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ReactionMechanismGenerator / AutoTST

AutoTST: A framework to perform automated transition state theory calculations
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Many import changes, and save databases in memory. #4

Closed rwest closed 6 years ago

rwest commented 6 years ago

I'm a bit confused by all the branches, so this is a PR onto vibrational_analysis, although I get the impression that's the new master? (or could be merged into master?)

Anyway, these commits are not really to do with vibrational analysis, but are general improvements (I hope).

Mostly, changes to import statements, making imports explicit. Otherwise you end up importing all sorts of stuff from one place to another and you have no idea or control over what is in your namespace. Please try to avoid import *.

Other change is making it only load the databases once. This makes a huge change to the speed. Where they are stored (currently class level variables on the AutoTST_Reaction class might want revisiting, but it's a minimal start).

nateharms commented 6 years ago

Also, will need changes in all files in the calculators and conformer directories to reflect the change from .ts and .distance_data to ._ts and ._distance_data

rwest commented 6 years ago

The .ts and .distance_data methods with @property decorators mean you should be able to access .ts and .distance_data exactly as was previously done, with no harm to downstream codes. The only concerns will be if downstream code (other than the currently implemented functions) wants to modify these attributes. If it does, we can create a setter method for each - but I couldn't see any instances.