FixUp to Errors introduced in recent Vibrational Analysis PRs

[nateharms]

A few previous PRs made errors occur when a user tried to call Vibrational Analysis methods. This PR addresses them by doing the following:

• Separates the creation of the TS._pesudo_geometry (used for Vibrational Analysis) and the creation of the TS.rdkit_molecule (used in geometry optimizations.
• Adds a line of code needed to correct the introduced error from before.

[nateharms]

@davidfarinajr can you take a look at this when you get a chance?

[nateharms]

Changes were made per @davidfarinajr's requests. Can you take a quick look so I can merge this in?

[codecov[bot]]

Codecov Report

:exclamation: No coverage uploaded for pull request base (master@d8dc7ca). Click here to learn what that means. The diff coverage is 88.00%.

@@            Coverage Diff            @@
##             master      #82   +/-   ##
=========================================
  Coverage          ?   65.18%           
=========================================
  Files             ?       27           
  Lines             ?     4774           
  Branches          ?        0           
=========================================
  Hits              ?     3112           
  Misses            ?     1662           
  Partials          ?        0           

Impacted Files	Coverage Δ
autotst/species.py	72.18% <ø> (ø)
autotst/reaction.py	82.19% <86.95%> (ø)
autotst/calculator/gaussian_test.py	94.91% <100.00%> (ø)
autotst/calculator/vibrational_analysis.py	77.41% <100.00%> (ø)
autotst/geometry_test.py	98.59% <0.00%> (ø)
autotst/species_test.py	98.73% <0.00%> (ø)
autotst/reaction_test.py	99.52% <0.00%> (ø)
autotst/calculator/orca.py	83.51% <0.00%> (ø)
autotst/data/update_test.py	93.33% <0.00%> (ø)
... and 21 more

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