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Crawl data of compounds from PubChem by CID based on PubChem PUG REST API.
pip install requestsGit clonethe repo.
git clone https://github.com/XavierJiezou/python-pubchem-api.gitCdto the root path.
cd python-pubchem-api- Write cid list to
cid.txt. - Run
python pubchem.py. - Results can be seen in
data.jsonordata.csv. - You can also modify the variable
self.property_listin pubchem.py according to theCompound Property Tablesbelow.
self.property_list = [
'IUPACName',
'IsomericSMILES',
'MolecularFormula',
'MolecularWeight',
'HBondDonorCount',
'HBondAcceptorCount'
]More than one property may be requested, in a comma-separated list of property tags in the request URL. Valid output formats for the property table are: XML, ASNT/B, JSON(P), CSV, and TXT (limited to a single property). Available properties are:
| Property | Notes |
|---|---|
| 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. |
| Title | The title used for the compound summary page. |
| 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 |
| 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. |
Get the property from cid.
Get the synonym from cid.
Example: https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/1,2,3,4,5/synonyms/JSON
git clone https://github.com/XavierJiezou/python-pubchem-api.git
cd python-pubchem-api
pip install pipenv
pipenv install
pipenv shell
pip install requests
pip install pyinstaller
pyinstaller -F -i favicon.ico pubchem.py- Github: pubchem-1.0.2-win64.zip
- Lanzou: pubchem-1.0.2-win64.zip
| HTTP Status | Error Code | General Error Category |
|---|---|---|
| 200 | (none) | Success |
| 202 | (none) | Accepted (asynchronous operation pending) |
| 400 | PUGREST.BadRequest | Request is improperly formed (syntax error in the URL, POST body, etc.) |
| 404 | PUGREST.NotFound | The input record was not found (e.g. invalid CID) |
| 405 | PUGREST.NotAllowed | Request not allowed (such as invalid MIME type in the HTTP Accept header) |
| 504 | PUGREST.Timeout | The request timed out, from server overload or too broad a request |
| 503 | PUGREST.ServerBusy | Too many requests or server is busy, retry later |
| 501 | PUGREST.Unimplemented | The requested operation has not (yet) been implemented by the server |
| 500 | PUGREST.ServerError | Some problem on the server side (such as a database server down, etc.) |
| 500 | PUGREST.Unknown | An unknown error occurred |