`chemistry_tools.pubchem.compound`

Attention

This package has the following additional requirements:

cawdrey>=0.1.7
mathematical>=0.1.13
pillow>=7.0.0
pyparsing>=2.4.6
tabulate>=0.8.9

These can be installed as follows:

python -m pip install chemistry-tools[pubchem]

Represents a chemical compound.

Data:

`C`	Invariant `TypeVar` bound to `chemistry_tools.pubchem.compound.Compound`.

Classes:

Compound(title, CID, description, **_)

Represents a single record from the PubChem Compound database.

Functions:

compounds_to_frame(compounds)

Construct a DataFrame from a list of Compound objects.

C = TypeVar(C, bound=Compound)

Type: TypeVar

Invariant TypeVar bound to chemistry_tools.pubchem.compound.Compound.

class Compound(title, CID, description, **_)[source]

Bases: Dictable

Represents a single record from the PubChem Compound database.

The PubChem Compound database is constructed from the Substance database using a standardization and deduplication process. Each Compound is uniquely identified by a CID.

Parameters

title (str) – The title of the compound record (usually the name of the compound)
CID (int)
description (str)

Methods:

`__repr__`()	Return a string representation of the `Compound`.
`from_cid`(cid[, record_type])	Returns the Compound objects for the compound with the given CID.
`get_iupac_name`([type_])	Return the IUPAC name of this compound.
`get_properties`(properties)	Returns the requested properties for the Compound.
`get_property`(prop)	Get a single property for the compound.
`precache`()	Precache all properties for this compound.
`to_series`()	Return a pandas `Series` containing Compound data.

Attributes:

`atoms`	List of `Atoms` in this Compound.
`bonds`	List of `Bonds` between `Atoms` in this Compound.
`cactvs_fingerprint`	PubChem CACTVS fingerprint.
`canonical_smiles`	Canonical SMILES, with no stereochemistry information.
`canonicalized`	Whether the compound is canonicalized.
`charge`	The charge of the compound.
`cid`	Returns the ID of this compound.
`coordinate_type`	The coordinate type of this compound.
`elements`	List of element symbols for atoms in this Compound.
`fingerprint`	Raw padded and hex-encoded fingerprint, as returned by the PUG REST API.
`has_full_record`	Returns whether this compound has a full record available.
`iupac_name`	The preferred IUPAC name of this compound.
`molecular_formula`	Molecular formula.
`molecular_mass`	Molecular Weight.
`molecular_weight`	Molecular Weight.
`smiles`	Canonical SMILES, with no stereochemistry information.
`synonyms`	Returns a list of synonyms for the Compound.
`systematic_name`	The systematic IUPAC name of this compound.

__repr__()[source]

Return a string representation of the Compound.

Return type: str

property atoms

List of Atoms in this Compound.

Return type: List[Atom]

property bonds

List of Bonds between Atoms in this Compound.

Return type: List[Bond]

property cactvs_fingerprint

PubChem CACTVS fingerprint.

Each bit in the fingerprint represents the presence or absence of one of 881 chemical substructures.

Return type: Optional[str]

property canonical_smiles

Canonical SMILES, with no stereochemistry information.

Return type: str

property canonicalized

Whether the compound is canonicalized.

Return type: bool

property charge

The charge of the compound.

Return type: int

property cid

Returns the ID of this compound.

Return type: int

property coordinate_type

The coordinate type of this compound.

Return type: Optional[str]

property elements

List of element symbols for atoms in this Compound.

Return type: List[str]

property fingerprint

Raw padded and hex-encoded fingerprint, as returned by the PUG REST API.

Return type: Optional[str]

classmethod from_cid(cid, record_type='2d')[source]

Returns the Compound objects for the compound with the given CID.

Parameters

cid (Union[str, int])
record_type (str) – Default '2d'.

Return type

Compound

get_iupac_name(type_='Systematic')[source]

Return the IUPAC name of this compound.

Parameters: type_ (str) – The type of IUPAC name. Default 'Systematic'.
Return type: Optional[str]

get_properties(properties)[source]

Returns the requested properties for the Compound.

Parameters: properties (Union[Sequence[str], str]) – The properties to retrieve for the compound. Can be either a comma-separated string or a list. See the table at the start of this chapter for a list of valid properties.
Return type: Dict[str, Any]
Returns: Dictionary mapping the property names to their values

get_property(prop)[source]

Get a single property for the compound.

Parameters: prop (str) – The property to retrieve for the compound. See the table at the start of this chapter for a list of valid properties.
Return type: Any

property has_full_record

Returns whether this compound has a full record available.

Return type: bool

property iupac_name

The preferred IUPAC name of this compound.

Return type: Optional[str]

property molecular_formula

Molecular formula.

Return type: Formula

property molecular_mass

Molecular Weight.

Return type: float

property molecular_weight

Molecular Weight.

Return type: float

precache()[source]: Precache all properties for this compound.

property smiles

Canonical SMILES, with no stereochemistry information.

Return type: str

property synonyms

Returns a list of synonyms for the Compound.

Return type: Optional[List[str]]

property systematic_name

The systematic IUPAC name of this compound.

Return type: Optional[str]

to_series()[source]

Return a pandas Series containing Compound data.

Return type: Series

compounds_to_frame(compounds)[source]

Construct a DataFrame from a list of Compound objects.

Parameters: compounds (Union[Compound, List[Compound]])
Return type: DataFrame

chemistry_tools.pubchem.compound

`chemistry_tools.pubchem.compound`