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Hydrolysis families and tests #770

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242e3d0
Minor: CI style modifications
alongd Jun 29, 2024
283dd12
Removed RMG-Py and RMG-database repo paths from common
alongd Jul 1, 2024
6a95e5b
Relocated reaction into a sub module
alongd Jun 29, 2024
f4fdf54
Added RMG_DB_PATH to settings
alongd Jul 2, 2024
e005c51
Added clean_text() to common
alongd Jun 29, 2024
9036d5c
Tests: common.clean_text()
alongd Jun 29, 2024
b40a4cb
Added hydrolysis as an ARC reaction family
alongd Jul 2, 2024
cbdfaed
Added the reaction family module
alongd Jul 2, 2024
2014a43
Tests: Added reaction family tests
alongd Jul 2, 2024
6612eaf
Removed rmgdb from reaction
alongd Jul 2, 2024
4794958
Tests: Adaptations to reaction tests
alongd Jul 2, 2024
b4e7453
Corrected import in arkane test
alongd Jul 2, 2024
c567e2d
Don't consider additional TS conformers if there's just one
alongd Jul 3, 2024
3c56dc3
Removed the determine_family() function from the rmgdb module
alongd Jul 3, 2024
1f76df4
Don't use RMGDatabase to determine reaction family
alongd Jul 3, 2024
76d4aa1
Tests: Removed RMGDatabase from tests
alongd Jul 3, 2024
17e0b91
Modifications to how reaction family is used in ARC
alongd Jul 3, 2024
eac7ff5
Make family a property of reaction
alongd Jul 3, 2024
3f1efa4
Tests: Adaptations to ARC tests
alongd Jul 3, 2024
c049a99
f! fam
alongd Jul 3, 2024
30ff156
f! fam test
alongd Jul 5, 2024
60870da
fam
alongd Jul 6, 2024
e2ce840
f! tst
alongd Jul 6, 2024
225dbd5
f tst
alongd Jul 7, 2024
2d77ce8
f fam
alongd Jul 7, 2024
da46e64
TMP
alongd Jul 11, 2024
d6f1c31
Removed hard-coded no-mol-perception for triplet O2/S2
alongd Jul 29, 2024
a15f4ec
Tests: Perceive triplet O2 properly
alongd Jul 29, 2024
79c4655
f! fam resonance
alongd Jul 29, 2024
66e1b84
f! fam tests
alongd Jul 29, 2024
363f571
TMP
alongd Aug 8, 2024
80bd77c
TMP
alongd Aug 11, 2024
50e0396
TMP
alongd Aug 12, 2024
9205c54
f!
alongd Oct 10, 2024
622c70d
Call hydrolysis function (still doesn't exist)
alongd Oct 10, 2024
8d3763f
Temporary commit
LeenFahoum Nov 6, 2024
f37d582
Add condition to filter ARC families by excluding hidden files and di…
LeenFahoum Nov 11, 2024
40467e1
Filter ARC families to exclude hidden files and directories
LeenFahoum Nov 11, 2024
e751642
new ester__hydrolysis family
LeenFahoum Nov 13, 2024
0f98d35
new imine hydrolysis family
LeenFahoum Nov 13, 2024
de6f175
new nitrite hydrolysis family
LeenFahoum Nov 13, 2024
178d8d2
new ether hydrolysis family
LeenFahoum Nov 13, 2024
3174e05
tests for new hydrolysis families
LeenFahoum Nov 13, 2024
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new imine hydrolysis family
  • Loading branch information
LeenFahoum committed Nov 13, 2024
commit 0f98d351888ff192c44a02fa2d775f6a1aae5ebc
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "imine/groups"
name = "imine_hydrolysis/groups"
shortDesc = u"imine_hydrolysis"
longDesc = u"""
A generic bimolecular ester hydrolysis reaction: R1-A(R2)=N-R3 + H2O <=> R1-A(R2)(OH)-N(H)-R3
A generic bimolecular imine hydrolysis reaction: R1-A(R2)=N-R3 + H2O <=> R1-A(R2)(OH)-N(H)-R3

Where:
- A can be C (carbonyl) or P (phosphoryl).
Expand All @@ -11,14 +11,14 @@

"""

template(reactants=["imine", "H2O"], products=["acid", "alcohol"], ownReverse=False)
template(reactants=["imine", "H2O"], products=["acid"], ownReverse=False)

reverse = "condensation"
#reverse = "condensation"

reversible = True
#reversible = True

recipe(actions=[
['CHANGE_BOND', '*1', 1, '*2'],
['CHANGE_BOND', '*1', -1, '*2'],
['BREAK_BOND', '*3', 1, '*4'],
['FORM_BOND', '*1', 1, '*4'],
['FORM_BOND', '*2', 1, '*3'],
Expand All @@ -29,11 +29,9 @@
label = "imine",
group =
"""
1 R u0 p0 c0 {2}
2 *1 [C,P] u0 p0 c0 {1}{3}{4,D}
3 R u0 p0 c0 {2}
4 *2 N u0 p0 c0 {2,D}
5 R u0 p0 c0 {4,S}
1 *1 [C,P] u0 {2,D}
2 *2 N u0 {1,D} {3,S}
3 R u0 {2,S}
""",
kinetics = None,
)
Expand Down