rdkit / mmpdb

A package to identify matched molecular pairs and use them to predict property changes.

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ujson is not appreciably faster than json

adalke opened this issue · comments

In Python 2.7 the built-in json module was significantly slower than the third-party ujson and cjson modules at parsing the fragment file. If one of the latter two is not found, mmpdb prints a warning message to suggest installing one of those two modules, then falls back to using the json module.

It appears that Python 3.6's json module, while still slower than cjson, is no longer sufficiently slower as to warrant having that warning message. In one test, json took 2m09s while cjson took 2m04s.

Need to re-run the timing tests with Python 3.5, 3.6, and 3.7. If it's no longer needed then have the warning message only for Python 2.7.