Use `rdkit` for SSSR and RCs (bug fix + Python upgrade) #2796

JacksonBurns · 2025-05-25T21:43:19Z

Currently we use RingDecomposerLib for finding the Smallest Set of Smallest Rings and getting the Relevant Cycles. This package does not support Python 3.10+ and is thus blocking further upgrades to RMG.

@KnathanM in particular is looking to get RMG to Python 3.11 so as to add support for ChemProp v2.

I believe we can just use RDKit to do these operations instead. The original paper mentions that the functionality was being moved upstream to RDKit. With the help of AI I've taken just a first pass at reimplementing, with the special note that:

I opted to use the Symmetric SSSR in place of the 'true' SSSR. This is because the latter is non-unique (see RDKit's "The SSSR Problem"). This should actually resolve get_deterministic_sssr is not really deterministic #2562
I need to read more about the "Relevant Cycles"

This PR will be a draft for now, as it is predicated on Python 3.9 already being available (which it nearly is in #2741)

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JacksonBurns · 2025-05-25T21:50:37Z

Cantera 2.6 isn't available for Python 3.12, so this PR will also need to upgrade the Cantera version to 3 as mostly completed in #2751

JacksonBurns · 2025-05-26T00:07:45Z

A note for the path forward on this PR - the get_relevant_cycles and get_smallest_set_of_smallest_rings functions will need to be moved to Molecule. Currently they are in Graph, and Graph has no way to send itself to RDKit in order to be subject to RDKit GetSymmSSSR but Molecule can be converted to RDKit via converted.to_rdkit_mol (also exposed as Molecule.to_rdkit_mol, and then RDKit can be used. This may have implications for inheritance elsewhere in the codebase, but should be OK.

jonwzheng · 2025-07-07T23:39:52Z

I ended up moving all the functions in Graph that call get_relevant_cycles or get_smallest_set_of_smallest_rings to Molecule as well. Still have a couple of unit tests to update, but if this is the direction we want to take, hopefully this should be adequate

jonwzheng · 2025-07-16T21:39:51Z

Addressed some of the failures, but still a few nontrivial challenges:

TODO list:

address e / electron representation if integrating to the new RDKit workflow
fix missing vdW bond order
make sure ring algorithms are implemented correctly
certain bond types like R need some sort of RDKit definition; or just never parse them into an RDKit mol object in the first places
how to represent certain surface bonds?
bond orders without definitions? issue from rdkit side or something else?
fill in remaining placeholder unit tests

The tests are just failing mainly for the aromatic compounds, indicating there's some issue with the implementation of the code. Since everything runs, the code "flow" seems clean, just need to iron out the implementation.

jonwzheng · 2025-07-18T19:15:09Z

We are now very close to passing all of the unit tests. There are just a couple major bugs to resolve, namely:

~~how to handle the R/L cutting fragment labels in the RDKit mol object? need to replace with placeholder atom? also with surfaces?~~
~~some bond orders are weird now, so need to investigate where something is going wrong. Due to sanitization maybe?~~
~~I think we can undo the changes to AtomTypeTest~~
~~some surface glitches~~
~~can't kekulize some molecules: if this occurs, maybe back-up is to use increasingly strict flags? e.g. turn kekulization off, and finally turn all sanitize off?~~

jonwzheng · 2025-07-23T21:00:14Z

One of the last failing tests is test_draw_hydrogen_bond_adsorbate, which actually fails due to an assertion error in the codebase:

https://github.com/ReactionMechanismGenerator/RMG-Py/blame/d0d95b3a6bb9cd5d873c8d5b552ec112d6ba9283/rmgpy/molecule/draw.py#L541

@rwest, since you're the last remaining dev who was involved in some capacity with this part of the code, do you know why we have that assert statement? I would think it's better to just plot a "dot" than to outright crash out.
I'm also not sure why this only popped up in this PR - maybe better to address any underlying problem in this code - but thought I'd ask, since this assert might cause problems in the future. There's no safeguards against passing a molecule with no backbone, unless there's something about how this is called that I'm not getting.

While we're at it, the _generate_coordinates also didn't use RDKit to draw if the charge != 0, but maybe that can be relaxed with new versions?

rwest · 2025-07-24T01:43:02Z

One of the last failing tests is test_draw_hydrogen_bond_adsorbate, which actually fails due to an assertion error in the codebase:

https://github.com/ReactionMechanismGenerator/RMG-Py/blame/d0d95b3a6bb9cd5d873c8d5b552ec112d6ba9283/rmgpy/molecule/draw.py#L541

@rwest, since you're the last remaining dev who was involved in some capacity with this part of the code, do you know why we have that assert statement?

I don't. I can see that if there is no straight chain backbone that a function to _find_straight_chain_backbone shouldn't work. It should either fail, and whatever called it deals with the exception (maybe a ValueError is better than AssertError, but either way it's an error to be handled). Or it could return None, but then the calling code would also have to be modified to handle that without crashing. Or the calling code shouldn't try calling it - but then it'd have to know there is no straight chain backbone (and perhaps the easiest way to find that out is to ask for it and fail.) So I think either way the calling code needs updating.

There's no safeguards against passing a molecule with no backbone, unless there's something about how this is called that I'm not getting.

I haven't investigated the full stack trace. But some safeguard, or exception handling, sounds appropriate.

While we're at it, the _generate_coordinates also didn't use RDKit to draw if the charge != 0, but maybe that can be relaxed with new versions?

We can try it. I expect RDKit at the time wasn't being helpful. Hopefully the commit messages offer clues? (this is why we should write helpful commit messages that explain why things are being done).

rwest · 2025-07-24T12:28:26Z

Is this related?

#2744

jonwzheng · 2025-07-24T18:15:26Z

regarding the draw unit test

@rwest yes, thanks, #2744 looks relevant. The test that's failing is for this charged species:

maybe failing due to the missing X-O connectivity, and so no backbone?
I see the discussion in the thread. I'll move any further discussion about this to that issue.
Maybe a separate PR can fix that issue, merged in, and then this can be rebased onto main.

Edit: I tried modifying the connectivity s.t. there is an apparent backbone. But, I still run into this problem even after changing the adjacency list to

1  O u0 p3 c-1 {2,S} {10,H}
2  N u0 p1 c0 {1,S} {3,S} {4,S}
3  O u0 p2 c0 {2,S} {11,S}
4  O u0 p2 c0 {2,S} {7,S}
5  N u0 p1 c0 {6,S} {8,S} {9,S} {7,H}
6  O u0 p2 c0 {5,S} {10,S}
7  H u0 p0 c0 {4,S} {5,H}
8  H u0 p0 c0 {5,S}
9  H u0 p0 c0 {5,S}
10 H u0 p0 c0 {6,S} {1,H}
11 X u0 p0 c0 {3,S}

So it is more fundamentally a problem with the species , than a unit-test specific one.

Note about sanitization

For posterity: some molecules that fail the first kekulization step include:

Can't kekulize mol.  Unkekulized atoms
[H]C1=C([H])C([H])([H])C([H])([H])[c]([H])c1[c]([H])[H]
[H]C([H])=C([H])C1([H])[c]([H])c([H])[c]([H])C1([H])[H]
[H]C([H])=C1c([c]([H])[H])[c]([H])C([H])([H])C1([H])[H]
[H]C1=C([H])C([H])([H])C2([H])[c]([H])c([H])[c]([H])C2([H])C([H])=C1[H]
[H]C1~[C]([H])C2([H])[c](c([H])[c]~1[H])~C([H])~[C]([H])C2([H])C([H])([H])[H]
[H][c]1c([H])[c]([H])C([H])(C([H])([H])[H])C1([H])[H]
[H][c]([H])c1[c]([H])C([H])([H])c2c([H])c([H])c([H])c([H])c-12
[H][C]1~C([H])~[C]([H])C2([H])[C](C([H])([H])[c]([H])c2[c]([H])[H])~C~1[H]
[H][c]([H])c1[c]([H])C([H])([H])c2c([H])c([H])c([H])c([H])c-12
[H][c]1c([H])[c]([H])C([H])(C([H])([H])[H])C1([H])[H]
[H]C1~[C]([H])C2([H])[c](c([H])[c]~1[H])~C([H])~[C]([H])C2([H])[H]
[H][c]([H])c1[c]([H])C1([H])[H]
non-ring atom marked aromatic:
[H][C]~c[c]([H])C([H])([H])C1=C([H])C([H])=C([H])C([H])=C1[H]
[H]c1=c([H])-c([H])=C(C([H])([H])[c]([H])c([H])[c]([H])[H])c([H])=c-1[H]

As implemented in this PR, the RDKit sanitization step will fallback to not use kekulization.

jonwzheng · 2025-07-24T18:42:21Z

Regarding the draw issue, I think I've figured out what's happening...

The test case is drawn as a cyclic molecule, even though it's not truly "cyclic". So it should take the find_cyclic_backbone branch rather than the find_straight_chain_backbone branch.

However, it thinks that len(self.cycles) = 0 because of the changes to ring perception, specifically molecule.get_smallest_set_of_smallest_rings: the H bonds are treated as RDKit hydrogen bonds which don't "count" toward the ring. So in RDKit world it's treated like a non-cyclic species, whereas RMG treats it as cyclic.

So, how to proceed? a few options...

Prefer RDKit drawing: if ring perception is through RDKit, then drawing with RDKit is going to generally be safer. Probably the easiest option, as all we need to do is get rid of the check for if there's charged species. (I think it should work alright personally!)
Change ring perception: instead of treating the H bonds as hydrogen bonds, treat them as an explicit bond?
Create a separate function from SSSR that is used purely to see if there's "ring-like" structure regardless of the nature of the bonds, purely for drawing/graph structure type analysis.

rwest · 2025-07-24T19:52:37Z

I think using RDKit for drawing as much as possible is fine, if it does a good job. Probably we ran into issues in the past that may not persist with more recent versions of RDKit, so it's fine to revisit past decisions. We should continue to put reasons for things in commit messages, to make life easier for future developers (our future selves included).

jonwzheng · 2025-07-24T20:02:26Z

OK. Maybe we can incorporate the fix into #2838 and then rebase onto main once it's merged in.

In ReactionMechanismGenerator#2744 and ReactionMechanismGenerator#2796 it was found that charge-separated bidentate species can have issues due to ring perception conflicts. The previous implementation also by default did not use the rdkit backend for charged species, but this was decided many years ago (~10 years!) In the meantime, RDKit conformer generation has improved and likely this we can just use RDKit by default, which would avoid the pesky edge-case issues for ions/zwitterions. In case the old behavior is desired, use_rdkit can be set to False.

In #2744 and #2796 it was found that charge-separated bidentate species can have issues due to ring perception conflicts. The previous implementation also by default did not use the rdkit backend for charged species, but this was decided many years ago (~10 years!) In the meantime, RDKit conformer generation has improved and likely this we can just use RDKit by default, which would avoid the pesky edge-case issues for ions/zwitterions. In case the old behavior is desired, use_rdkit can be set to False.

JacksonBurns · 2025-08-04T01:52:40Z

With the merger of e92bec0 this PR's CI should now pass - let's see!

JacksonBurns · 2025-08-04T13:30:14Z

@jonwzheng the overnight test failures look spurious - re-running them now.

… RDKit adjacency list parsing rules" This reverts commit 86e15b6.

Some RMG molecule representations are not representable in RDKit. This commit makes it so that if the kekulization step fails during sanitization, then RDKit will try to sanitize with less stringent sanitization criteria. This was necessary because some species from adjacency lists would pop up and crash out due to failed sanitization.

simps was deprecated in scipy 1.6 in favor of simpson. This updates the function call so that it doesn't break workflows.

3.12 needs cantera update, which is not yet ready.

This aligns the RDKit conversion process. A relaxed sanitization process is required to avoid kekulization/sanitization/valence issues which would prevent a molecule from being created. Especially relevant in the context of `draw`, which has an RDKit backend that calls this function. We don't want it to fail drawing simple because it doesn't follow the sanitization rules.

In #2744 and #2796 it was found that charge-separated bidentate species can have issues due to ring perception conflicts. The previous implementation also by default did not use the rdkit backend for charged species, but this was decided many years ago (~10 years!) In the meantime, RDKit conformer generation has improved and likely this we can just use RDKit by default, which would avoid the pesky edge-case issues for ions/zwitterions. In case the old behavior is desired, use_rdkit can be set to False.

Accompanies changes to `draw.py` to use `rdkit` backend, which traditionally was not well-supported for ions (but now might be a better option than the default drawing algorithm).

The molecule to_rdkit_mol now allows for and calls sanitize. The fragment code previously had hardcoded args. This commit just makes the args flexible so that they get passed directly to `converter` regardless of what the arguments are.

After changing to_rdkit_mol to kwargs format in Fragment, some of the existing code that relied on the previous function defaults broke. Namely, return_mapping must be True.

This reverts commit 7ac5fd4.

Fragments will sometimes call `get_smallest_set_of_smallest_rings` (e.g. for drawing), which will then call the _fragment_ version of `to_rdkit_mol` (rather than Molecule, since Fragment inherits from Molecule), which returns a _tuple_ rather than a _mol_. This causes a crash. I considerd just replacing this with `converter.to_rdkit_mol` without the checks, but then you'd lose out on any fragment-related benefits from to_rdkit_mol (for example, you need to replace the fragments with H atoms). This commit also adds a check so that the user is at least aware that the default behavior is to change the kwarg to forcibly return mapping=True for fragments.

Some compounds with resonance form resonance hybrids, which create non-integer bond orders that then call ring perception (via get_symmetry_number). Because non-integer bond orders are not recognized, we handle them as `unspecified`. Alternatively, the kekulization rules for RMG may sometimes differ from those of RDKit, which also logged a warning. For ring perception, these 'warnings' do not impact performance, and for nearly all users should not raise any concerns. So this demotes the logging level from `warning` to `debug`

jonwzheng · 2025-09-19T18:47:42Z

@rwest do you have any unaddressed thoughts/concerns about this PR?

github-actions · 2025-09-19T23:46:26Z

Regression Testing Results

⚠️ One or more regression tests failed.
Please download the failed results and run the tests locally or check the log to see why.

Detailed regression test results.

Regression test aromatics:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:50
Current: Execution time (DD:HH:MM:SS): 00:00:01:15
Reference: Memory used: 747.09 MB
Current: Memory used: 762.36 MB

aromatics Passed Core Comparison ✅

Original model has 15 species.
Test model has 15 species. ✅
Original model has 11 reactions.
Test model has 11 reactions. ✅

aromatics Failed Edge Comparison ❌

Original model has 106 species.
Test model has 106 species. ✅
Original model has 358 reactions.
Test model has 358 reactions. ✅

Non-identical thermo! ❌
original: C1=CC2C=CC=1C=C2
tested: C1=CC2C=CC=1C=C2

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
164.90	80.93	22.21	28.97	35.25	40.69	48.70	53.97	64.36
148.68	54.21	25.46	34.24	42.29	49.12	58.39	63.30	72.16

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsCsH) + group(Cdd-CdsCds) + Estimated bicyclic component: polycyclic(s4_6_6_ane) - ring(Cyclohexane) - ring(Cyclohexane) + ring(124cyclohexatriene) + ring(124cyclohexatriene)
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsCsH) + group(Cdd-CdsCds) + polycyclic(s4_6_6)

Non-identical thermo! ❌
original: C1=CC2C=CC1=CC2
tested: C1=CC2C=CC1=CC2

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
56.66	79.96	24.39	32.69	40.44	47.15	56.86	63.03	75.30
108.21	56.81	27.43	37.29	46.38	54.14	64.77	70.51	80.83

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + Estimated bicyclic component: polycyclic(s4_6_6_ane) - ring(Cyclohexane) - ring(Cyclohexane) + ring(1,3-Cyclohexadiene) + ring(1,4-Cyclohexadiene)
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + polycyclic(s4_6_6)

Non-identical thermo! ❌
original: [CH]=CC1C=C2C=CC1C=C2
tested: [CH]=CC1C=C2C=CC1C=C2

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
134.28	94.17	33.50	43.19	51.79	59.11	69.91	77.10	90.41
185.84	71.01	36.54	47.79	57.73	66.08	77.82	84.60	95.93

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds- CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsHH) + Estimated bicyclic component: polycyclic(s4_6_6_ane) - ring(Cyclohexane) - ring(Cyclohexane) + ring(1,4-Cyclohexadiene) + ring(1,3-Cyclohexadiene) + radical(Cds_P)
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds- CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsHH) + polycyclic(s4_6_6) + radical(Cds_P)

Non-identical thermo! ❌
original: C=CC1C=C2C=CC1C=C2
tested: C=CC1C=C2C=CC1C=C2

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
75.19	92.78	33.68	43.92	53.13	61.03	72.77	80.56	94.93
126.74	69.62	36.73	48.52	59.07	68.01	80.68	88.07	100.46

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds- CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsHH) + Estimated bicyclic component: polycyclic(s4_6_6_ane) - ring(Cyclohexane) - ring(Cyclohexane) + ring(1,4-Cyclohexadiene) + ring(1,3-Cyclohexadiene)
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds- CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsHH) + polycyclic(s4_6_6)

Non-identical kinetics! ❌
original:
rxn: benzene(1) + C1=CC2C=C[C]1C=C2(49) <=> [c]1ccccc1(3) + C1=CC2C=CC1=CC2(83) origin: H_Abstraction
tested:
rxn: benzene(1) + C1=CC2C=C[C]1C=C2(49) <=> [c]1ccccc1(3) + C1=CC2C=CC1=CC2(83) origin: H_Abstraction

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-17.84	-11.76	-8.01	-5.45	-2.13	-0.05	2.94	4.59
k(T):	-49.97	-35.85	-27.28	-21.51	-14.18	-9.68	-3.49	-0.23

kinetics: Arrhenius(A=(0.387,'cm^3/(mol*s)'), n=4.34, Ea=(30.45,'kcal/mol'), T0=(1,'K'), comment="""From training reaction 1694 used for Cb_H;C_rad/H/CdCs Exact match found for rate rule [Cb_H;C_rad/H/CdCs] Euclidian distance = 0 Multiplied by reaction path degeneracy 18.0 family: H_Abstraction""")
kinetics: Arrhenius(A=(0.387,'cm^3/(mol*s)'), n=4.34, Ea=(74.548,'kcal/mol'), T0=(1,'K'), comment="""From training reaction 1694 used for Cb_H;C_rad/H/CdCs Exact match found for rate rule [Cb_H;C_rad/H/CdCs] Euclidian distance = 0 Multiplied by reaction path degeneracy 18.0 family: H_Abstraction Ea raised from 310.7 to 311.9 kJ/mol to match endothermicity of reaction.""")
kinetics: From training reaction 1694 used for Cb_H;C_rad/H/CdCs
Exact match found for rate rule [Cb_H;C_rad/H/CdCs]
Euclidian distance = 0
Multiplied by reaction path degeneracy 18.0
family: H_Abstraction
kinetics: From training reaction 1694 used for Cb_H;C_rad/H/CdCs
Exact match found for rate rule [Cb_H;C_rad/H/CdCs]
Euclidian distance = 0
Multiplied by reaction path degeneracy 18.0
family: H_Abstraction
Ea raised from 310.7 to 311.9 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: ethyne(2) + C1=CC2C=C[C]1C=C2(49) <=> [CH]=CC1C=C2C=CC1C=C2(85) origin: R_Addition_MultipleBond
tested:
rxn: ethyne(2) + C1=CC2C=C[C]1C=C2(49) <=> [CH]=CC1C=C2C=CC1C=C2(85) origin: R_Addition_MultipleBond

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-4.50	-1.87	-0.23	0.89	2.36	3.30	4.65	5.42
k(T):	-22.62	-15.46	-11.10	-8.17	-4.43	-2.14	1.03	2.70

kinetics: Arrhenius(A=(73800,'cm^3/(mol*s)'), n=2.41, Ea=(12.82,'kcal/mol'), T0=(1,'K'), comment="""From training reaction 2258 used for Ct-H_Ct-H;CsJ-CdCsH Exact match found for rate rule [Ct-H_Ct-H;CsJ-CdCsH] Euclidian distance = 0 Multiplied by reaction path degeneracy 6.0 family: R_Addition_MultipleBond""")
kinetics: Arrhenius(A=(73800,'cm^3/(mol*s)'), n=2.41, Ea=(37.693,'kcal/mol'), T0=(1,'K'), comment="""From training reaction 2258 used for Ct-H_Ct-H;CsJ-CdCsH Exact match found for rate rule [Ct-H_Ct-H;CsJ-CdCsH] Euclidian distance = 0 Multiplied by reaction path degeneracy 6.0 family: R_Addition_MultipleBond Ea raised from 152.0 to 157.7 kJ/mol to match endothermicity of reaction.""")
kinetics: From training reaction 2258 used for Ct-H_Ct-H;CsJ-CdCsH
Exact match found for rate rule [Ct-H_Ct-H;CsJ-CdCsH]
Euclidian distance = 0
Multiplied by reaction path degeneracy 6.0
family: R_Addition_MultipleBond
kinetics: From training reaction 2258 used for Ct-H_Ct-H;CsJ-CdCsH
Exact match found for rate rule [Ct-H_Ct-H;CsJ-CdCsH]
Euclidian distance = 0
Multiplied by reaction path degeneracy 6.0
family: R_Addition_MultipleBond
Ea raised from 152.0 to 157.7 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: [c]1ccccc1(3) + C1=CC2C=C[C]1C=C2(49) <=> benzene(1) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation
tested:
rxn: [c]1ccccc1(3) + C1=CC2C=C[C]1C=C2(49) <=> benzene(1) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-3.00	-0.74	0.70	1.71	3.07	3.97	5.33	6.15
k(T):	4.06	4.56	4.94	5.25	5.72	6.09	6.75	7.21

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(9.943,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 38.5 to 41.6 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(0.239,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 38.5 to 41.6 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌
original:
rxn: [c]1ccccc1(3) + C1=CC2C=C[C]1C=C2(49) <=> C1#CC=CC=C1(10) + C1=CC2C=CC1=CC2(83) origin: Disproportionation
tested:
rxn: [c]1ccccc1(3) + C1=CC2C=C[C]1C=C2(49) <=> C1#CC=CC=C1(10) + C1=CC2C=CC1=CC2(83) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	0.84	2.04	2.82	3.38	4.15	4.67	5.49	6.00
k(T):	-26.90	-18.77	-13.83	-10.49	-6.25	-3.65	-0.06	1.84

kinetics: Arrhenius(A=(4050,'cm^3/(mol*s)'), n=2.7, Ea=(4.743,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_N-Sp-5R!H=1R!H_Ext-4CHNS-R_N-6R!H->S_4CHNS->C_N- Sp-6BrBrBrCCCClClClFFFIIINNNOOOPPPSiSiSi#4C_6BrCClFINOPSi->C_1R!H-inRing in family Disproportionation. Multiplied by reaction path degeneracy 6.0""")
kinetics: Arrhenius(A=(4050,'cm^3/(mol*s)'), n=2.7, Ea=(42.829,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_N-Sp-5R!H=1R!H_Ext-4CHNS-R_N-6R!H->S_4CHNS->C_N- Sp-6BrBrBrCCCClClClFFFIIINNNOOOPPPSiSiSi#4C_6BrCClFINOPSi->C_1R!H-inRing in family Disproportionation. Multiplied by reaction path degeneracy 6.0 Ea raised from 178.7 to 179.2 kJ/mol to match endothermicity of reaction.""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_N-Sp-5R!H=1R!H_Ext-4CHNS-R_N-6R!H->S_4CHNS->C_N- Sp-6BrBrBrCCCClClClFFFIIINNNOOOPPPSiSiSi#4C_6BrCClFINOPSi->C_1R!H-inRing in family Disproportionation.
Multiplied by reaction path degeneracy 6.0
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_N-Sp-5R!H=1R!H_Ext-4CHNS-R_N-6R!H->S_4CHNS->C_N- Sp-6BrBrBrCCCClClClFFFIIINNNOOOPPPSiSiSi#4C_6BrCClFINOPSi->C_1R!H-inRing in family Disproportionation.
Multiplied by reaction path degeneracy 6.0
Ea raised from 178.7 to 179.2 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: [H](4) + C1=CC2C=C[C]1C=C2(49) <=> [H][H](11) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation
tested:
rxn: [H](4) + C1=CC2C=C[C]1C=C2(49) <=> [H][H](11) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-7.44	-4.08	-2.05	-0.69	1.02	2.06	3.46	4.18
k(T):	4.57	4.93	5.15	5.31	5.52	5.66	5.86	5.98

kinetics: Arrhenius(A=(4.06926e+10,'cm^3/(mol*s)'), n=0.47, Ea=(18.137,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 75.2 to 75.9 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(4.06926e+10,'cm^3/(mol*s)'), n=0.47, Ea=(1.659,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 0.0 to 6.9 kJ/mol to match endothermicity of reaction.""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 75.2 to 75.9 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 0.0 to 6.9 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: [CH]=C(7) + C1=CC2C=C[C]1C=C2(49) <=> C=C(13) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation
tested:
rxn: [CH]=C(7) + C1=CC2C=C[C]1C=C2(49) <=> C=C(13) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-7.17	-3.66	-1.56	-0.16	1.60	2.65	4.05	4.75
k(T):	-0.85	1.07	2.23	3.00	3.97	4.55	5.32	5.70

kinetics: Arrhenius(A=(7.23e+12,'cm^3/(mol*s)'), n=0, Ea=(19.262,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_N-Sp-6R!H-4CHNS in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
kinetics: Arrhenius(A=(7.23e+12,'cm^3/(mol*s)'), n=0, Ea=(10.587,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_N-Sp-6R!H-4CHNS in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
Identical kinetics comments:
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_N-Sp-6R!H-4CHNS in family Disproportionation.
Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌
original:
rxn: [CH]=C(7) + C1=CC2C=C[C]1C=C2(49) <=> ethyne(2) + C1=CC2C=CC1=CC2(83) origin: Disproportionation
tested:
rxn: [CH]=C(7) + C1=CC2C=C[C]1C=C2(49) <=> ethyne(2) + C1=CC2C=CC1=CC2(83) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	7.18	7.15	7.12	7.10	7.07	7.05	7.00	6.97
k(T):	1.39	2.81	3.65	4.21	4.90	5.31	5.85	6.10

kinetics: Arrhenius(A=(6.31914e+13,'cm^3/(mol*s)'), n=-0.251, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_N-4R->H_4CNOS-u1_N-1R!H->O_N-4CNOS->O_Ext-4CNS-R_N-Sp-5R!H#4CCCNNNSSS_N-2R!H->S_N-5R!H->O_Sp-5CS-4CCNSS in family Disproportionation. Multiplied by reaction path degeneracy 6.0""")
kinetics: Arrhenius(A=(6.31914e+13,'cm^3/(mol*s)'), n=-0.251, Ea=(7.948,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_N-4R->H_4CNOS-u1_N-1R!H->O_N-4CNOS->O_Ext-4CNS-R_N-Sp-5R!H#4CCCNNNSSS_N-2R!H->S_N-5R!H->O_Sp-5CS-4CCNSS in family Disproportionation. Multiplied by reaction path degeneracy 6.0""")
Identical kinetics comments:
kinetics: Estimated from node Root_N-4R->H_4CNOS-u1_N-1R!H->O_N-4CNOS->O_Ext-4CNS-R_N-Sp-5R!H#4CCCNNNSSS_N-2R!H->S_N-5R!H->O_Sp-5CS-4CCNSS in family Disproportionation.
Multiplied by reaction path degeneracy 6.0

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2CC2=C1(27) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation
tested:
rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2CC2=C1(27) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-30.48	-21.35	-15.79	-12.03	-7.23	-4.28	-0.16	2.03
k(T):	-18.48	-12.34	-8.58	-6.02	-2.73	-0.67	2.24	3.83

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(47.659,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 195.4 to 199.4 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(31.181,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 127.5 to 130.5 kJ/mol to match endothermicity of reaction.""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 195.4 to 199.4 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 127.5 to 130.5 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2=CC2=C1(22) + C1=CC2C=CC1=CC2(83) origin: Disproportionation
tested:
rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2=CC2=C1(22) + C1=CC2C=CC1=CC2(83) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	6.29	6.36	6.39	6.40	6.40	6.38	6.34	6.30
k(T):	-6.48	-3.22	-1.28	0.01	1.61	2.55	3.79	4.38

kinetics: Arrhenius(A=(1.57744e+14,'cm^3/(mol*s)'), n=-0.55, Ea=(0.75,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Ext-1R!H-R_4CHNS->C_Ext-4C-R_N-Sp-7R!H#4C_7R!H->C_Ext-4C-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
kinetics: Arrhenius(A=(1.57744e+14,'cm^3/(mol*s)'), n=-0.55, Ea=(18.28,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Ext-1R!H-R_4CHNS->C_Ext-4C-R_N-Sp-7R!H#4C_7R!H->C_Ext-4C-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
Identical kinetics comments:
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Ext-1R!H-R_4CHNS->C_Ext-4C-R_N-Sp-7R!H#4C_7R!H->C_Ext-4C-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=C2C1(29) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation
tested:
rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=C2C1(29) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-31.23	-21.91	-16.23	-12.40	-7.51	-4.50	-0.31	1.91
k(T):	-19.22	-12.90	-9.03	-6.40	-3.01	-0.90	2.09	3.71

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(48.686,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 202.2 to 203.7 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(32.207,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 134.3 to 134.8 kJ/mol to match endothermicity of reaction.""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 202.2 to 203.7 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 134.3 to 134.8 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2=CC2C=1(26) + C1=CC2C=CC1=CC2(83) origin: Disproportionation
tested:
rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2=CC2C=1(26) + C1=CC2C=CC1=CC2(83) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-21.38	-14.52	-10.33	-7.48	-3.82	-1.55	1.66	3.39
k(T):	-58.94	-42.69	-32.86	-26.25	-17.90	-12.81	-5.85	-2.24

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(35.17,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(86.72,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
Identical kinetics comments:
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2=CC2C1(28) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation
tested:
rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2=CC2C1(28) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-27.24	-18.91	-13.84	-10.40	-6.02	-3.30	0.48	2.51
k(T):	-15.31	-9.97	-6.68	-4.44	-1.54	0.27	2.87	4.30

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(43.208,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 180.2 to 180.8 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(26.837,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 180.2 to 180.8 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌
original:
rxn: [CH]=CC=C(15) + C1=CC2C=C[C]1C=C2(49) <=> C=CC=C(17) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation
tested:
rxn: [CH]=CC=C(15) + C1=CC2C=C[C]1C=C2(49) <=> C=CC=C(17) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-11.95	-7.61	-5.01	-3.27	-1.10	0.20	1.93	2.80
k(T):	-5.85	-3.04	-1.35	-0.22	1.18	2.03	3.15	3.71

kinetics: Arrhenius(A=(2.529e+11,'cm^3/(mol*s)'), n=0, Ea=(23.821,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
kinetics: Arrhenius(A=(2.529e+11,'cm^3/(mol*s)'), n=0, Ea=(15.45,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
Identical kinetics comments:
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌
original:
rxn: [CH]=CC=C(15) + C1=CC2C=C[C]1C=C2(49) <=> C#CC=C(38) + C1=CC2C=CC1=CC2(83) origin: Disproportionation
tested:
rxn: [CH]=CC=C(15) + C1=CC2C=C[C]1C=C2(49) <=> C#CC=C(38) + C1=CC2C=CC1=CC2(83) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	6.93	6.88	6.85	6.82	6.77	6.73	6.67	6.62
k(T):	2.09	3.26	3.95	4.40	4.96	5.28	5.70	5.90

kinetics: Arrhenius(A=(7.08174e+13,'cm^3/(mol*s)'), n=-0.372, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_N-Sp-5R!H=1R!H_Ext-4CHNS-R_N-6R!H->S_4CHNS->C_N- Sp-6BrBrBrCCCClClClFFFIIINNNOOOPPPSiSiSi#4C_6BrCClFINOPSi->C_N-1R!H-inRing_Ext-4C-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
kinetics: Arrhenius(A=(7.08174e+13,'cm^3/(mol*s)'), n=-0.372, Ea=(6.637,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_N-Sp-5R!H=1R!H_Ext-4CHNS-R_N-6R!H->S_4CHNS->C_N- Sp-6BrBrBrCCCClClClFFFIIINNNOOOPPPSiSiSi#4C_6BrCClFINOPSi->C_N-1R!H-inRing_Ext-4C-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
Identical kinetics comments:
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_N-Sp-5R!H=1R!H_Ext-4CHNS-R_N-6R!H->S_4CHNS->C_N- Sp-6BrBrBrCCCClClClFFFIIINNNOOOPPPSiSiSi#4C_6BrCClFINOPSi->C_N-1R!H-inRing_Ext-4C-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]=Cc1ccccc1(12) <=> C1=CC2C=CC=1C=C2(79) + C=Cc1ccccc1(16) origin: Disproportionation
tested:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]=Cc1ccccc1(12) <=> C1=CC2C=CC=1C=C2(79) + C=Cc1ccccc1(16) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-12.28	-7.86	-5.21	-3.44	-1.23	0.10	1.87	2.75
k(T):	-6.11	-3.23	-1.51	-0.35	1.09	1.95	3.10	3.68

kinetics: Arrhenius(A=(2.529e+11,'cm^3/(mol*s)'), n=0, Ea=(24.273,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
kinetics: Arrhenius(A=(2.529e+11,'cm^3/(mol*s)'), n=0, Ea=(15.805,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
Identical kinetics comments:
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]=Cc1ccccc1(12) <=> C#Cc1ccccc1(51) + C1=CC2C=CC1=CC2(83) origin: Disproportionation
tested:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]=Cc1ccccc1(12) <=> C#Cc1ccccc1(51) + C1=CC2C=CC1=CC2(83) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	6.93	6.88	6.85	6.82	6.77	6.73	6.67	6.62
k(T):	3.05	3.98	4.52	4.88	5.32	5.57	5.89	6.04

kinetics: Arrhenius(A=(7.08174e+13,'cm^3/(mol*s)'), n=-0.372, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_N-Sp-5R!H=1R!H_Ext-4CHNS-R_N-6R!H->S_4CHNS->C_N- Sp-6BrBrBrCCCClClClFFFIIINNNOOOPPPSiSiSi#4C_6BrCClFINOPSi->C_N-1R!H-inRing_Ext-4C-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
kinetics: Arrhenius(A=(7.08174e+13,'cm^3/(mol*s)'), n=-0.372, Ea=(5.319,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_N-Sp-5R!H=1R!H_Ext-4CHNS-R_N-6R!H->S_4CHNS->C_N- Sp-6BrBrBrCCCClClClFFFIIINNNOOOPPPSiSiSi#4C_6BrCClFINOPSi->C_N-1R!H-inRing_Ext-4C-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
Identical kinetics comments:
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_N-Sp-5R!H=1R!H_Ext-4CHNS-R_N-6R!H->S_4CHNS->C_N- Sp-6BrBrBrCCCClClClFFFIIINNNOOOPPPSiSiSi#4C_6BrCClFINOPSi->C_N-1R!H-inRing_Ext-4C-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC(=C1)C2(69) origin: Disproportionation
tested:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC(=C1)C2(69) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-30.44	-21.32	-15.76	-12.01	-7.22	-4.26	-0.16	2.03
k(T):	-18.44	-12.31	-8.56	-6.00	-2.72	-0.66	2.24	3.83

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(47.606,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 195.1 to 199.2 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(31.128,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 127.2 to 130.2 kJ/mol to match endothermicity of reaction.""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 195.1 to 199.2 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 127.2 to 130.2 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2=CC(=C1)C=C2(60) + C1=CC2C=CC1=CC2(83) origin: Disproportionation
tested:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2=CC(=C1)C=C2(60) + C1=CC2C=CC1=CC2(83) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-56.32	-40.60	-31.18	-24.91	-17.08	-12.40	-6.18	-3.09
k(T):	-93.66	-68.61	-53.59	-43.58	-31.09	-23.60	-13.65	-8.69

kinetics: Arrhenius(A=(1.57744e+14,'cm^3/(mol*s)'), n=-0.55, Ea=(86.692,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Ext-1R!H-R_4CHNS->C_Ext-4C-R_N-Sp-7R!H#4C_7R!H->C_Ext-4C-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 358.9 to 362.7 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(1.57744e+14,'cm^3/(mol*s)'), n=-0.55, Ea=(137.957,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Ext-1R!H-R_4CHNS->C_Ext-4C-R_N-Sp-7R!H#4C_7R!H->C_Ext-4C-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 574.6 to 577.2 kJ/mol to match endothermicity of reaction.""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Ext-1R!H-R_4CHNS->C_Ext-4C-R_N-Sp-7R!H#4C_7R!H->C_Ext-4C-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 358.9 to 362.7 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Ext-1R!H-R_4CHNS->C_Ext-4C-R_N-Sp-7R!H#4C_7R!H->C_Ext-4C-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 574.6 to 577.2 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC(=C2)C1(70) origin: Disproportionation
tested:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC(=C2)C1(70) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-32.11	-22.57	-16.76	-12.84	-7.84	-4.76	-0.49	1.78
k(T):	-20.10	-13.56	-9.56	-6.84	-3.34	-1.16	1.91	3.58

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(49.895,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 205.2 to 208.8 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(33.417,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 137.3 to 139.8 kJ/mol to match endothermicity of reaction.""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 205.2 to 208.8 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 137.3 to 139.8 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2=CC(C=1)C=C2(64) + C1=CC2C=CC1=CC2(83) origin: Disproportionation
tested:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2=CC(C=1)C=C2(64) + C1=CC2C=CC1=CC2(83) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-8.04	-4.52	-2.32	-0.81	1.18	2.46	4.32	5.39
k(T):	-45.39	-32.53	-24.73	-19.48	-12.82	-8.75	-3.15	-0.21

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(16.86,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 65.8 to 70.5 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(68.125,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 281.4 to 285.0 kJ/mol to match endothermicity of reaction.""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 65.8 to 70.5 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 281.4 to 285.0 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2=CC(C=C2)C1(71) origin: Disproportionation
tested:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2=CC(C=C2)C1(71) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-33.97	-23.97	-17.88	-13.77	-8.54	-5.32	-0.86	1.50
k(T):	-21.97	-14.96	-10.68	-7.77	-4.04	-1.72	1.54	3.30

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(52.457,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 214.4 to 219.5 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(35.979,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 146.5 to 150.5 kJ/mol to match endothermicity of reaction.""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 214.4 to 219.5 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 146.5 to 150.5 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC1C=C2(82) origin: Disproportionation
tested:
rxn: C1=CC2C=C[C]1C=C2(49) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC1C=C2(82) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-30.48	-21.35	-15.79	-12.03	-7.23	-4.28	-0.16	2.03
k(T):	-18.48	-12.34	-8.58	-6.02	-2.73	-0.67	2.24	3.83

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(47.659,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 195.4 to 199.4 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(31.181,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 127.5 to 130.5 kJ/mol to match endothermicity of reaction.""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 195.4 to 199.4 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 127.5 to 130.5 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC1=CC2(83) origin: Disproportionation
tested:
rxn: C1=CC2C=C[C]1C=C2(49) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC1=CC2(83) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-19.49	-12.98	-9.00	-6.29	-2.81	-0.64	2.42	4.08
k(T):	-44.83	-31.99	-24.20	-18.96	-12.32	-8.25	-2.65	0.28

kinetics: Arrhenius(A=(51.5097,'cm^3/(mol*s)'), n=3.635, Ea=(33.226,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 9.0 Ea raised from 133.4 to 139.0 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(51.5097,'cm^3/(mol*s)'), n=3.635, Ea=(68.012,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 9.0 Ea raised from 281.2 to 284.6 kJ/mol to match endothermicity of reaction.""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 9.0
Ea raised from 133.4 to 139.0 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 9.0
Ea raised from 281.2 to 284.6 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2=CC=C1C=C2(81) + C1=CC2C=CC1=CC2(83) origin: Disproportionation
tested:
rxn: C1=CC2C=C[C]1C=C2(49) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2=CC=C1C=C2(81) + C1=CC2C=CC1=CC2(83) origin: Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-63.63	-46.08	-35.57	-28.56	-19.82	-14.59	-7.64	-4.19
k(T):	-101.11	-74.19	-58.05	-47.30	-33.88	-25.83	-15.14	-9.81

kinetics: Arrhenius(A=(1.57744e+14,'cm^3/(mol*s)'), n=-0.55, Ea=(96.732,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Ext-1R!H-R_4CHNS->C_Ext-4C-R_N-Sp-7R!H#4C_7R!H->C_Ext-4C-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 404.3 to 404.7 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(1.57744e+14,'cm^3/(mol*s)'), n=-0.55, Ea=(148.174,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Ext-1R!H-R_4CHNS->C_Ext-4C-R_N-Sp-7R!H#4C_7R!H->C_Ext-4C-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Ext-1R!H-R_4CHNS->C_Ext-4C-R_N-Sp-7R!H#4C_7R!H->C_Ext-4C-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 404.3 to 404.7 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Ext-1R!H-R_4CHNS->C_Ext-4C-R_N-Sp-7R!H#4C_7R!H->C_Ext-4C-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌
original:
rxn: C#Cc1ccccc1(51) + C1=CC2C=C[C]1C=C2(49) <=> C#Cc1[c]cccc1(88) + C1=CC2C=CC1=CC2(83) origin: H_Abstraction
tested:
rxn: C#Cc1ccccc1(51) + C1=CC2C=C[C]1C=C2(49) <=> C#Cc1[c]cccc1(88) + C1=CC2C=CC1=CC2(83) origin: H_Abstraction

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-18.32	-12.23	-8.49	-5.92	-2.61	-0.52	2.46	4.11
k(T):	-50.45	-36.33	-27.76	-21.99	-14.66	-10.16	-3.97	-0.71

kinetics: Arrhenius(A=(0.129,'cm^3/(mol*s)'), n=4.34, Ea=(30.45,'kcal/mol'), T0=(1,'K'), comment="""From training reaction 1694 used for Cb_H;C_rad/H/CdCs Exact match found for rate rule [Cb_H;C_rad/H/CdCs] Euclidian distance = 0 Multiplied by reaction path degeneracy 6.0 family: H_Abstraction""")
kinetics: Arrhenius(A=(0.129,'cm^3/(mol*s)'), n=4.34, Ea=(74.548,'kcal/mol'), T0=(1,'K'), comment="""From training reaction 1694 used for Cb_H;C_rad/H/CdCs Exact match found for rate rule [Cb_H;C_rad/H/CdCs] Euclidian distance = 0 Multiplied by reaction path degeneracy 6.0 family: H_Abstraction Ea raised from 310.7 to 311.9 kJ/mol to match endothermicity of reaction.""")
kinetics: From training reaction 1694 used for Cb_H;C_rad/H/CdCs
Exact match found for rate rule [Cb_H;C_rad/H/CdCs]
Euclidian distance = 0
Multiplied by reaction path degeneracy 6.0
family: H_Abstraction
kinetics: From training reaction 1694 used for Cb_H;C_rad/H/CdCs
Exact match found for rate rule [Cb_H;C_rad/H/CdCs]
Euclidian distance = 0
Multiplied by reaction path degeneracy 6.0
family: H_Abstraction
Ea raised from 310.7 to 311.9 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: C#Cc1ccccc1(51) + C1=CC2C=C[C]1C=C2(49) <=> C#Cc1c[c]ccc1(89) + C1=CC2C=CC1=CC2(83) origin: H_Abstraction
tested:
rxn: C#Cc1ccccc1(51) + C1=CC2C=C[C]1C=C2(49) <=> C#Cc1c[c]ccc1(89) + C1=CC2C=CC1=CC2(83) origin: H_Abstraction

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-18.32	-12.23	-8.49	-5.92	-2.61	-0.52	2.46	4.11
k(T):	-50.45	-36.33	-27.76	-21.99	-14.66	-10.16	-3.97	-0.71

kinetics: Arrhenius(A=(0.129,'cm^3/(mol*s)'), n=4.34, Ea=(30.45,'kcal/mol'), T0=(1,'K'), comment="""From training reaction 1694 used for Cb_H;C_rad/H/CdCs Exact match found for rate rule [Cb_H;C_rad/H/CdCs] Euclidian distance = 0 Multiplied by reaction path degeneracy 6.0 family: H_Abstraction""")
kinetics: Arrhenius(A=(0.129,'cm^3/(mol*s)'), n=4.34, Ea=(74.548,'kcal/mol'), T0=(1,'K'), comment="""From training reaction 1694 used for Cb_H;C_rad/H/CdCs Exact match found for rate rule [Cb_H;C_rad/H/CdCs] Euclidian distance = 0 Multiplied by reaction path degeneracy 6.0 family: H_Abstraction Ea raised from 310.7 to 311.9 kJ/mol to match endothermicity of reaction.""")
kinetics: From training reaction 1694 used for Cb_H;C_rad/H/CdCs
Exact match found for rate rule [Cb_H;C_rad/H/CdCs]
Euclidian distance = 0
Multiplied by reaction path degeneracy 6.0
family: H_Abstraction
kinetics: From training reaction 1694 used for Cb_H;C_rad/H/CdCs
Exact match found for rate rule [Cb_H;C_rad/H/CdCs]
Euclidian distance = 0
Multiplied by reaction path degeneracy 6.0
family: H_Abstraction
Ea raised from 310.7 to 311.9 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: C#Cc1ccccc1(51) + C1=CC2C=C[C]1C=C2(49) <=> C#Cc1cc[c]cc1(90) + C1=CC2C=CC1=CC2(83) origin: H_Abstraction
tested:
rxn: C#Cc1ccccc1(51) + C1=CC2C=C[C]1C=C2(49) <=> C#Cc1cc[c]cc1(90) + C1=CC2C=CC1=CC2(83) origin: H_Abstraction

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-18.62	-12.53	-8.79	-6.22	-2.91	-0.83	2.16	3.81
k(T):	-50.75	-36.63	-28.06	-22.29	-14.96	-10.46	-4.27	-1.01

kinetics: Arrhenius(A=(0.0645,'cm^3/(mol*s)'), n=4.34, Ea=(30.45,'kcal/mol'), T0=(1,'K'), comment="""From training reaction 1694 used for Cb_H;C_rad/H/CdCs Exact match found for rate rule [Cb_H;C_rad/H/CdCs] Euclidian distance = 0 Multiplied by reaction path degeneracy 3.0 family: H_Abstraction""")
kinetics: Arrhenius(A=(0.0645,'cm^3/(mol*s)'), n=4.34, Ea=(74.548,'kcal/mol'), T0=(1,'K'), comment="""From training reaction 1694 used for Cb_H;C_rad/H/CdCs Exact match found for rate rule [Cb_H;C_rad/H/CdCs] Euclidian distance = 0 Multiplied by reaction path degeneracy 3.0 family: H_Abstraction Ea raised from 310.7 to 311.9 kJ/mol to match endothermicity of reaction.""")
kinetics: From training reaction 1694 used for Cb_H;C_rad/H/CdCs
Exact match found for rate rule [Cb_H;C_rad/H/CdCs]
Euclidian distance = 0
Multiplied by reaction path degeneracy 3.0
family: H_Abstraction
kinetics: From training reaction 1694 used for Cb_H;C_rad/H/CdCs
Exact match found for rate rule [Cb_H;C_rad/H/CdCs]
Euclidian distance = 0
Multiplied by reaction path degeneracy 3.0
family: H_Abstraction
Ea raised from 310.7 to 311.9 kJ/mol to match endothermicity of reaction.

Observables Test Case: Aromatics Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

aromatics Passed Observable Testing ✅

Regression test liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:57
Current: Execution time (DD:HH:MM:SS): 00:00:02:32
Reference: Memory used: 846.98 MB
Current: Memory used: 852.01 MB

liquid_oxidation Passed Core Comparison ✅

Original model has 37 species.
Test model has 37 species. ✅
Original model has 241 reactions.
Test model has 241 reactions. ✅

liquid_oxidation Failed Edge Comparison ❌

Original model has 214 species.
Test model has 214 species. ✅
Original model has 1593 reactions.
Test model has 1590 reactions. ❌
The original model has 6 reactions that the tested model does not have. ❌
rxn: C[CH]CC(C)OO(31) <=> [OH](22) + CCCC(C)=O(28) origin: intra_H_migration
rxn: CC(C[CH]COO)OO(118) <=> CC(CC[CH]OO)OO(133) origin: intra_H_migration
rxn: CC(C[CH]COO)OO(118) <=> C[C](CCCOO)OO(132) origin: intra_H_migration
rxn: CC(CC(C)OO)O[O](90) + CC(CCCOO)O[O](108) <=> oxygen(1) + CC([O])CC(C)OO(110) + CC([O])CCCOO(123) origin: Peroxyl_Disproportionation
rxn: CC(CC(C)OO)O[O](90) + CC(CCCOO)O[O](108) <=> oxygen(1) + CC(=O)CC(C)OO(105) + CC(O)CCCOO(152) origin: Peroxyl_Termination
rxn: CC(CC(C)OO)O[O](90) + CC(CCCOO)O[O](108) <=> oxygen(1) + CC(=O)CCCOO(115) + CC(O)CC(C)OO(143) origin: Peroxyl_Termination
The tested model has 3 reactions that the original model does not have. ❌
rxn: C[CH]CC(C)OO(32) <=> CCC[C](C)OO(78) origin: intra_H_migration
rxn: CC(C[CH]COO)OO(115) <=> [OH](22) + CC(CCC=O)OO(116) origin: intra_H_migration
rxn: CC(C[CH]COO)OO(115) <=> [OH](22) + CC(=O)CCCOO(112) origin: intra_H_migration

Observables Test Case: liquid_oxidation Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

liquid_oxidation Passed Observable Testing ✅

Regression test nitrogen:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:02
Current: Execution time (DD:HH:MM:SS): 00:00:01:13
Reference: Memory used: 848.72 MB
Current: Memory used: 852.89 MB

nitrogen Failed Core Comparison ❌

Original model has 41 species.
Test model has 41 species. ✅
Original model has 359 reactions.
Test model has 360 reactions. ❌
The tested model has 1 reactions that the original model does not have. ❌
rxn: HNO(48) + HCO(13) <=> NO(38) + CH2O(18) origin: H_Abstraction

nitrogen Failed Edge Comparison ❌

Original model has 133 species.
Test model has 133 species. ✅
Original model has 981 reactions.
Test model has 983 reactions. ❌
The tested model has 2 reactions that the original model does not have. ❌
rxn: HNO(48) + HCO(13) <=> NO(38) + CH2O(18) origin: H_Abstraction
rxn: HON(T)(83) + HCO(13) <=> NO(38) + CH2O(18) origin: Disproportionation

Observables Test Case: NC Comparison

✅ All Observables varied by less than 0.200 on average between old model and new model in all conditions!

nitrogen Passed Observable Testing ✅

Regression test oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:48
Current: Execution time (DD:HH:MM:SS): 00:00:02:09
Reference: Memory used: 733.56 MB
Current: Memory used: 739.12 MB

oxidation Passed Core Comparison ✅

Original model has 59 species.
Test model has 59 species. ✅
Original model has 694 reactions.
Test model has 694 reactions. ✅

oxidation Passed Edge Comparison ✅

Original model has 230 species.
Test model has 230 species. ✅
Original model has 1526 reactions.
Test model has 1526 reactions. ✅

Observables Test Case: Oxidation Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

oxidation Passed Observable Testing ✅

Errors occurred during observable testing ⚠️

WARNING:root:Initial mole fractions do not sum to one; normalizing.

Regression test sulfur:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:40
Current: Execution time (DD:HH:MM:SS): 00:00:00:47
Reference: Memory used: 837.21 MB
Current: Memory used: 850.78 MB

sulfur Passed Core Comparison ✅

Original model has 27 species.
Test model has 27 species. ✅
Original model has 74 reactions.
Test model has 74 reactions. ✅

sulfur Failed Edge Comparison ❌

Original model has 89 species.
Test model has 89 species. ✅
Original model has 227 reactions.
Test model has 227 reactions. ✅
The original model has 1 reactions that the tested model does not have. ❌
rxn: O(4) + SO2(15) (+N2) <=> SO3(16) (+N2) origin: primarySulfurLibrary
The tested model has 1 reactions that the original model does not have. ❌
rxn: O(4) + SO2(15) (+N2) <=> SO3(16) (+N2) origin: primarySulfurLibrary

Observables Test Case: SO2 Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

sulfur Passed Observable Testing ✅

Regression test superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:25
Current: Execution time (DD:HH:MM:SS): 00:00:00:27
Reference: Memory used: 933.86 MB
Current: Memory used: 930.11 MB

superminimal Passed Core Comparison ✅

Original model has 13 species.
Test model has 13 species. ✅
Original model has 21 reactions.
Test model has 21 reactions. ✅

superminimal Passed Edge Comparison ✅

Original model has 18 species.
Test model has 18 species. ✅
Original model has 28 reactions.
Test model has 28 reactions. ✅

Regression test RMS_constantVIdealGasReactor_superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:18
Current: Execution time (DD:HH:MM:SS): 00:00:02:59
Reference: Memory used: 2227.68 MB
Current: Memory used: 2463.94 MB

RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅

Original model has 13 species.
Test model has 13 species. ✅
Original model has 19 reactions.
Test model has 19 reactions. ✅

RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅

Original model has 13 species.
Test model has 13 species. ✅
Original model has 19 reactions.
Test model has 19 reactions. ✅

Observables Test Case: RMS_constantVIdealGasReactor_superminimal Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_constantVIdealGasReactor_superminimal Passed Observable Testing ✅

Regression test RMS_CSTR_liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:17:40
Current: Execution time (DD:HH:MM:SS): 00:00:16:59
Reference: Memory used: 2551.98 MB
Current: Memory used: 3403.06 MB

RMS_CSTR_liquid_oxidation Failed Core Comparison ❌

Original model has 35 species.
Test model has 35 species. ✅
Original model has 130 reactions.
Test model has 126 reactions. ❌
The original model has 1 species that the tested model does not have. ❌
spc: [CH2]C(CCC)OO(33)
The tested model has 1 species that the original model does not have. ❌
spc: [CH2]CCC(9)
The original model has 11 reactions that the tested model does not have. ❌
rxn: CCCC(C)O[O](22) <=> [CH2]C(CCC)OO(33) origin: intra_H_migration
rxn: [O]O(13) + [CH2]C(CCC)OO(33) <=> oxygen(1) + CCCC(C)OO(27) origin: H_Abstraction
rxn: OO(23) + [CH2]C(CCC)OO(33) <=> [O]O(13) + CCCC(C)OO(27) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(33) + pentane(2) <=> CC[CH]CC(7) + CCCC(C)OO(27) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(33) + pentane(2) <=> C[CH]CCC(11) + CCCC(C)OO(27) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(33) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCCC(C)OO(27) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(33) + CCC(CC)OO(26) <=> CCC(CC)O[O](21) + CCCC(C)OO(27) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(33) + pentane(2) <=> [CH2]CCCC(12) + CCCC(C)OO(27) origin: H_Abstraction
rxn: [O]O(13) + C=CCCC(18) <=> [CH2]C(CCC)OO(33) origin: R_Addition_MultipleBond
rxn: [CH2]CCCC(12) + [CH2]C(CCC)OO(33) <=> C=CCCC(18) + CCCC(C)OO(27) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]C(CCC)OO(33) <=> C=CCCC(18) + CCCC(C)OO(27) origin: Disproportionation
The tested model has 7 reactions that the original model does not have. ❌
rxn: CCC(CC)O[O](22) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(27) origin: H_Abstraction
rxn: CCCC(C)O[O](21) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(26) origin: H_Abstraction
rxn: C[CH]CC(C)OO(34) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CC(CC)OO(38) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]C(CC)OO(37) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(27) origin: H_Abstraction
rxn: CC[CH]C(C)OO(32) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH3](10) + [CH2]CCC(9) <=> pentane(2) origin: R_Recombination

RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌

Original model has 77 species.
Test model has 77 species. ✅
Original model has 256 reactions.
Test model has 266 reactions. ❌
The tested model has 10 reactions that the original model does not have. ❌
rxn: CCC(CC)O[O](22) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(27) origin: H_Abstraction
rxn: CCCC(C)O[O](21) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(26) origin: H_Abstraction
rxn: C[CH]CC(C)OO(34) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CC(CC)OO(38) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]C(CC)OO(37) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(27) origin: H_Abstraction
rxn: CC[CH]C(C)OO(32) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(26) origin: H_Abstraction
rxn: CC[C](CC)OO(52) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(27) origin: H_Abstraction
rxn: CCC[C](C)OO(58) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(33) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CCC(C)OO(35) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(26) origin: H_Abstraction

Observables Test Case: RMS_CSTR_liquid_oxidation Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_CSTR_liquid_oxidation Passed Observable Testing ✅

Regression test fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:30
Current: Execution time (DD:HH:MM:SS): 00:00:00:46
Reference: Memory used: 699.72 MB
Current: Memory used: 706.53 MB

fragment Passed Core Comparison ✅

Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Original model has 10 species.
Test model has 10 species. ✅
Original model has 2 reactions.
Test model has 2 reactions. ✅

fragment Passed Edge Comparison ✅

Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Fragment to_rdkit_mol expects to return a tuple. Setting return_mapping = True; please double-check your code to ensure this is what you want.
Original model has 33 species.
Test model has 33 species. ✅
Original model has 47 reactions.
Test model has 47 reactions. ✅

Observables Test Case: fragment Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

fragment Passed Observable Testing ✅

Errors occurred during observable testing ⚠️

WARNING:root:Initial mole fractions do not sum to one; normalizing.

Regression test RMS_constantVIdealGasReactor_fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:42
Current: Execution time (DD:HH:MM:SS): 00:00:03:30
Reference: Memory used: 2438.17 MB
Current: Memory used: 2440.85 MB

RMS_constantVIdealGasReactor_fragment Passed Core Comparison ✅

Original model has 10 species.
Test model has 10 species. ✅
Original model has 2 reactions.
Test model has 2 reactions. ✅

RMS_constantVIdealGasReactor_fragment Passed Edge Comparison ✅

Original model has 27 species.
Test model has 27 species. ✅
Original model has 24 reactions.
Test model has 24 reactions. ✅

Observables Test Case: RMS_constantVIdealGasReactor_fragment Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_constantVIdealGasReactor_fragment Passed Observable Testing ✅

Errors occurred during observable testing ⚠️

WARNING:root:Initial mole fractions do not sum to one; normalizing.

Regression test minimal_surface:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:31
Current: Execution time (DD:HH:MM:SS): 00:00:00:39
Reference: Memory used: 849.97 MB
Current: Memory used: 857.27 MB

minimal_surface Passed Core Comparison ✅

Original model has 11 species.
Test model has 11 species. ✅
Original model has 3 reactions.
Test model has 3 reactions. ✅

minimal_surface Passed Edge Comparison ✅

Original model has 38 species.
Test model has 38 species. ✅
Original model has 38 reactions.
Test model has 38 reactions. ✅

Observables Test Case: minimal_surface Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

minimal_surface Passed Observable Testing ✅

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JacksonBurns marked this pull request as draft May 25, 2025 21:43

JacksonBurns force-pushed the feat/rdkit_sssr branch from 99bf00c to 8d6fe64 Compare May 25, 2025 21:49

JacksonBurns mentioned this pull request May 29, 2025

Add T-Dependent and ML Options for Solvation Corrections #2798

Draft

Base automatically changed from feat/py39_rebase to main May 29, 2025 19:55

jonwzheng self-assigned this Jun 30, 2025

jonwzheng mentioned this pull request Jun 30, 2025

Update Jupyter notebooks and associated codebase [RMG-Py] #2815

Open

13 tasks

JacksonBurns mentioned this pull request Jul 9, 2025

Make RMG-Py conda Work Again 🎉 #2820

Merged

jonwzheng mentioned this pull request Jul 24, 2025

Updates to draw.py are causing a crash for charge separated bidentates #2744

Open

jonwzheng mentioned this pull request Jul 25, 2025

Fix drawing errors for charged species by moving to rdkit geometry generation #2838

Merged

jonwzheng force-pushed the feat/rdkit_sssr branch from 7598c98 to 019362c Compare July 25, 2025 17:09

JacksonBurns force-pushed the feat/rdkit_sssr branch from 6e6490a to e92bec0 Compare August 4, 2025 01:51

JacksonBurns mentioned this pull request Aug 4, 2025

Status Tracking: chemprop and ML Thermochemistry Prediction #2559

Open

1 task

jonwzheng and others added 27 commits September 19, 2025 14:25

make test_make_sample_molecule test logic more clear

a4d2777

remove erroneously malformed sanitize arg

fac0daf

Revert "remove some tests that appear backwards-incompatible with new…

510e654

… RDKit adjacency list parsing rules" This reverts commit 86e15b6.

add support for RDKit fragment atom w/ dummy molecule

81a43af

fix pesky type error in rdkit mol creation due to type cython coercion

afc2fdf

update test_get_largest_ring

e02491d

fix error in test_Get_all_polycyclic_vertices

fa75457

make rdkit parsing more lenient with weird bond orders

09e975a

update scipy simps to sipmson

32e0b86

simps was deprecated in scipy 1.6 in favor of simpson. This updates the function call so that it doesn't break workflows.

remove python3.12 from CI for now

8d6307c

3.12 needs cantera update, which is not yet ready.

update setup.py to also exclude python 3.12

09e395a

added a test for drawing bidentates with charge separation

df78a8b

add ion test cases to drawTest

62b6f54

Accompanies changes to `draw.py` to use `rdkit` backend, which traditionally was not well-supported for ions (but now might be a better option than the default drawing algorithm).

remove pyrdl from conda recipe as well

6e3780d

add more python versions to conda build

a801068

Make fragment code compatible with RDKit changes

f5ace28

The molecule to_rdkit_mol now allows for and calls sanitize. The fragment code previously had hardcoded args. This commit just makes the args flexible so that they get passed directly to `converter` regardless of what the arguments are.

Fix fragment error due to non-default return type

22eafd7

After changing to_rdkit_mol to kwargs format in Fragment, some of the existing code that relied on the previous function defaults broke. Namely, return_mapping must be True.

add missing remove_h=False required flag to fragment to_rdkit_mol calls

d3d365a

fix test_to_rdkit_mol because default args were changed

2253294

update test expectted return type

2ae3c3f

Revert "update test expectted return type"

e156394

This reverts commit 7ac5fd4.

set default

1699791

jonwzheng force-pushed the feat/rdkit_sssr branch from 46c8460 to 55f8fc4 Compare September 19, 2025 18:25

Use rdkit for SSSR and RCs (bug fix + Python upgrade) #2796

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Use rdkit for SSSR and RCs (bug fix + Python upgrade) #2796

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JacksonBurns commented May 25, 2025

Motivation or Problem

Description of Changes

Testing

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regarding the draw unit test

Note about sanitization

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github-actions bot commented Sep 19, 2025

Regression Testing Results

Regression test aromatics:

Regression test liquid_oxidation:

Regression test nitrogen:

Regression test oxidation:

Regression test sulfur:

Regression test superminimal:

Regression test RMS_constantVIdealGasReactor_superminimal:

Regression test RMS_CSTR_liquid_oxidation:

Regression test fragment:

Regression test RMS_constantVIdealGasReactor_fragment:

Regression test minimal_surface:

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Use `rdkit` for SSSR and RCs (bug fix + Python upgrade) #2796

Use `rdkit` for SSSR and RCs (bug fix + Python upgrade) #2796

jonwzheng commented Jul 16, 2025 •

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