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Is there a publicly available API that serves physical property data for organic molecules?

Pubchem does not serve properties, ChemSpider closes property access to API calls, and Toxnet only serves html. Im basically looking for a free programmatic interface to the kind of info in a CRC handbook. Thanks for any suggestions.

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    $\begingroup$ I'd be curious what kinds of properties you want to know. But chemical databases with public web APIs are few. $\endgroup$ – Geoff Hutchison Jan 1 '15 at 22:26
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ChEMBL database provides API access: https://www.ebi.ac.uk/chembl/ws properties can be retrieved from the 'molecule' endpoint, for example aspirin:

https://www.ebi.ac.uk/chembl/api/data/molecule/CHEMBL25.json

Disclaimer: I'm the author of this API.

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I am not sure this is what you are looking for, but there is the Padel descriptor software that calculates a whole slew of properties for compounds you throw at it. Nothing empirical though, all calculated values.

See here: http://www.yapcwsoft.com/dd/padeldescriptor/

If you are willing to use a tool like KNIME, there is a Padel KNIME extension available on de Padel website. It is somewhat fiddly to get working properly in KNIME without conflicts, but once you have that going you can pump millions of molecules through this pipeline.

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Your question is rather broad. So the answers can't be too narrow. If you look for material properties like DoS and phase diagrams, try The Materials Project. Working with Pymatgen to brigde to programs like VASP and Gaussian «to compute further», the API is briefly described here.

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PubChem now have a REST API serving properties as part of their PUG REST service.

There's a table of available 2D and 3D properties that can be selected, and a variety of input and output formats supported, including database ID, SMILES and SDF input, and JSON/XML/CSV outputs.

For example, to GET a set of properties for a SMILES string for benzene, in JSON output format:

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/c1ccccc1/property/MolecularFormula,MolecularWeight,InChIKey/JSON

Result:

{
  "PropertyTable": {
    "Properties": [
      {
        "CID": 241,
        "MolecularFormula": "C6H6",
        "MolecularWeight": 78.11,
        "InChIKey": "UHOVQNZJYSORNB-UHFFFAOYSA-N"
      }
    ]
  }
}

You can also move request parameters into a POST request body, allowing POSTing of SDF format molecules.

For example, using curl on the command line to determine the 3D volume of methane:

$ curl --url 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/sdf/property/MolecularFormula,Volume3D/JSON' \
  --form 'sdf=Untitled
  xed2sdf_05210316543D

  1  0  0  0  0  0  0  0  0  0999 V2000
   -5.1559    1.5833    1.7170 C   0  0  0  0  0  0  0  0  0  0  0  0
M  END

$$$$'

Result:

{
  "PropertyTable": {
    "Properties": [
      {
        "CID": 297,
        "MolecularFormula": "CH4",
        "Volume3D": 20.6
      }
    ]
  }
}

From a quick test, it appears that properties are pre-calculated for CID database entries matching the query, so it appears that any 3D properties are not calculated on the input conformation, but rather the PubChem database's conformation. The docs suggest this, saying 3D properties are for the "first diverse conformer (default conformer)".

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