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Improved output runtime; now prints old positions (indices+1) before…

Authored by matt on Fri, Nov 12, 13:37.

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Improved output runtime; now prints old positions (indices+1) before preprocessing

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mattFri, Nov 12, 13:37
Pushed
mattFri, Nov 12, 13:37
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R11301:cad06c9aec83: Modifed preprocessing to remove hydrogens; various changes on onepass (i forgot…
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