chemistry_tools.pubchem

This module provides a wrapper around the PubChem PUG_REST API.

Data for compounds can be accessed using the pubchem.lookup.get_compounds function.

The following table lists the various properties that can be obtained from the PubChem API:

Click to expand

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.

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]