Initial support for constraints

[kantundpeterpan]

ToDo

• change range expressions in switch statements
• crosscheck include statements
• source file headers (licenses, copyrights, etc ...)
• remove legacy Avogadro source files
• change to enum for constraint mapping
• change to nlohmann::json

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[welcome]

Thanks for opening this pull request! Please check out our contributing guidelines and check for the automated tests.

[avo-bot]

This pull request has been mentioned on Avogadro Discussion. There might be relevant details there:

https://discuss.avogadro.cc/t/constraints-in-avogadro2/3072/10

[ghutchis]

I'm on a short trip with the family, but I'll take a look on Wednesday.

A few quick notes

• you'll want to use an enum instead of an int for the different types. It's much easier to read, e.g. FreezeAtom or FreezeBond.
• you want to use using json = nlohmann::json; instead of the Qt JSON code, which is very slow
  • See https://github.com/OpenChemistry/avogadrolibs/blob/master/avogadro/io/cjsonformat.cpp for example

[ghutchis]

I'd like to see if I can help you finish this up, particularly as I'm finishing force field code (which could use the freeze atom, etc. bits).

Could you take care of the DCO sign-off?
https://github.com/OpenChemistry/avogadrolibs/pull/481/checks?check_run_id=841303208

If you've got some time to work on it, I'd be happy to help. If not, please take care of the DCO and I can pick it up from here.

[ghutchis]

I'll ping again. I'd really like to build on this. Could you please fix the sign-off for the DCO. It should take a minute or two.
https://github.com/OpenChemistry/avogadrolibs/pull/481/checks?check_run_id=841303208

[kantundpeterpan]

Hello. Sorry for the late answer, I was caught up in writing my thesis last year and missed the notifications from here. I signed off the commits.

Best

[ghutchis]

Thanks. I'll probably cherry-pick your changes into another pull-request, but it'll keep your history and authorship. Might be a few days, but this is really helpful.

[ghutchis]

Okay, I rebased this into #841 - I'll go with the merge there, but this is really helpful. Thanks for your contribution!