A00', '#940094', '#429EB0', '#57178F', '#00C900', '#70D4FF', '#FFFFC7', '#D9FFC7', '#C7FFC7', '#A3FFC7', '#8FFFC7', '#61FFC7', '#45FFC7', '#30FFC7', '#1FFFC7', '#00FF9C', '#00E675', '#00D452', '#00BF38', '#00AB24', '#4DC2FF', '#4DA6FF', '#2194D6', '#267DAB', '#266696', '#175487', '#D0D0E0', '#FFD123', '#B8B8D0', '#A6544D', '#575961', '#9E4FB5', '#AB5C00', '#754F45', '#428296', '#420066', '#007D00', '#70ABFA', '#00BAFF', '#00A1FF', '#008FFF', '#0080FF', '#006BFF', '#545CF2', '#785CE3', '#8A4FE3', '#A136D4', '#B31FD4', '#B31FBA', '#B30DA6', '#BD0D87', '#C70066', '#CC0059', '#D1004F', '#D90045', '#E00038', '#E6002E', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026'), dx_ci: float = 0.05, dy_ci: float = 0.2, triple_space: float = 0.13, aromatic_dashes: Tuple[float, float] = (0.15, 0.05), dy_nh: float = 0.15, formed_color: str = 'green', monochrome: bool = False, atom_radius: float = 0.2, dy_m: float = 0.2, symbols_font_style: str = 'sans-serif', other_size: float = 0.3, double_space: float = 0.06, dx_m: float = 0.05, span_dy: float = 0.15, span_size: float = 0.35, dx_nh: float = 0.075, other_font_style: str = 'monospace', cgr_aromatic_space: float = 0.18, aam_size: float = 0.25, other_color: str = 'black', broken_color: str = 'red', aromatic_space: float = 0.14, bond_radius=0.02)

Settings for depict of chemical structures

Parameters

carbon – if True, depict atom C
font_size – font size
aam_size – atom-to-atom mapping font size
span_size – font size for hydrogen count
other_size – isotope, radical, charges, neighbors and hybridization symbols size
bond_width – bond width
bond_color – color of bonds
aam_color – atom-to-atom mapping color
query_color – hybridization and neighbors color
atoms_colors – atom colors where key is atomic number - 1, value is atom color (str)
broken_color – only CGRContainer: color of broken bond
formed_color – only CGRContainer: color of formed bond
other_color – color for charges, radicals, isotopes
symbols_font_style – font style for atom symbols
other_font_style – font style for mapping, charges, radicals, isotopes, hybridization and neighbors
aam – if True, depict mapping
monochrome – if True, colors of items in molecule not used
dashes – first value is long of visible line, second is long of invisible line
aromatic_space – space between simple and aromatic bonds
triple_space – space between simple and triple bonds
double_space – space between simple and double bonds
cgr_aromatic_space – only CGRContainer: space between simple and aromatic bonds
aromatic_dashes – first value is long of visible line, second is long of invisible line
atom_radius – radius of atoms spheres in depict3d. if negative is multiplier to covalent radii
bond_radius – radius of bonds spheres in depict3d
dx_ci – x-axis offset relative to the center of the atom symbol for radical, charges, isotope
dy_ci – y-axis offset relative to the center of the atom symbol for radical, charges, isotope
dx_m – x-axis offset relative to the center of the atom symbol for atom-to-atom mapping
dy_m – y-axis offset relative to the center of the atom symbol for atom-to-atom mapping
dx_nh – x-axis offset relative to the center of the atom symbol for neighbors and hybridization
dy_nh – y-axis offset relative to the center of the atom symbol for neighbors and hybridization
span_dy – y-axis offset relative to the center of the atom symbol for hydrogen count

environment(atom: int, include_bond: bool = True, include_atom: bool = True) → Tuple[Union[Tuple[int, Union[Bond, DynamicBond], Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, DynamicAnyElement, ListElement]], Tuple[int, Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, DynamicAnyElement, ListElement]], Tuple[int, Union[Bond, DynamicBond]], int], ...]

groups of (atom_number, bond, atom) connected to atom or groups of (atom_number, bond) connected to atom or groups of (atom_number, atom) connected to atom or neighbors atoms connected to atom

Parameters

atom – number
include_atom – include atom object
include_bond – include bond object

flush_cache()

get_automorphism_mapping() → Iterator[Dict[int, int]]: Iterator of all possible automorphism mappings.

get_mapping(other: Union[QueryCGRContainer, CGRContainer], **kwargs)

Get self to other substructure mapping generator.

Parameters

automorphism_filter – Skip matches to same atoms.
optimize – Morgan weights based automorphism preventing.
fallback – Try without optimization then nothing matched.

get_mcs_mapping(other: Union[QueryCGRContainer, CGRContainer], **kwargs)

find maximum common substructure. based on clique searching in product graph.

Parameters: limit – limit tested cliques

has_atom(n: int) → bool

has_bond(n: int, m: int) → bool

is_automorphic(): Test for automorphism symmetry of graph.

is_equal(other) → bool: Test self is same structure as other

is_substructure(other) → bool: Test self is substructure of other

property meta: Dict

property name: str

classmethod pickle_save_cache(arg: bool): Store cache of Graph into pickle for speedup loading

remap(mapping, *, copy=False) → QueryCGRContainer

ring_atoms: Atoms in rings

rings_count: SSSR rings count.

skin_atoms: Atoms of rings and rings linkers [without terminal atoms]

skin_graph: Graph without terminal atoms. Only rings and linkers

smiles_atoms_order: Atoms order in canonic SMILES.

split(meta: bool = False) → List[Graph]

split disconnected structure to connected substructures

Parameters: meta – copy metadata to each substructure
Returns: list of substructures

sssr

Smallest Set of Smallest Rings.

:return rings atoms numbers

substructure(atoms, **kwargs) → QueryCGRContainer

create substructure containing atoms from atoms list

Parameters

atoms – list of atoms numbers of substructure
meta – if True metadata will be copied to substructure

union(other, **kwargs) → QueryCGRContainer

Merge Graphs into one.

Parameters: remap – if atoms has collisions then remap other graph atoms else raise exception.

class CGRtools.containers.QueryContainer

add_atom(atom: Union[QueryElement, AnyElement, Element, int, str], *args, neighbors: Optional[Union[int, List[int], Tuple[int, ...]]] = None, hybridization: Optional[Union[int, List[int], Tuple[int, ...]]] = None, hydrogens: Optional[Union[int, List[int], Tuple[int, ...]]] = None, rings_sizes: Optional[Union[int, List[int], Tuple[int, ...]]] = None, heteroatoms: Optional[Union[int, List[int], Tuple[int, ...]]] = None, **kwargs): new atom addition

add_bond(n, m, bond: Union[QueryBond, Bond, int, Tuple[int, ...]]): new bond addition

adjacency_matrix(set_bonds=False)

Adjacency matrix of Graph.

Parameters: set_bonds – if True set bond orders instead of 1.

aromatic_rings: Aromatic rings atoms numbers

atom(n: int) → Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, DynamicAnyElement, ListElement]

atoms() → Iterator[Tuple[int, Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, DynamicAnyElement, ListElement]]]: iterate over all atoms

atoms_count

atoms_numbers

atoms_order

Morgan like algorithm for graph nodes ordering

Returns: dict of atom-order pairs

atoms_rings: Dict of atoms rings which contains it.

atoms_rings_sizes: Sizes of rings containing atom.

augmented_substructure(atoms: Iterable[int], deep: int = 1, **kwargs) → Graph

create substructure containing atoms and their neighbors

Parameters

atoms – list of core atoms in graph
deep – number of bonds between atoms and neighbors
meta – copy metadata to each substructure
as_query – return Query object based on graph substructure. for Molecule and CGR only

augmented_substructures(atoms: Iterable[int], deep: int = 1, **kwargs) → List[Graph]

create list of substructures containing atoms and their neighbors

Parameters

atoms – list of core atoms in graph
deep – number of bonds between atoms and neighbors
meta – copy metadata to each substructure
as_query – return Query object based on graph substructure. for Molecule and CGR only

Returns

list of graphs containing atoms, atoms + first circle, atoms + 1st + 2nd, etc up to deep or while new nodes available

bond(n: int, m: int) → Union[Bond, DynamicBond]

bonds() → Iterator[Tuple[int, int, Union[Bond, DynamicBond]]]: iterate other all bonds

bonds_count

clean2d(): Calculate 2d layout of graph. https://pubs.acs.org/doi/10.1021/acs.jcim.7b00425 JS implementation used.

clean_stereo(): Remove stereo data

connected_components: Isolated components of single graph. E.g. salts as ion pair.

property connected_components_count: int: Number of components in graph

connected_rings: Rings groups with common atoms. E.g. naphthalene has two connected rings. Rings not atom ordered like sssr.

connected_rings_cumulenes: Connected ring with attached cumulenes.

copy(**kwargs) → QueryContainer

copy of graph

Parameters: meta – include metadata

cumulenes: Alkenes, allenes and cumulenes atoms numbers

delete_atom(n): implementation of atom removing

delete_bond(n, m): implementation of bond removing

depict(*, embedding=False)

classmethod depict_settings(*, carbon: bool = False, bond_color: str = 'black', font_size: float = 0.5, aam: bool = True, aam_color: str = '#0305A7', bond_width: float = 0.04, dashes: Tuple[float, float] = (0.2, 0.1), query_color: str = '#5D8AA8', atoms_colors: tuple = ('#909090', '#D9FFFF', '#CC80FF', '#C2FF00', '#FFB5B5', '#101010', '#3050F8', '#FF0D0D', '#90E050', '#B3E3F5', '#AB5CF2', '#8AFF00', '#BFA6A6', '#F0C8A0', '#FF8000', '#C6C600', '#1FF01F', '#80D1E3', '#8F40D4', '#3DFF00', '#E6E6E6', '#BFC2C7', '#A6A6AB', '#8A99C7', '#9C7AC7', '#E06633', '#F090A0', '#50D050', '#C88033', '#7D80B0', '#C28F8F', '#668F8F', '#BD80E3', '#FFA100', '#A62929', '#5CB8D1', '#702EB0', '#00FF00', '#94FFFF', '#94E0E0', '#73C2C9', '#54B5B5', '#3B9E9E', '#248F8F', '#0A7D8C', '#006985', '#C0C0C0', '#FFD98F', '#A67573', '#668080', '#9E63B5', '#D47A00', '#940094', '#429EB0', '#57178F', '#00C900', '#70D4FF', '#FFFFC7', '#D9FFC7', '#C7FFC7', '#A3FFC7', '#8FFFC7', '#61FFC7', '#45FFC7', '#30FFC7', '#1FFFC7', '#00FF9C', '#00E675', '#00D452', '#00BF38', '#00AB24', '#4DC2FF', '#4DA6FF', '#2194D6', '#267DAB', '#266696', '#175487', '#D0D0E0', '#FFD123', '#B8B8D0', '#A6544D', '#575961', '#9E4FB5', '#AB5C00', '#754F45', '#428296', '#420066', '#007D00', '#70ABFA', '#00BAFF', '#00A1FF', '#008FFF', '#0080FF', '#006BFF', '#545CF2', '#785CE3', '#8A4FE3', '#A136D4', '#B31FD4', '#B31FBA', '#B30DA6', '#BD0D87', '#C70066', '#CC0059', '#D1004F', '#D90045', '#E00038', '#E6002E', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026', '#EB0026'), dx_ci: float = 0.05, dy_ci: float = 0.2, triple_space: float = 0.13, aromatic_dashes: Tuple[float, float] = (0.15, 0.05), dy_nh: float = 0.15, formed_color: str = 'green', monochrome: bool = False, atom_radius: float = 0.2, dy_m: float = 0.2, symbols_font_style: str = 'sans-serif', other_size: float = 0.3, double_space: float = 0.06, dx_m: float = 0.05, span_dy: float = 0.15, span_size: float = 0.35, dx_nh: float = 0.075, other_font_style: str = 'monospace', cgr_aromatic_space: float = 0.18, aam_size: float = 0.25, other_color: str = 'black', broken_color: str = 'red', aromatic_space: float = 0.14, bond_radius=0.02)

Settings for depict of chemical structures

Parameters

carbon – if True, depict atom C
font_size – font size
aam_size – atom-to-atom mapping font size
span_size – font size for hydrogen count
other_size – isotope, radical, charges, neighbors and hybridization symbols size
bond_width – bond width
bond_color – color of bonds
aam_color – atom-to-atom mapping color
query_color – hybridization and neighbors color
atoms_colors – atom colors where key is atomic number - 1, value is atom color (str)
broken_color – only CGRContainer: color of broken bond
formed_color – only CGRContainer: color of formed bond
other_color – color for charges, radicals, isotopes
symbols_font_style – font style for atom symbols
other_font_style – font style for mapping, charges, radicals, isotopes, hybridization and neighbors
aam – if True, depict mapping
monochrome – if True, colors of items in molecule not used
dashes – first value is long of visible line, second is long of invisible line
aromatic_space – space between simple and aromatic bonds
triple_space – space between simple and triple bonds
double_space – space between simple and double bonds
cgr_aromatic_space – only CGRContainer: space between simple and aromatic bonds
aromatic_dashes – first value is long of visible line, second is long of invisible line
atom_radius – radius of atoms spheres in depict3d. if negative is multiplier to covalent radii
bond_radius – radius of bonds spheres in depict3d
dx_ci – x-axis offset relative to the center of the atom symbol for radical, charges, isotope
dy_ci – y-axis offset relative to the center of the atom symbol for radical, charges, isotope
dx_m – x-axis offset relative to the center of the atom symbol for atom-to-atom mapping
dy_m – y-axis offset relative to the center of the atom symbol for atom-to-atom mapping
dx_nh – x-axis offset relative to the center of the atom symbol for neighbors and hybridization
dy_nh – y-axis offset relative to the center of the atom symbol for neighbors and hybridization
span_dy – y-axis offset relative to the center of the atom symbol for hydrogen count

environment(atom: int, include_bond: bool = True, include_atom: bool = True) → Tuple[Union[Tuple[int, Union[Bond, DynamicBond], Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, DynamicAnyElement, ListElement]], Tuple[int, Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, DynamicAnyElement, ListElement]], Tuple[int, Union[Bond, DynamicBond]], int], ...]

groups of (atom_number, bond, atom) connected to atom or groups of (atom_number, bond) connected to atom or groups of (atom_number, atom) connected to atom or neighbors atoms connected to atom

Parameters

atom – number
include_atom – include atom object
include_bond – include bond object

flush_cache()

get_automorphism_mapping() → Iterator[Dict[int, int]]: Iterator of all possible automorphism mappings.

get_mapping(other: Union[QueryContainer, MoleculeContainer], **kwargs)

Get self to other substructure mapping generator.

Parameters

automorphism_filter – Skip matches to same atoms.
optimize – Morgan weights based automorphism preventing.
fallback – Try without optimization then nothing matched.

get_mcs_mapping(other: Union[QueryContainer, MoleculeContainer], **kwargs)

find maximum common substructure. based on clique searching in product graph.

Parameters: limit – limit tested cliques

has_atom(n: int) → bool

has_bond(n: int, m: int) → bool

is_automorphic(): Test for automorphism symmetry of graph.

is_equal(other) → bool: Test self is same structure as other

is_substructure(other) → bool: Test self is substructure of other

property meta: Dict

property name: str

classmethod pickle_save_cache(arg: bool): Store cache of Graph into pickle for speedup loading

remap(mapping, *, copy=False) → QueryContainer

ring_atoms: Atoms in rings

rings_count: SSSR rings count.

skin_atoms: Atoms of rings and rings linkers [without terminal atoms]

skin_graph: Graph without terminal atoms. Only rings and linkers

smiles_atoms_order: Atoms order in canonic SMILES.

split(meta: bool = False) → List[Graph]

split disconnected structure to connected substructures

Parameters: meta – copy metadata to each substructure
Returns: list of substructures

sssr

Smallest Set of Smallest Rings.

:return rings atoms numbers

substructure(atoms, **kwargs) → QueryContainer

create substructure containing atoms from atoms list

Parameters

atoms – list of atoms numbers of substructure
meta – if True metadata will be copied to substructure

tetrahedrons: Carbon sp3 atoms numbers

union(other, **kwargs) → QueryContainer

Merge Graphs into one.

Parameters: remap – if atoms has collisions then remap other graph atoms else raise exception.

class CGRtools.containers.ReactionContainer(reactants: Iterable[Union[MoleculeContainer, QueryContainer, CGRContainer, QueryCGRContainer]] = (), products: Iterable[Union[MoleculeContainer, QueryContainer, CGRContainer, QueryCGRContainer]] = (), reagents: Iterable[Union[MoleculeContainer, QueryContainer, CGRContainer, QueryCGRContainer]] = (), meta: Optional[Dict] = None, name: Optional[str] = None)

Reaction storage. Contains reactants, products and reagents lists.

Reaction storage hashable and comparable. based on reaction unique signature (SMIRKS).

New reaction object creation

Parameters

reactants – list of MoleculeContainers [or other Structure Containers] in left side of reaction
products – right side of reaction. see reactants
reagents – middle side of reaction: solvents, catalysts, etc. see reactants
meta – dictionary of metadata. like DTYPE-DATUM in RDF

canonicalize(fix_mapping: bool = True, *, logging=False) → Union[bool, Tuple[int, Tuple[int, ...], int, str]]

Convert molecules to canonical forms of functional groups and aromatic rings without explicit hydrogens. Works only for Molecules. Return True if in any molecule found not canonical group.

Parameters

fix_mapping – Search AAM errors of functional groups.
logging – return log from molecules with index of molecule at first position. Otherwise return True if these groups found in any molecule.

centers_list: Reaction centers with leaving and coming groups.

check_valence() → List[Tuple[int, Tuple[int, ...]]]

Check valences of all atoms of all molecules.

Works only on molecules with aromatic rings in Kekule form. :return: list of invalid molecules with invalid atoms lists

clean2d(): Recalculate 2d coordinates

clean_isotopes() → bool: Clean isotope marks for all molecules in reaction. Returns True if in any molecule found isotope.

clean_stereo(): Remove stereo data

compose() → CGRContainer

Get CGR of reaction

Reagents will be presented as unchanged molecules :return: CGRContainer

contract_ions() → bool

Contract ions into salts (Molecules with disconnected components). Note: works only for unambiguous cases. e.g. equal anions/cations and different or equal cations/anions.

Return True if any ions contracted.

copy() → ReactionContainer: Get copy of object

depict()

static depict_settings(**kwargs): Settings for depict of chemical structures

enumerate_centers() → Iterator[ReactionContainer]: Get all possible single stage reactions from multistage. Note multicomponent molecules (salts etc) can be treated incorrectly.

explicify_hydrogens() → int

Add explicit hydrogens to atoms

Returns: number of added atoms

extended_centers_list

Additionally to centers_list include: * First environment of dynamic atoms. * Whole formed cycles. For condensed cycles smallest is taken. * Whole aromatic cycle with at least one dynamic atom. * Whole small (3, 4) cycle with at least one dynamic atom. * Double or triple bonds connected to previous atoms.

Note for multiple RCs intersection possible. Use enumerate_centers to prevent unobvious RCs.

fix_mapping(*, logging: bool = False) → bool: Fix atom-to-atom mapping of some functional groups. Return True if found AAM errors.

fix_positions(): Fix coordinates of molecules in reaction

flush_cache()

classmethod from_cgr(cgr: CGRContainer) → ReactionContainer: Decompose CGR into reaction

implicify_hydrogens() → int

Remove explicit hydrogens if possible

Returns: number of removed hydrogens

kekule() → bool: Convert structures to kekule form. Works only for Molecules. Return True if in any molecule found aromatic ring

classmethod load_remapping_rules(reactions): Load AAM fixing rules. Required pairs of bad mapped and good mapped reactions. Reactants in pairs should be fully equal (equal molecules and equal atom orders). Products should be equal but with different atom numbers.

property meta: Dict: Dictionary of metadata. Like DTYPE-DATUM in RDF

molecules() → Iterator[Union[MoleculeContainer, QueryContainer, CGRContainer, QueryCGRContainer]]: Iterator of all reaction molecules

property name: str

neutralize(*, logging=False) → Union[bool, Tuple[int, Tuple[int, ...]]]

Transform biradical or dipole resonance structures into neutral form. Works only for Molecules.

Parameters: logging – return log from molecules with index of molecule at first position. Otherwise return True if these groups found in any molecule.

classmethod pickle_save_cache(arg: bool): Store cache of reaction into pickle for speedup loading

property products: Tuple[Union[MoleculeContainer, QueryContainer, CGRContainer, QueryCGRContainer], ...]

property reactants: Tuple[Union[MoleculeContainer, QueryContainer, CGRContainer, QueryCGRContainer], ...]

property reagents: Tuple[Union[MoleculeContainer, QueryContainer, CGRContainer, QueryCGRContainer], ...]

remove_reagents(*, keep_reagents: bool = False) → bool

Preprocess reaction according to mapping, using the following idea: molecules(each separated graph) will be placed to reagents if it is not changed in the reaction (no bonds, charges reorders)

Return True if any reagent found.

standardize(fix_mapping: bool = True, *, logging=False) → Union[bool, Tuple[int, Tuple[int, ...], int, str]]

Standardize functional groups. Works only for Molecules.

Parameters

fix_mapping – Search AAM errors of functional groups.
logging – return log from molecules with index of molecule at first position. Otherwise return True if these groups found in any molecule.

thiele() → bool: Convert structures to aromatic form. Works only for Molecules. Return True if in any molecule found kekule ring