Draw Hydrogen bonds (again) #2734

rwest · 2024-11-20T05:11:48Z

Motivation or Problem

Pull request #1961 introduced the ability to draw hydrogen bonds.

To do so, Hydrogen atoms that have H bonds shouldn't be removed from the drawings.
This check was removed without explanation in ec95153
which was designed to make drawing work for fragments.
That broke drawing of hydrogen bonds.
The unit test for drawing hydrogen bonds exists, but just checks that a PDF is made, not what it looks like.
So the regression was not detected.

Description of Changes

This restores the check that H atoms in H-bonds are not removed from drawings.
It also removes code duplication that was introduced in #1961 through erroneous rebasing, that @bjkreitz noticed and removed in a different PR.

Testing

It was while testing the second commit (Bjarne's commit that removes the code duplication)
that I found the title problem (the H bonds being broken). Now I've tested both, by running the original tests from #1961

example =  Molecule().from_adjacency_list("""
example
1  O u0 p3 c-1 {2,S} {10,H}
2  N u0 p0 c+1 {1,S} {3,D} {4,S}
3  O u0 p2 c0 {2,D}
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}
""")
example
display(example)
for m in example.generate_h_bonded_structures():
    display(m)

Restoring the check makes the H bonds work. This particular molecule still looks ugly, as it always did. Removing the duplicate code doesn't make them worse.

Reviewer Tips

Not a big change, and not worth a lot of time.

This was added in PR #1961 which indroduced the ability to draw hydrogen bonds. It was removed without explanation in ec95153 which made drawing work for fragments. That broke drawing of hydrogen bonds. The unit test for drawing hydrogen bonds exists, but just checks that a PDF is made, not what it looks like. So this wasn't detected.

github-actions · 2024-11-20T07:34:51Z

Regression Testing Results

WARNING:root:Initial mole fractions do not sum to one; normalizing.
WARNING:root:Initial mole fractions do not sum to one; normalizing.
WARNING:root:Initial mole fractions do not sum to one; normalizing.
⚠️ 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): 00:00:01:05
Current: Execution time (DD:HH:MM:SS): 00:00:01:04
Reference: Memory used: 2759.25 MB
Current: Memory used: 2789.68 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 Passed Edge Comparison ✅

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

Details

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): 00:00:02:08
Current: Execution time (DD:HH:MM:SS): 00:00:02:06
Reference: Memory used: 2890.78 MB
Current: Memory used: 2898.54 MB

liquid_oxidation Passed Core Comparison ✅

Original model has 37 species.
Test model has 37 species. ✅
Original model has 216 reactions.
Test model has 216 reactions. ✅

liquid_oxidation Passed Edge Comparison ✅

Original model has 202 species.
Test model has 202 species. ✅
Original model has 1610 reactions.
Test model has 1610 reactions. ✅

Details

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): 00:00:01:25
Current: Execution time (DD:HH:MM:SS): 00:00:01:24
Reference: Memory used: 2897.56 MB
Current: Memory used: 2900.09 MB

nitrogen Failed Core Comparison ❌

Original model has 41 species.
Test model has 41 species. ✅
Original model has 360 reactions.
Test model has 359 reactions. ❌
The original model has 1 reactions that the tested 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 983 reactions.
Test model has 981 reactions. ❌

Non-identical thermo! ❌
original: O1[C]=N1
tested: O1[C]=N1

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
141.64	58.66	12.26	12.27	12.09	11.96	12.26	12.72	12.15
116.46	53.90	11.62	12.71	13.49	13.96	14.14	13.85	13.58

thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(oxirene) + radical(CdJ-NdO)
thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(Cyclopropene) + radical(CdJ-NdO)
The original model has 2 reactions that the tested 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

Non-identical kinetics! ❌
original:
rxn: NCO(66) <=> O1[C]=N1(126) origin: Intra_R_Add_Endocyclic
tested:
rxn: NCO(66) <=> O1[C]=N1(126) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-66.25	-46.19	-34.19	-26.21	-16.28	-10.36	-2.54	1.31
k(T):	-49.54	-33.65	-24.16	-17.85	-10.01	-5.35	0.80	3.82

kinetics: Arrhenius(A=(6.95187e+18,'s^-1'), n=-1.628, Ea=(111.271,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H""")
kinetics: Arrhenius(A=(6.95187e+18,'s^-1'), n=-1.628, Ea=(88.327,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H""")
Identical kinetics comments:
kinetics: Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H

Details

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): 00:00:02:26
Current: Execution time (DD:HH:MM:SS): 00:00:02:19
Reference: Memory used: 2748.37 MB
Current: Memory used: 2765.68 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. ✅

Details

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 ✅

Regression test sulfur:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:53
Current: Execution time (DD:HH:MM:SS): 00:00:00:52
Reference: Memory used: 2847.88 MB
Current: Memory used: 2878.36 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

Details

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): 00:00:00:35
Current: Execution time (DD:HH:MM:SS): 00:00:00:34
Reference: Memory used: 2965.46 MB
Current: Memory used: 2956.12 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): 00:00:02:24
Current: Execution time (DD:HH:MM:SS): 00:00:02:19
Reference: Memory used: 3522.57 MB
Current: Memory used: 3486.84 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. ✅

Details

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): 00:00:05:55
Current: Execution time (DD:HH:MM:SS): 00:00:05:44
Reference: Memory used: 3414.52 MB
Current: Memory used: 3411.63 MB

RMS_CSTR_liquid_oxidation Failed Core Comparison ❌

Original model has 37 species.
Test model has 37 species. ✅
Original model has 233 reactions.
Test model has 232 reactions. ❌
The original model has 1 reactions that the tested model does not have. ❌
rxn: CCO[O](34) <=> [OH](21) + CC=O(62) origin: intra_H_migration

RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌

Original model has 206 species.
Test model has 206 species. ✅
Original model has 1508 reactions.
Test model has 1508 reactions. ✅
The original model has 2 reactions that the tested model does not have. ❌
rxn: CCO[O](34) <=> [OH](21) + CC=O(62) origin: intra_H_migration
rxn: CCCO[O](35) <=> [OH](21) + CCC=O(44) origin: intra_H_migration
The tested model has 2 reactions that the original model does not have. ❌
rxn: CCCO[O](34) <=> CC[CH]OO(45) origin: intra_H_migration
rxn: CCO[O](36) <=> C[CH]OO(62) origin: intra_H_migration

Non-identical kinetics! ❌
original:
rxn: CCCO[O](35) + CCCC(C)O[O](33) <=> oxygen(1) + CCC[O](92) + CCCC(C)[O](65) origin: Peroxyl_Disproportionation
tested:
rxn: CCCO[O](34) + CCCC(C)O[O](33) <=> oxygen(1) + CCC[O](94) + CCCC(C)[O](61) origin: Peroxyl_Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	7.83	7.49	7.23	7.02	6.68	6.42	5.95	5.61
k(T):	3.69	4.39	4.82	5.10	5.45	5.66	5.94	6.08

kinetics: Arrhenius(A=(3.18266e+20,'cm^3/(mol*s)'), n=-2.694, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing""")
kinetics: Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(3.866,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R""")
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R

Details

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): 00:00:00:40
Current: Execution time (DD:HH:MM:SS): 00:00:00:39
Reference: Memory used: 2680.55 MB
Current: Memory used: 2697.44 MB

fragment Passed Core Comparison ✅

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

fragment Passed Edge Comparison ✅

Original model has 33 species.
Test model has 33 species. ✅
Original model has 47 reactions.
Test model has 47 reactions. ✅

Details

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 ✅

Regression test RMS_constantVIdealGasReactor_fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:03:04
Current: Execution time (DD:HH:MM:SS): 00:00:02:58
Reference: Memory used: 3652.67 MB
Current: Memory used: 3630.89 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. ✅

Details

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 ✅

Regression test minimal_surface:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:43
Current: Execution time (DD:HH:MM:SS): 00:00:00:42
Reference: Memory used: 2852.16 MB
Current: Memory used: 2877.33 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. ✅

Details

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 ✅

beep boop this comment was written by a bot 🤖

bjkreitz

This change looks good to me. The structures of the example molecule are indeed pretty ugly, but reintroducing this check allows to draw the hydrogen bonds again. RMG also works normally.

rwest and others added 2 commits November 19, 2024 23:55

Remove code duplicate

6f5c1c8

bjkreitz self-requested a review November 21, 2024 15:12

bjkreitz approved these changes Nov 21, 2024

View reviewed changes

rwest merged commit 5397e7f into main Nov 21, 2024

rwest deleted the drawHbonds branch November 21, 2024 15:17

JacksonBurns mentioned this pull request Jul 10, 2025

RMG-Py Version 3.3.0 #2826

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Draw Hydrogen bonds (again) #2734

Draw Hydrogen bonds (again) #2734

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rwest commented Nov 20, 2024

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github-actions bot commented Nov 20, 2024

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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Draw Hydrogen bonds (again) #2734

Draw Hydrogen bonds (again) #2734

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rwest commented Nov 20, 2024

Motivation or Problem

Description of Changes

Testing

Reviewer Tips

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github-actions bot commented Nov 20, 2024

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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