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Arg fix #2504

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Arg fix #2504

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Commits on Jul 1, 2022

  1. Fix issue with protonating charged ARG 

    OB was placing a third H on NH1 using a random bond vector.  The
AssignBonds, which is suppose to match known protein residue bonding
patterns, was not working because atom names were not stripped of
whitespace. Also, the original pattern in resdata.txt does not match the
convention of the double bond going to NH1 (it has NH2). Then, even if
AssignBonds sets the right bond order, the
PerceivedBonds fragment matching code undoes it, so refined the bond
typer patterns.
    @dkoes
    dkoes committed Jul 1, 2022
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  2. tests for ARG fix 

    need to change gzip test since it processed 1ubq - the new output is
more correct
    @dkoes
    dkoes committed Jul 1, 2022
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    523c775 View commit details
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