[Bug 252309] science/openbabel: upgrade to 3.1.1

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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=252309

            Bug ID: 252309
           Summary: science/openbabel: upgrade to 3.1.1
           Product: Ports & Packages
           Version: Latest
          Hardware: Any
                OS: Any
            Status: New
          Severity: Affects Some People
          Priority: ---
         Component: Individual Port(s)
          Assignee: yuri at freebsd.org
          Reporter: thierry at FreeBSD.org
          Assignee: yuri at freebsd.org
             Flags: maintainer-feedback?(yuri at freebsd.org)

Created attachment 221136
  --> https://bugs.freebsd.org/bugzilla/attachment.cgi?id=221136&action=edit
Patch to upgrade OpenBabel to 3.1.1

To upgrade science/v_sim, OpenBabel 3 is needed (see PR 252308), but ATM the
port has 2.4.1.

Release notes are available at
<https://github.com/openbabel/openbabel/releases>.

We could keep the actual port, and repocopy it to science/openbabel3, but since
it only has 5 consumers in the ports tree, this does not seem very useful.

The proposed patch upgrade science/openbabel to 3.1.1, and 4 other patches are
attached for the consumers to chase this upgrade.

- science_kalzium.diff for science/kalzium
        (since I'm there, it also define the licenses)

- science_gchemutils.diff for science/gchemutils

- science_molsketch.diff for science/molsketch
        simple upgrade to 0.7.0 which knows OpenBabel3

- science_xdrawchem.diff for science/xdrawchem
        with patches from https://github.com/bryanherger/xdrawchem/pull/17

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