xyz to smiles

[alongd]

Added an iPy notebook with an xyz to SMILES script

Also specify numpy and RDKit version

Also, don't load the RMG database if not necessary

[alongd]

Added pydot-ng to environment.yml, see ReactionMechanismGenerator/RMG-Py#1644

[codecov]

Codecov Report

Merging #141 into master will decrease coverage by 1.82%.
The diff coverage is 0%.

@@            Coverage Diff             @@
##           master     #141      +/-   ##
==========================================
- Coverage   42.63%   40.81%   -1.83%     
==========================================
  Files          27       27              
  Lines        6105     6106       +1     
  Branches     1578     1579       +1     
==========================================
- Hits         2603     2492     -111     
- Misses       3120     3245     +125     
+ Partials      382      369      -13

Impacted Files	Coverage Δ
arc/processor.py	38.88% <0%> (-20.88%)	⬇️
arc/plotter.py	18.76% <0%> (-11.83%)	⬇️
arc/common.py	80.98% <0%> (-2.12%)	⬇️
arc/rmgdb.py	72.36% <0%> (-1.32%)	⬇️
arc/main.py	46.1% <0%> (-0.8%)	⬇️
arc/species/species.py	60.94% <0%> (-0.31%)	⬇️
arc/reaction.py	41.92% <0%> (ø)	⬆️

---

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[codecov]

Codecov Report

Merging #141 into master will decrease coverage by <.01%.
The diff coverage is 33.33%.

@@            Coverage Diff             @@
##           master     #141      +/-   ##
==========================================
- Coverage   42.63%   42.63%   -0.01%     
==========================================
  Files          27       27              
  Lines        6105     6106       +1     
  Branches     1578     1579       +1     
==========================================
  Hits         2603     2603              
+ Misses       3120     3118       -2     
- Partials      382      385       +3

Impacted Files	Coverage Δ
arc/processor.py	59.52% <33.33%> (-0.24%)	⬇️
arc/reaction.py	41.92% <0%> (ø)	⬆️

---

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 ce32cac...224e31f. Read the comment docs.