ChemSpiPy provides a number of different ways to search ChemSpider.
The main ChemSpiPy search method functions in a similar way to the main search box on the ChemSpider website. Just provide any type of query, and ChemSpider will interpret it and provide the most relevant results:
>>> cs.search('O=C(OCC)C') Results([Compound(8525)]) >>> cs.search('glucose') Results([Compound(5589), Compound(58238), Compound(71358), Compound(96749), Compound(2006622), Compound(5341883), Compound(5360239), Compound(9129332), Compound(9281077), Compound(9312824), Compound(9484839), Compound(9655623)]) >>> cs.search('2157') Results([Compound(2157)])
The supported query types include systematic names, synonyms, trade names, registry numbers, molecular formula, SMILES, InChI and InChIKey.
Results object that is returned can be treated just like any regular python list. For
example, you can iterate over the results:
>>> for result in cs.search('Glucose'): ... print(result.record_id) 5589 58238 71358 96749 2006622 5341883 5360239 9129332 9281077 9312824 9484839 9655623
Results object also provides the time taken to perform the search, and a message that
explains how the query type was resolved:
>>> r = cs.search('Glucose') >>> print(r.duration) 0:00:00.513406 >>> print(r.message) Found by approved synonym
Certain types of search can sometimes take slightly longer, which can be inconvenient if the search method blocks the Python interpreter until the search results are returned. Fortunately, the ChemSpiPy search method works asynchronously.
Once a search is executed, ChemSpiPy immediately returns the
Results object, which is
actually empty at first:
>>> results = cs.search('O=C(OCC)C') >>> print(results.ready()) False
In a background thread, ChemSpiPy is making the search request and waiting for the response. But in the meantime, it is
possible to continue performing other tasks in the main Python interpreter process. Call
ready() at any point to check if the results have been returned and are available.
Any attempt to access the results will just block until the results are ready, like a simple synchronous search. To
manually block the main thread until the results are ready, use the
>>> results.wait() >>> results.ready() True
For more detailed information about the status of a search, use the
>>> results.status 'Created' >>> results.wait() >>> results.status 'Complete'
The possible statuses are
Search by Formula¶
Searching by molecular formula is supported by the main
search() method, but there is
the possibility that a formula could be interpreted as a name or SMILES or another query type. To specifically search
by formula, use:
>>> cs.search_by_formula('C44H30N4Zn') [Compound(436642), Compound(3232330), Compound(24746832), Compound(26995124)]
Search by Mass¶
It is also possible to search ChemSpider by mass by specifying a certain range:
>>> cs.search_by_mass(680, 0.001) [Compound(8298180), Compound(12931939), Compound(12931969), Compound(21182158)]
The first parameter specifies the desired molecular mass, while the second parameter specifies the allowed ± range of values.