`chemistry_tools.pubchem.compound`¶

Attention

This module has the following additional requirements:

cawdrey>=0.1.7
mathematical>=0.1.13
pillow>=7.0.0; platform_python_implementation == "PyPy" and python_version != "3.6"
pillow>=7.0.0; platform_python_implementation != "PyPy"
pillow<=8.0.0,>=7.0.0; platform_python_implementation == "PyPy" and python_version == "3.6"
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, **_)

Corresponds to a single record from the PubChem Compound database.

Functions:

compounds_to_frame(compounds)

Construct a pandas.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

Corresponds to 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

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.

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. See the table below. Can be either a comma-separated string or a list.

Property	Description
MolecularFormula	Molecular formula.
MolecularWeight	The molecular weight is the sum of all atomic weights of the constituent atoms in a compound, measured in g/mol. In the absence of explicit isotope labelling, averaged natural abundance is assumed. If an atom bears an explicit isotope label, 100% isotopic purity is assumed at this location.
CanonicalSMILES	Canonical SMILES (Simplified Molecular Input Line Entry System) string. It is a unique SMILES string of a compound, generated by a “canonicalization” algorithm.
IsomericSMILES	Isomeric SMILES string. It is a SMILES string with stereochemical and isotopic specifications.
InChI	Standard IUPAC International Chemical Identifier (InChI). It does not allow for user selectable options in dealing with the stereochemistry and tautomer layers of the InChI string.
InChIKey	Hashed version of the full standard InChI, consisting of 27 characters.
IUPACName	Chemical name systematically determined according to the IUPAC nomenclatures.
XLogP	Computationally generated octanol-water partition coefficient or distribution coefficient. XLogP is used as a measure of hydrophilicity or hydrophobicity of a molecule.
ExactMass	The mass of the most likely isotopic composition for a single molecule, corresponding to the most intense ion/molecule peak in a mass spectrum.
MonoisotopicMass	The mass of a molecule, calculated using the mass of the most abundant isotope of each element.
TPSA	Topological polar surface area, computed by the algorithm described in the paper by Ertl et al.
Complexity	The molecular complexity rating of a compound, computed using the Bertz/Hendrickson/Ihlenfeldt formula.
Charge	The total (or net) charge of a molecule.
HBondDonorCount	Number of hydrogen-bond donors in the structure.
HBondAcceptorCount	Number of hydrogen-bond acceptors in the structure.
RotatableBondCount	Number of rotatable bonds.
HeavyAtomCount	Number of non-hydrogen atoms.
IsotopeAtomCount	Number of atoms with enriched isotope(s)
AtomStereoCount	Total number of atoms with tetrahedral (sp3) stereo [e.g., (R)- or (S)-configuration]
DefinedAtomStereoCount	Number of atoms with defined tetrahedral (sp3) stereo.
UndefinedAtomStereoCount	Number of atoms with undefined tetrahedral (sp3) stereo.
BondStereoCount	Total number of bonds with planar (sp2) stereo [e.g., (E)- or (Z)-configuration].
DefinedBondStereoCount	Number of atoms with defined planar (sp2) stereo.
UndefinedBondStereoCount	Number of atoms with undefined planar (sp2) stereo.
CovalentUnitCount	Number of covalently bound units.
Volume3D	Analytic volume of the first diverse conformer (default conformer) for a compound.
XStericQuadrupole3D	The x component of the quadrupole moment (Qx) of the first diverse conformer (default conformer) for a compound.
YStericQuadrupole3D	The y component of the quadrupole moment (Qy) of the first diverse conformer (default conformer) for a compound.
ZStericQuadrupole3D	The z component of the quadrupole moment (Qz) of the first diverse conformer (default conformer) for a compound.
FeatureCount3D	Total number of 3D features (the sum of FeatureAcceptorCount3D, FeatureDonorCount3D, FeatureAnionCount3D, FeatureCationCount3D, FeatureRingCount3D and FeatureHydrophobeCount3D)
FeatureAcceptorCount3D	Number of hydrogen-bond acceptors of a conformer.
FeatureDonorCount3D	Number of hydrogen-bond donors of a conformer.
FeatureAnionCount3D	Number of anionic centers (at pH 7) of a conformer.
FeatureCationCount3D	Number of cationic centers (at pH 7) of a conformer.
FeatureRingCount3D	Number of rings of a conformer.
FeatureHydrophobeCount3D	Number of hydrophobes of a conformer.
ConformerModelRMSD3D	Conformer sampling RMSD in Å.
EffectiveRotorCount3D	Total number of 3D features (the sum of FeatureAcceptorCount3D, FeatureDonorCount3D, FeatureAnionCount3D, FeatureCationCount3D, FeatureRingCount3D and FeatureHydrophobeCount3D)
ConformerCount3D	The number of conformers in the conformer model for a compound.
Fingerprint2D	Base64-encoded PubChem Substructure Fingerprint of a molecule.

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 below.

Property	Description
MolecularFormula	Molecular formula.
MolecularWeight	The molecular weight is the sum of all atomic weights of the constituent atoms in a compound, measured in g/mol. In the absence of explicit isotope labelling, averaged natural abundance is assumed. If an atom bears an explicit isotope label, 100% isotopic purity is assumed at this location.
CanonicalSMILES	Canonical SMILES (Simplified Molecular Input Line Entry System) string. It is a unique SMILES string of a compound, generated by a “canonicalization” algorithm.
IsomericSMILES	Isomeric SMILES string. It is a SMILES string with stereochemical and isotopic specifications.
InChI	Standard IUPAC International Chemical Identifier (InChI). It does not allow for user selectable options in dealing with the stereochemistry and tautomer layers of the InChI string.
InChIKey	Hashed version of the full standard InChI, consisting of 27 characters.
IUPACName	Chemical name systematically determined according to the IUPAC nomenclatures.
XLogP	Computationally generated octanol-water partition coefficient or distribution coefficient. XLogP is used as a measure of hydrophilicity or hydrophobicity of a molecule.
ExactMass	The mass of the most likely isotopic composition for a single molecule, corresponding to the most intense ion/molecule peak in a mass spectrum.
MonoisotopicMass	The mass of a molecule, calculated using the mass of the most abundant isotope of each element.
TPSA	Topological polar surface area, computed by the algorithm described in the paper by Ertl et al.
Complexity	The molecular complexity rating of a compound, computed using the Bertz/Hendrickson/Ihlenfeldt formula.
Charge	The total (or net) charge of a molecule.
HBondDonorCount	Number of hydrogen-bond donors in the structure.
HBondAcceptorCount	Number of hydrogen-bond acceptors in the structure.
RotatableBondCount	Number of rotatable bonds.
HeavyAtomCount	Number of non-hydrogen atoms.
IsotopeAtomCount	Number of atoms with enriched isotope(s)
AtomStereoCount	Total number of atoms with tetrahedral (sp3) stereo [e.g., (R)- or (S)-configuration]
DefinedAtomStereoCount	Number of atoms with defined tetrahedral (sp3) stereo.
UndefinedAtomStereoCount	Number of atoms with undefined tetrahedral (sp3) stereo.
BondStereoCount	Total number of bonds with planar (sp2) stereo [e.g., (E)- or (Z)-configuration].
DefinedBondStereoCount	Number of atoms with defined planar (sp2) stereo.
UndefinedBondStereoCount	Number of atoms with undefined planar (sp2) stereo.
CovalentUnitCount	Number of covalently bound units.
Volume3D	Analytic volume of the first diverse conformer (default conformer) for a compound.
XStericQuadrupole3D	The x component of the quadrupole moment (Qx) of the first diverse conformer (default conformer) for a compound.
YStericQuadrupole3D	The y component of the quadrupole moment (Qy) of the first diverse conformer (default conformer) for a compound.
ZStericQuadrupole3D	The z component of the quadrupole moment (Qz) of the first diverse conformer (default conformer) for a compound.
FeatureCount3D	Total number of 3D features (the sum of FeatureAcceptorCount3D, FeatureDonorCount3D, FeatureAnionCount3D, FeatureCationCount3D, FeatureRingCount3D and FeatureHydrophobeCount3D)
FeatureAcceptorCount3D	Number of hydrogen-bond acceptors of a conformer.
FeatureDonorCount3D	Number of hydrogen-bond donors of a conformer.
FeatureAnionCount3D	Number of anionic centers (at pH 7) of a conformer.
FeatureCationCount3D	Number of cationic centers (at pH 7) of a conformer.
FeatureRingCount3D	Number of rings of a conformer.
FeatureHydrophobeCount3D	Number of hydrophobes of a conformer.
ConformerModelRMSD3D	Conformer sampling RMSD in Å.
EffectiveRotorCount3D	Total number of 3D features (the sum of FeatureAcceptorCount3D, FeatureDonorCount3D, FeatureAnionCount3D, FeatureCationCount3D, FeatureRingCount3D and FeatureHydrophobeCount3D)
ConformerCount3D	The number of conformers in the conformer model for a compound.
Fingerprint2D	Base64-encoded PubChem Substructure Fingerprint of a molecule.

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 pandas.DataFrame from a list of Compound objects.

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

chemistry_tools.pubchem.compound¶

`chemistry_tools.pubchem.compound`¶