CGRtools.periodictable package

Contains classes of all elements used in containers: common for MoleculeContainer, Dynamic for CGRContainer, Query and DynamicQuery for QueryContainer and QueryCGRContainer respectively. Also available 3 special query atom types: AnyElement, DynamicAnyElement and ListElement

Below only carbon atom classes shown.

class CGRtools.periodictable.C(isotope: Optional[int] = None)

Bases: Element, PeriodII, GroupXIV

Element object with specified isotope

Parameters: isotope – Isotope number of element

__eq__(other): compare attached to molecules elements

__hash__(): Return hash(self).

__int__(): Same as hash

property atomic_mass: float

property atomic_number: Element number

property atomic_radius: Valence radius of atom

property atomic_symbol: str

property charge: int: Charge of atom

copy() → Core: Detached from graph copy of element

property explicit_hydrogens: int

classmethod from_atom(atom: Element) → Element: get Element copy

classmethod from_atomic_number(number: int) → Type[Element]: get Element class by its number

classmethod from_symbol(symbol: str) → Type[Element]: get Element class by its symbol

property heteroatoms: int

property hybridization: 1 - if atom has zero or only single bonded neighbors, 2 - if has only one double bonded neighbor and any amount of single bonded, 3 - if has one triple bonded and any amount of double and single bonded neighbors or two double bonded and any amount of single bonded neighbors, 4 - if atom in aromatic ring.

property implicit_hydrogens: Optional[int]

property in_ring: bool: Atom in any ring.

property is_radical: bool: Radical state of atoms

property isotope: Optional[int]: Isotope number

property isotopes_distribution: Isotopes distribution in earth

property isotopes_masses: Isotopes masses

property neighbors: int: Neighbors count of atom

property ring_sizes: Tuple[int, ...]: Atom rings sizes.

property total_hydrogens: int

valence_rules(charge: int, is_radical: bool, valence: int) → List[Tuple[Set[Tuple[int, Element]], Dict[Tuple[int, Element], int], int]]: valence rules for element with specific charge/radical state

property x: float: X coordinate of atom on 2D plane

property xy: Tuple[float, float]: (X, Y) coordinates of atom on 2D plane

property y: float: Y coordinate of atom on 2D plane

class CGRtools.periodictable.DynamicC(isotope: Optional[int] = None)

Bases: DynamicElement, PeriodII, GroupXIV

Element object with specified isotope

Parameters: isotope – Isotope number of element

__eq__(other): compare attached to molecules dynamic elements

__hash__(): Return hash(self).

__int__(): Same as hash

property atomic_mass: float

property atomic_number: Element number

property atomic_radius: Valence radius of atom

property atomic_symbol: str

property charge: int: Charge of atom

copy() → Core: Detached from graph copy of element

classmethod from_atom(atom: Union[Element, DynamicElement]) → DynamicElement: get DynamicElement object from Element object or copy of DynamicElement object

classmethod from_atomic_number(number: int) → Type[DynamicElement]: get DynamicElement class by its number

classmethod from_symbol(symbol: str) → Type[DynamicElement]: get DynamicElement class by its symbol

property hybridization: 1 - if atom has zero or only single bonded neighbors, 2 - if has only one double bonded neighbor and any amount of single bonded, 3 - if has one triple bonded and any amount of double and single bonded neighbors or two double bonded and any amount of single bonded neighbors, 4 - if atom in aromatic ring.

property in_ring: bool: Atom in any ring.

property is_radical: bool: Radical state of atoms

property isotope: Optional[int]: Isotope number

property isotopes_distribution: Isotopes distribution in earth

property isotopes_masses: Isotopes masses

property neighbors: Neighbors count of atom

property p_charge: int

property p_hybridization: Product state hybridization of atom

property p_is_radical: bool

property p_neighbors

property ring_sizes: Tuple[int, ...]: Atom rings sizes.

property x: float: X coordinate of atom on 2D plane

property xy: Tuple[float, float]: (X, Y) coordinates of atom on 2D plane

property y: float: Y coordinate of atom on 2D plane

class CGRtools.periodictable.QueryC(isotope: Optional[int] = None)

Bases: QueryElement, PeriodII, GroupXIV

Element object with specified isotope

Parameters: isotope – Isotope number of element

__eq__(other): compare attached to molecules elements and query elements

__hash__(): Return hash(self).

__int__(): Same as hash

property atomic_mass: float

property atomic_number: Element number

property atomic_radius: Valence radius of atom

property atomic_symbol: str

property charge: int: Charge of atom

copy() → Core: Detached from graph copy of element

classmethod from_atom(atom: Union[Element, QueryElement, AnyElement]) → Union[QueryElement, AnyElement]: get QueryElement or AnyElement object from Element object or copy of QueryElement or AnyElement

classmethod from_atomic_number(number: int) → Type[Union[QueryElement, AnyElement]]: get Element class by its number

classmethod from_symbol(symbol: str) → Type[Union[QueryElement, AnyElement]]: get Element class by its symbol

property heteroatoms: Tuple[int, ...]

property hybridization: 1 - if atom has zero or only single bonded neighbors, 2 - if has only one double bonded neighbor and any amount of single bonded, 3 - if has one triple bonded and any amount of double and single bonded neighbors or two double bonded and any amount of single bonded neighbors, 4 - if atom in aromatic ring.

property implicit_hydrogens: Tuple[int, ...]

property in_ring: bool: Atom in any ring.

property is_radical: bool: Radical state of atoms

property isotope: Optional[int]: Isotope number

property isotopes_distribution: Isotopes distribution in earth

property isotopes_masses: Isotopes masses

property neighbors: Tuple[int, ...]: Neighbors count of atom

property ring_sizes: Tuple[int, ...]: Atom rings sizes.

property x: float: X coordinate of atom on 2D plane

property xy: Tuple[float, float]: (X, Y) coordinates of atom on 2D plane

property y: float: Y coordinate of atom on 2D plane

class CGRtools.periodictable.DynamicQueryC(isotope: Optional[int] = None)

Bases: DynamicQueryElement, PeriodII, GroupXIV

Element object with specified isotope

Parameters: isotope – Isotope number of element

__eq__(other): Return self==value.

__hash__(): Return hash(self).

__int__(): Same as hash

property atomic_mass: float

property atomic_number: Element number

property atomic_radius: Valence radius of atom

property atomic_symbol: str

property charge: int: Charge of atom

copy() → Core: Detached from graph copy of element

classmethod from_atom(atom: Union[Element, DynamicElement, DynamicQueryElement, DynamicAnyElement, QueryElement, AnyElement]) → Union[DynamicQueryElement, DynamicAnyElement]: get DynamicQueryElement or DynamicAnyElement object from Element or DynamicElement or QueryElement object or copy of DynamicQueryElement or DynamicAnyElement

classmethod from_atomic_number(number: int) → Type[Union[DynamicQueryElement, DynamicAnyElement]]: get Element class by its number

classmethod from_symbol(symbol: str) → Type[Union[DynamicQueryElement, DynamicAnyElement]]: get Element class by its symbol

property hybridization: 1 - if atom has zero or only single bonded neighbors, 2 - if has only one double bonded neighbor and any amount of single bonded, 3 - if has one triple bonded and any amount of double and single bonded neighbors or two double bonded and any amount of single bonded neighbors, 4 - if atom in aromatic ring.

property in_ring: bool: Atom in any ring.

property is_radical: bool: Radical state of atoms

property isotope: Optional[int]: Isotope number

property isotopes_distribution: Isotopes distribution in earth

property isotopes_masses: Isotopes masses

property neighbors: Tuple[int, ...]: Number of neighbors of atom in reactant state.

property p_charge: int

property p_hybridization: Product state hybridization of atom

property p_is_radical: bool

property p_neighbors: Tuple[int, ...]: Number of neighbors of atom in product state.

property ring_sizes: Tuple[int, ...]: Atom rings sizes.

property x: float: X coordinate of atom on 2D plane

property xy: Tuple[float, float]: (X, Y) coordinates of atom on 2D plane

property y: float: Y coordinate of atom on 2D plane

class CGRtools.periodictable.AnyElement(*args, **kwargs)

Bases: Query

Element object with specified isotope

Parameters: isotope – Isotope number of element

__eq__(other): Compare attached to molecules elements and query elements

__hash__(): Return hash(self).

__int__(): Same as hash

property atomic_mass: float

property atomic_number: int: Element number

property atomic_radius: Valence radius of atom

property atomic_symbol: str

property charge: int: Charge of atom

copy() → Core: Detached from graph copy of element

property heteroatoms: Tuple[int, ...]

property hybridization: 1 - if atom has zero or only single bonded neighbors, 2 - if has only one double bonded neighbor and any amount of single bonded, 3 - if has one triple bonded and any amount of double and single bonded neighbors or two double bonded and any amount of single bonded neighbors, 4 - if atom in aromatic ring.

property implicit_hydrogens: Tuple[int, ...]

property in_ring: bool: Atom in any ring.

property is_radical: bool: Radical state of atoms

property isotope: Optional[int]: Isotope number

property isotopes_distribution: Dict[int, float]: Isotopes distribution in earth

property isotopes_masses: Dict[int, float]: Isotopes masses

property neighbors: Tuple[int, ...]: Neighbors count of atom

property ring_sizes: Tuple[int, ...]: Atom rings sizes.

property x: float: X coordinate of atom on 2D plane

property xy: Tuple[float, float]: (X, Y) coordinates of atom on 2D plane

property y: float: Y coordinate of atom on 2D plane

class CGRtools.periodictable.DynamicAnyElement(*args, **kwargs)

Bases: DynamicQuery

Element object with specified isotope

Parameters: isotope – Isotope number of element

__eq__(other): Return self==value.

__hash__(): Return hash(self).

__int__(): Same as hash

property atomic_mass: float

property atomic_number: int: Element number

property atomic_radius: Valence radius of atom

property atomic_symbol: str

property charge: int: Charge of atom

copy() → Core: Detached from graph copy of element

property hybridization: 1 - if atom has zero or only single bonded neighbors, 2 - if has only one double bonded neighbor and any amount of single bonded, 3 - if has one triple bonded and any amount of double and single bonded neighbors or two double bonded and any amount of single bonded neighbors, 4 - if atom in aromatic ring.

property in_ring: bool: Atom in any ring.

property is_radical: bool: Radical state of atoms

property isotope: Optional[int]: Isotope number

property isotopes_distribution: Dict[int, float]: Isotopes distribution in earth

property isotopes_masses: Dict[int, float]: Isotopes masses

property neighbors: Tuple[int, ...]: Number of neighbors of atom in reactant state.

property p_charge: int

property p_hybridization: Product state hybridization of atom

property p_is_radical: bool

property p_neighbors: Tuple[int, ...]: Number of neighbors of atom in product state.

property ring_sizes: Tuple[int, ...]: Atom rings sizes.

property x: float: X coordinate of atom on 2D plane

property xy: Tuple[float, float]: (X, Y) coordinates of atom on 2D plane

property y: float: Y coordinate of atom on 2D plane

class CGRtools.periodictable.ListElement(elements: List[str], *args, **kwargs)

Bases: AnyElement

Elements list

__eq__(other): Compare attached to molecules elements and query elements

__hash__(): 13bit = 4bit | 1bit | 4bit | 4bit

__int__(): Same as hash

property atomic_mass: float

property atomic_number: int: Element number

property atomic_radius: Valence radius of atom

property atomic_symbol: str

property charge: int: Charge of atom

copy() → ListElement: Detached from graph copy of element

property heteroatoms: Tuple[int, ...]

property hybridization: 1 - if atom has zero or only single bonded neighbors, 2 - if has only one double bonded neighbor and any amount of single bonded, 3 - if has one triple bonded and any amount of double and single bonded neighbors or two double bonded and any amount of single bonded neighbors, 4 - if atom in aromatic ring.

property implicit_hydrogens: Tuple[int, ...]

property in_ring: bool: Atom in any ring.

property is_radical: bool: Radical state of atoms

property isotope: Optional[int]: Isotope number

property isotopes_distribution: Dict[int, float]: Isotopes distribution in earth

property isotopes_masses: Dict[int, float]: Isotopes masses

property neighbors: Tuple[int, ...]: Neighbors count of atom

property ring_sizes: Tuple[int, ...]: Atom rings sizes.

property x: float: X coordinate of atom on 2D plane

property xy: Tuple[float, float]: (X, Y) coordinates of atom on 2D plane

property y: float: Y coordinate of atom on 2D plane