Fix of Conformer Analysis Issues for Migration TSs

[nateharms]

When I was digging into why AutoTST had a weirdly high failure rate for migration reactions, I dove into some of the results for the conformer analysis and saw conformers that look like the following:

For reaction

The conformer generation outputted this as one of the low energy conformers where the stars are the reacting atoms:

Diving into this I saw that one of the stared atoms is identified as a chiral center and is therefore inverted during the conformer generation process and this flips the geometry out of its ring-like TS. This PR will ignore chiral centers and CisTrans bonds in rings by looking at the _pseudo_geometry which has a fake single bond drawn between reacting atoms. An example of what the _pseudo_geometry looks like is below.

[codecov[bot]]

Codecov Report

Merging #85 into master will increase coverage by 0.06%. The diff coverage is 78.94%.

@@            Coverage Diff             @@
##           master      #85      +/-   ##
==========================================
+ Coverage   65.18%   65.24%   +0.06%     
==========================================
  Files          27       27              
  Lines        4774     4791      +17     
==========================================
+ Hits         3112     3126      +14     
- Misses       1662     1665       +3     

Impacted Files	Coverage Δ
autotst/conformer/systematic.py	75.11% <78.94%> (+0.61%)	:arrow_up:

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update b90d4d9...10c602b. Read the comment docs.

[nateharms]

Hi, could someone take a look at this PR? @rwest @davidfarinajr @skrsna

[nateharms]

Sweet, I'm going to merge this in since @skrsna approved.