Adding Fluorine as a new element in RMG #1543
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alongd
reviewed
Jan 25, 2019
rmgpy/reaction.py
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| # Sort the reactants and products by C/O/N/S numbers | ||
| reactants = [(carbon, oxygen, nitrogen, silicon, sulfur, chlorine, iodine, reactant) for carbon, oxygen, nitrogen, silicon, sulfur, chlorine, iodine, reactant | ||
| reactants = [(carbon, oxygen, nitrogen, silicon, sulfur, chlorine, iodine, fluorine, reactant) for carbon, oxygen, nitrogen, silicon, sulfur, chlorine, iodine, reactant |
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I think this should be:
Suggested change
| reactants = [(carbon, oxygen, nitrogen, silicon, sulfur, chlorine, iodine, fluorine, reactant) for carbon, oxygen, nitrogen, silicon, sulfur, chlorine, iodine, reactant | |
| reactants = [(carbon, oxygen, nitrogen, silicon, sulfur, chlorine, iodine, fluorine, reactant) for carbon, oxygen, nitrogen, silicon, sulfur, chlorine, iodine, fluorine, reactant |
(same for products below)
rmgpy/reaction.py
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| # Sort the reactants and products by C/O/N/S numbers | ||
| reactants = [(carbon, oxygen, nitrogen, silicon, sulfur, chlorine, iodine, reactant) for carbon, oxygen, nitrogen, silicon, sulfur, chlorine, iodine, reactant | ||
| reactants = [(carbon, oxygen, nitrogen, silicon, sulfur, chlorine, iodine, fluorine, reactant) for carbon, oxygen, nitrogen, silicon, sulfur, chlorine, iodine, reactant | ||
| in zip(reactantCarbons,reactantOxygens,reactantNitrogens,reactantSilicons,reactantSulfurs,reactantChlorines, reactantIodines, reactants)] |
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I think reactantFluorines should be added to the zip here, same for products below
| reactantIodines = [sum([1 for atom in reactant.molecule[0].atoms if atom.isIodine()]) for reactant in reactants] | ||
| productIodines = [sum([1 for atom in product.molecule[0].atoms if atom.isIodine()]) for product in products ] | ||
| reactantFluorines = [sum([1 for atom in reactant.molecule[0].atoms if atom.isFluorine()]) for reactant in reactants] | ||
| productFluorines = [sum([1 for atom in product.molecule[0].atoms if atom.isFluorine()]) for product in products ] |
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Do we have the isFluorine() method already defined?
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Which file should I modify to define this function?
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We do already have isFluorine(), it's here
Codecov Report
@@ Coverage Diff @@
## master #1543 +/- ##
==========================================
+ Coverage 42% 42.01% +<.01%
==========================================
Files 165 165
Lines 27867 27873 +6
Branches 5680 5680
==========================================
+ Hits 11706 11711 +5
- Misses 15375 15377 +2
+ Partials 786 785 -1
Continue to review full report at Codecov.
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alongd
approved these changes
Jan 29, 2019
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Motivation or Problem
Adding Fluorine as an atomtype to RMG.
Description of Changes
Files related to atomtypes are changed.
Testing
Added Fluorine atomtype test.