[WIP] MBIS interface

[jthorton]

Description

This PR provides an interface to MBIS via the latest version of PSI4.

Todos

Notable points that this PR has either accomplished or will accomplish.

• Add an MBIS interface
• Add psi4 solvent calculations
• Add Gaussian solvent calculation support via QCEngine
• Update Vsites to be a pydantic stage
• Update Lennard Jones to be a pydantic stage

Questions

• Although we can not test the gaussian code in the CI should we add tests that we can run locally to make sure everything works?
• What should the default solvent be for PSI4 or should we just expose this will we fit new parameters?

Status

• Ready to go

[lgtm-com]

This pull request introduces 1 alert when merging 67af9d8 into b46ff91 - view on LGTM.com

new alerts:

• 1 for Conflicting attributes in base classes

[codecov]

Codecov Report

Merging #259 (33123aa) into master (b46ff91) will increase coverage by 0.33%.
The diff coverage is 65.50%.

@@            Coverage Diff             @@
##           master     #259      +/-   ##
==========================================
+ Coverage   63.96%   64.29%   +0.33%     
==========================================
  Files          44       54      +10     
  Lines        4934     5165     +231     
==========================================
+ Hits         3156     3321     +165     
- Misses       1778     1844      +66     

Impacted Files	Coverage Δ
qubekit/molecules/ligand.py	96.61% <ø> (-0.01%)	⬇️
qubekit/proteins/protein_run.py	0.00% <0.00%> (ø)
qubekit/utils/configs.py	26.38% <ø> (+0.36%)	⬆️
qubekit/utils/file_handling.py	88.00% <ø> (+41.03%)	⬆️
qubekit/run.py	24.60% <17.24%> (-0.29%)	⬇️
qubekit/engines/gaussian_harness.py	83.23% <30.76%> (-3.72%)	⬇️
qubekit/charges/utils.py	34.96% <34.96%> (ø)
qubekit/charges/mbis.py	44.11% <44.11%> (ø)
qubekit/charges/ddec.py	58.92% <58.92%> (ø)
qubekit/charges/base.py	71.79% <71.79%> (ø)
... and 22 more

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[lgtm-com]

This pull request introduces 1 alert when merging 13ce576 into b46ff91 - view on LGTM.com

new alerts:

• 1 for Conflicting attributes in base classes