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Frag debug rebased 3 #3

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Frag debug rebased 3 #3

amarkpayne wants to merge 41 commits into from

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@amarkpayne amarkpayne commented Aug 26, 2019

Motivation or Problem

Draft PR to investigate how easy it would be to merge this branch into master

KEHANG and others added 30 commits July 11, 2019 11:18
@KEHANG @lily90502
[for fragment react] enable fragment to react
760b2a8
@KEHANG @lily90502
added a few Atom checks to make draw work for fragments
b13b033
@KEHANG @lily90502
enable ReactionDrawer to draw fragment reaction as well
2b15759
@KEHANG @lily90502
it's a safe change for RMG since atom has symbol attr already
5a1ee61 
and it makes the code more generally applicable to classes other
than Atom, e.g., CuttingLabel in fragment which doesn't have
element but can define symbol
@KEHANG @lily90502
allow atomIsotope instantiation to accept classes other than Atom
6ca2c61 
it's very helpful for fragment to make use of toAdjacencyList() method
@KEHANG @lily90502
changes needed for fragment to use fromAdj()
62dc240
@KEHANG @lily90502
enable fragment to generate aromatic resonance structures
2361016
@KEHANG @lily90502
try to make generate_resonance_structures work for fragment
2d2f0f3 
with clar_structure generation turned off
@KEHANG @lily90502
[import Fragment] let ensure_species&isIsomorphic work for fragment
706ad89
@KEHANG @lily90502
estimate thermo for fragment via it's repr_species
8318339
@KEHANG @lily90502
make pathfinder to accept fragment so that
7f867c4 
generate_adjacent_resonance_structures can be fully used by fragment
@KEHANG @lily90502
simplify the calculation of multiplicity
af13c1a 
also the original one is not an integer
@KEHANG @lily90502
from only accepting Molecule to Graph for mol.isIsomorphic()
22dd8a9
@KEHANG @lily90502
use fragment repr species to estimate transport data
0985bf2
@KEHANG @lily90502
allow Fragment in mol.util.retrieveElementCount()
c683e75
@KEHANG @lily90502
[tmp commit] this commit's change should be implemented in AFM
cc2c34d
@KEHANG @lily90502
allow RMG to generate clar structures for non-molecules e.g., fragments
4c88e88
@lily90502
modify get_octet_deviation to accept Fragment.
79af0f9
@lily90502
let fragment update to avoid error.
8d05e5a
@lily90502
modify cython declare for has_reactive_molecule
784ba0f
@lily90502
modify toRDKitMol so that it can accept toSMILES for Fragment.
d1d2409
@lily90502
Modify toRDKit for Fragment toSMILES.
68abe8a
@lily90502
Change thermo to make Fragment get correct thermo data.
befc46f
@lily90502
modify applyRecipe so that it can recognize Fragment and Molecule and…
fd73299 
… generate reactions.
@lily90502
let Species isIdentical acceptable for comparing Fragment and Molecule.
d688757
@lily90502
make RMG can read Fragment from library.
9fcc50c
@lily90502
Modify isBalanced so that it can handle library with Fragment.
4fae8ad
@lily90502
pass checkForDuplicates to accelerate library loading.
a6273ec
@lily90502
modify for loading Chemkin file and simulation in Cantera.
911660b
@lily90502
let Fragment to kekulize and debug duplicate reactions due to changin…
c375116 
…g Fragment to Molecule class.
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4 participants

@amarkpayne @KEHANG @lily90502