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Fix EPAM Indigo parsing so that the S groups needs to saved before collection block#3531

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sapiosciences-dev:yqiao_pr/CHEMBUGS-184
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Fix EPAM Indigo parsing so that the S groups needs to saved before collection block#3531
sapiosciences-dev wants to merge 5 commits into
epam:masterfrom
sapiosciences-dev:yqiao_pr/CHEMBUGS-184

CHEMBUGS-184 Fixed merge up on commons.cpp my changes.

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