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Added the "-r" option for the choice of atom/bond type prediction#134

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Added the "-r" option for the choice of atom/bond type prediction#134
Mishakolok wants to merge 1 commit intoalanwilter:masterfrom
Mishakolok:master

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@Mishakolok
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Mentioned in issue #26

Added new variable predIndex (for prediction Index) which transfers "-r" command line option to the Antechamber "-j" option for determining the type of bond/atom type prediction. The acpype "-j" option was already taken by the "chiral" option, so I took the free "-r" option.

@alanwilter
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I need some time to check this PR and thanks a lot for doing this.

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