Changed run_reactants() function to add a flag needExplicitHs
Put stereochemistry fixes inside run_reactants()

Previously actions required to use implemented stereochemistry fixes were
scattered across the code. Now I put evertyhing into run_reactants() function
and added two flags: 'needsExplicitHs' and 'needsEnvironments' allowing for
controlling its behavior. I have also modified testing script 'stereotest.py'
was also modified to reflect the changes in our API.
Merge branch 'master' of https://github.com/psuresearch/stereofix

Conflicts:
	NUtestcases.txt
	stereofix.py