`chemistry_tools.pubchem.properties`¶

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]

Functions and classes to access properties of compounds in the PubChem database.

Data:

`PROPERTY_MAP`	Allows properties to optionally be specified as underscore_separated, consistent with Compound attributes
`valid_properties`	Properties for PubChem REST API
`valid_property_descriptions`	Table giving descriptions of valid properties.

Classes:

`PropData`(name, description, type, attr_name)	Metadata about a property.
`PubChemProperty`(label[, name, value, dtype, …])	Represents a property parsed from the full PubChem record.

Functions:

`force_valid_properties`(properties)	Coerce `properties` into a list of strings and exclude any invalid properties, or raise a `ValueError` if that is not possible.
`get_properties`(identifier[, properties, …])	Returns the requested properties for the compound with the given identifier.
`get_property`(identifier[, property, namespace])	Returns the requested property for the compound with the given identifier.
`insert_valid_properties_table`()	Decorator to insert table of valid properties into the docstring of the decorated function.
`parse_properties`(property_data)	Parse raw data from the `property` endpoint of the REST API.
`rest_get_properties`(identifier[, namespace, …])	Returns the properties for the compound with the given identifier in the desired format.
`rest_get_properties_json`(identifier[, …])	Returns the properties for the compound with the given identifier as a dictionary.
`string_list`(val)	Coerce an iterable of values to a list of strings.

PROPERTY_MAP = {'atom_stereo_count': 'AtomStereoCount', 'bond_stereo_count': 'BondStereoCount', 'canonical_smiles': 'CanonicalSMILES', 'charge': 'Charge', 'complexity': 'Complexity', 'conformer_count_3d': 'ConformerCount3D', 'conformer_model_rmsd_3d': 'ConformerModelRMSD3D', 'covalent_unit_count': 'CovalentUnitCount', 'defined_atom_stereo_count': 'DefinedAtomStereoCount', 'defined_bond_stereo_count': 'DefinedBondStereoCount', 'effective_rotor_count_3d': 'EffectiveRotorCount3D', 'exact_mass': 'ExactMass', 'feature_acceptor_count_3d': 'FeatureAcceptorCount3D', 'feature_anion_count_3d': 'FeatureAnionCount3D', 'feature_cation_count_3d': 'FeatureCationCount3D', 'feature_count_3d': 'FeatureCount3D', 'feature_donor_count_3d': 'FeatureDonorCount3D', 'feature_hydrophobe_count_3d': 'FeatureHydrophobeCount3D', 'feature_ring_count_3d': 'FeatureRingCount3D', 'fingerprint_2d': 'Fingerprint2D', 'h_bond_acceptor_count': 'HBondAcceptorCount', 'h_bond_donor_count': 'HBondDonorCount', 'heavy_atom_count': 'HeavyAtomCount', 'inchi': 'InChI', 'inchikey': 'InChIKey', 'isomeric_smiles': 'IsomericSMILES', 'isotope_atom_count': 'IsotopeAtomCount', 'iupac_name': 'IUPACName', 'molecular_formula': 'MolecularFormula', 'molecular_weight': 'MolecularWeight', 'monoisotopic_mass': 'MonoisotopicMass', 'rotatable_bond_count': 'RotatableBondCount', 'tpsa': 'TPSA', 'undefined_atom_stereo_count': 'UndefinedAtomStereoCount', 'undefined_bond_stereo_count': 'UndefinedBondStereoCount', 'volume3d': 'Volume3D', 'volume_3d': 'XStericQuadrupole3D', 'x_steric_quadrupole_3d': 'YStericQuadrupole3D', 'xlogp': 'XLogP', 'y_steric_quadrupole_3d': 'ZStericQuadrupole3D'}¶

Type: Dict[str, str]

Allows properties to optionally be specified as underscore_separated, consistent with Compound attributes

namedtuple PropData(name, description, type, attr_name)[source]¶

Bases: NamedTuple

Metadata about a property.

Fields

name (str) – The name of the property.
description (str) – The description of the property.
type (Callable) – The type of the property.
attr_name (str) – The Python attribute name of the property in a chemistry_tools.pubchem.compound.Compound.

__repr__()¶: Return a nicely formatted representation string

namedtuple PubChemProperty(label, name=None, value=None, dtype=None, source=None)[source]¶

Bases: NamedTuple

Represents a property parsed from the full PubChem record.

Fields

label (str) – The label of the property.
name (str) – The name of the property.
value (Any) – The property’s value.
dtype (Callable) – The data type property’s value.
source (Dict) – Dictionary of property sources.

force_valid_properties(properties)[source]¶

Coerce properties into a list of strings and exclude any invalid properties, or raise a ValueError if that is not possible.

Parameters: properties (Union[str, Iterable[str]])
Return type: List[str]

get_properties(identifier, properties='', namespace=<PubChemNamespace.Name: 'name'>, as_dataframe=False)[source]¶

Returns the requested properties for the compound with the given identifier. As more than one compound may be identified the results are returned in a list.

Parameters

identifier (Union[str, int, Sequence[Union[str, int]]]) – Identifiers (e.g. name, CID) for the compound to look up. When using the CID namespace data for multiple compounds can be retrieved at once by supplying either a comma-separated string or a list.
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. Default ''.

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.

Parameters

namespace (Union[PubChemNamespace, str]) – The type of identifier to look up. Valid values are in PubChemNamespace. Default <PubChemNamespace.Name: 'name'>.
as_dataframe (bool) – Automatically extract the properties into a pandas DataFrame. Default False.

Raises

ValueError – If the response body does not contain valid JSON.
NotFoundError – If the compound with the requested identifier was not found in PubChem.

Return type

Union[List[Dict[str, Any]], DataFrame]

Returns

List of dictionaries mapping properties to values

get_property(identifier, property='', namespace=<PubChemNamespace.Name: 'name'>)[source]¶

Returns the requested property for the compound with the given identifier.

This convenience function only allows for a single property to be accessed at once, and for only a single compound. if you require multiple properties and/or properties for multiple compounds use chemistry_tools.pubchem.properties.get_properties, which helps reduce the burden on the PubChem servers.

Parameters

identifier (Union[str, int, Sequence[Union[str, int]]]) – Identifiers (e.g. name, CID) for the compound to look up.
property (str) – The property to retrieve for the compound. See the table below. Default ''.

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.

Parameters

namespace (Union[PubChemNamespace, str]) – The type of identifier to look up. Valid values are in PubChemNamespace. Default <PubChemNamespace.Name: 'name'>.

Raises

ValueError – If the response body does not contain valid JSON.
NotFoundError – If the compound with the requested identifier was not found in PubChem.

Return type

Any

Returns

The requested property. Type depends on the property requested

insert_valid_properties_table()[source]¶

Decorator to insert table of valid properties into the docstring of the decorated function.

Return type: Callable

parse_properties(property_data)[source]¶

Parse raw data from the property endpoint of the REST API.

Parameters: property_data (Dict)
Return type: List[Dict]
Returns: A list of dictionaries mapping the properties to values for each compound

rest_get_properties(identifier, namespace=<PubChemNamespace.Name: 'name'>, properties='', format_=<PubChemFormats.CSV: 'CSV'>)[source]¶

Returns the properties for the compound with the given identifier in the desired format.

Parameters

identifier (Union[str, int, Sequence[Union[str, int]]]) – Identifiers (e.g. name, CID) for the compound to look up. When using the CID namespace data for multiple compounds can be retrieved at once by supplying either a comma-separated string or a list.
namespace – The type of identifier to look up. Valid values are in PubChemNamespace. Default <PubChemNamespace.Name: 'name'>.
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. Default ''.

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.

Parameters: format_ (Union[PubChemFormats, str]) – The format to obtain the data in. Default <PubChemFormats.CSV: 'CSV'>.

rest_get_properties_json(identifier, namespace=<PubChemNamespace.Name: 'name'>, properties='', **kwargs)[source]¶

Returns the properties for the compound with the given identifier as a dictionary.

Parameters

identifier (Union[str, int, Sequence[Union[str, int]]]) – Identifiers (e.g. name, CID) for the compound to look up. When using the CID namespace data for multiple compounds can be retrieved at once by supplying either a comma-separated string or a list.
namespace – The type of identifier to look up. Valid values are in PubChemNamespace. Default <PubChemNamespace.Name: 'name'>.
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. Default ''.

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.

Parameters: kwargs – Optional arguments that json.loads takes.
Raises: ValueError – If the response body does not contain valid JSON.
Return type: Dict
Returns: Parsed JSON data

string_list(val)[source]¶

Coerce an iterable of values to a list of strings.

Parameters: val (Iterable[Any])
Return type: List[str]

valid_properties = {'AtomStereoCount': <class 'int'>, 'BondStereoCount': <class 'int'>, 'CanonicalSMILES': <class 'str'>, 'Charge': <class 'int'>, 'Complexity': <class 'float'>, 'ConformerCount3D': <class 'int'>, 'ConformerModelRMSD3D': <class 'float'>, 'CovalentUnitCount': <class 'int'>, 'DefinedAtomStereoCount': <class 'int'>, 'DefinedBondStereoCount': <class 'int'>, 'EffectiveRotorCount3D': <class 'int'>, 'ExactMass': <class 'float'>, 'FeatureAcceptorCount3D': <class 'int'>, 'FeatureAnionCount3D': <class 'int'>, 'FeatureCationCount3D': <class 'int'>, 'FeatureCount3D': <class 'int'>, 'FeatureDonorCount3D': <class 'int'>, 'FeatureHydrophobeCount3D': <class 'int'>, 'FeatureRingCount3D': <class 'int'>, 'Fingerprint2D': <class 'str'>, 'HBondAcceptorCount': <class 'int'>, 'HBondDonorCount': <class 'int'>, 'HeavyAtomCount': <class 'int'>, 'IUPACName': <class 'str'>, 'InChI': <class 'str'>, 'InChIKey': <class 'str'>, 'IsomericSMILES': <class 'str'>, 'IsotopeAtomCount': <class 'int'>, 'MolecularFormula': <bound method Formula.from_string of <class 'chemistry_tools.formulae.formula.Formula'>>, 'MolecularWeight': <class 'float'>, 'MonoisotopicMass': <class 'float'>, 'RotatableBondCount': <class 'int'>, 'TPSA': <class 'float'>, 'UndefinedAtomStereoCount': <class 'int'>, 'UndefinedBondStereoCount': <class 'int'>, 'Volume3D': <class 'str'>, 'XLogP': <class 'float'>, 'XStericQuadrupole3D': <class 'float'>, 'YStericQuadrupole3D': <class 'float'>, 'ZStericQuadrupole3D': <class 'float'>}¶

Type: Dict[str, Callable]

Properties for PubChem REST API

valid_property_descriptions = '======================== ===================================================================================================================================================================================================================================================================================================\nProperty Description\n======================== ===================================================================================================================================================================================================================================================================================================\nMolecularFormula Molecular formula.\nMolecularWeight 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.\nCanonicalSMILES Canonical SMILES (Simplified Molecular Input Line Entry System) string. It is a unique SMILES string of a compound, generated by a “canonicalization” algorithm.\nIsomericSMILES Isomeric SMILES string. It is a SMILES string with stereochemical and isotopic specifications.\nInChI 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.\nInChIKey Hashed version of the full standard InChI, consisting of 27 characters.\nIUPACName Chemical name systematically determined according to the IUPAC nomenclatures.\nXLogP Computationally generated octanol-water partition coefficient or distribution coefficient. XLogP is used as a measure of hydrophilicity or hydrophobicity of a molecule.\nExactMass The mass of the most likely isotopic composition for a single molecule, corresponding to the most intense ion/molecule peak in a mass spectrum.\nMonoisotopicMass The mass of a molecule, calculated using the mass of the most abundant isotope of each element.\nTPSA Topological polar surface area, computed by the algorithm described in the paper by Ertl et al.\nComplexity The molecular complexity rating of a compound, computed using the Bertz/Hendrickson/Ihlenfeldt formula.\nCharge The total (or net) charge of a molecule.\nHBondDonorCount Number of hydrogen-bond donors in the structure.\nHBondAcceptorCount Number of hydrogen-bond acceptors in the structure.\nRotatableBondCount Number of rotatable bonds.\nHeavyAtomCount Number of non-hydrogen atoms.\nIsotopeAtomCount Number of atoms with enriched isotope(s)\nAtomStereoCount Total number of atoms with tetrahedral (sp3) stereo [e.g., (R)- or (S)-configuration]\nDefinedAtomStereoCount Number of atoms with defined tetrahedral (sp3) stereo.\nUndefinedAtomStereoCount Number of atoms with undefined tetrahedral (sp3) stereo.\nBondStereoCount Total number of bonds with planar (sp2) stereo [e.g., (E)- or (Z)-configuration].\nDefinedBondStereoCount Number of atoms with defined planar (sp2) stereo.\nUndefinedBondStereoCount Number of atoms with undefined planar (sp2) stereo.\nCovalentUnitCount Number of covalently bound units.\nVolume3D Analytic volume of the first diverse conformer (default conformer) for a compound.\nXStericQuadrupole3D The x component of the quadrupole moment (Qx) of the first diverse conformer (default conformer) for a compound.\nYStericQuadrupole3D The y component of the quadrupole moment (Qy) of the first diverse conformer (default conformer) for a compound.\nZStericQuadrupole3D The z component of the quadrupole moment (Qz) of the first diverse conformer (default conformer) for a compound.\nFeatureCount3D Total number of 3D features (the sum of FeatureAcceptorCount3D, FeatureDonorCount3D, FeatureAnionCount3D, FeatureCationCount3D, FeatureRingCount3D and FeatureHydrophobeCount3D)\nFeatureAcceptorCount3D Number of hydrogen-bond acceptors of a conformer.\nFeatureDonorCount3D Number of hydrogen-bond donors of a conformer.\nFeatureAnionCount3D Number of anionic centers (at pH 7) of a conformer.\nFeatureCationCount3D Number of cationic centers (at pH 7) of a conformer.\nFeatureRingCount3D Number of rings of a conformer.\nFeatureHydrophobeCount3D Number of hydrophobes of a conformer.\nConformerModelRMSD3D Conformer sampling RMSD in Å.\nEffectiveRotorCount3D Total number of 3D features (the sum of FeatureAcceptorCount3D, FeatureDonorCount3D, FeatureAnionCount3D, FeatureCationCount3D, FeatureRingCount3D and FeatureHydrophobeCount3D)\nConformerCount3D The number of conformers in the conformer model for a compound.\nFingerprint2D Base64-encoded PubChem Substructure Fingerprint of a molecule.\n======================== ==================================================================================================================================================================================================================================================================================================='¶

Type: str

Table giving descriptions of valid properties.

chemistry_tools.pubchem.properties¶

`chemistry_tools.pubchem.properties`¶