Make CorrectForPH respect perceived chains. #2678
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This fixes #2677
CorrectForPH currently clears all perceived attributes through mol.EndModify(). In my change, I check if chains are perceived before hand and in that case sets them as perceived also after since normally the residues and chains shouldn't change through pH-correction.
However, this is a breaking change if someone previously relied on the old behavior. In that case they need to manually reperceive the chains after the call to CorrectForPH (or reset the flag before...).