Skip to content

Integration/implementation of RECAP algorithm #143

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
JonasSchaub wants to merge 43 commits into
base: production
Choose a base branch
from
Draft

Integration/implementation of RECAP algorithm #143

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
43 commits
Select commit Hold shift + click to select a range
591a00d
Starts RECAP implementation
JonasSchaub Nov 14, 2024
e37bd84
adds documentation i.e. explanations of the SMIRKS codes
JonasSchaub Nov 15, 2024
fe02b16
Fixes spotless complaint
JonasSchaub Nov 15, 2024
e5a615b
Merge branch 'production' into recap-integration
JonasSchaub Nov 20, 2024
312ed0b
updates CDK to version 2.10-SNAPSHOT and further work on RECAP
JonasSchaub Nov 20, 2024
92d6e0e
WIP, adds method for single-pass fragmentation and setting for minimu…
JonasSchaub Nov 21, 2024
d4cb29c
WIP, now trying the same way as RDKit via a hierarchy graph
JonasSchaub Nov 22, 2024
8917cd1
WIP, represents first working version of the RECAP hierarchy with a b…
JonasSchaub Nov 25, 2024
c59a0b7
WIP, only does a bit of refactoring
JonasSchaub Nov 25, 2024
6612743
excludes pseudo atoms from atom count for forbidden fragments and che…
JonasSchaub Dec 2, 2024
42eb297
WIP, adjusts the amine and cyclic amines cleavage rules so that they …
JonasSchaub Dec 2, 2024
757bffe
WIP, added more tests taken from RDKit
JonasSchaub Dec 4, 2024
4c227c6
WIP, adjusts ether SMIRKS code, adds two new functions to the hierarc…
JonasSchaub Dec 5, 2024
bacca59
WIP, restructures the class, moves cleavage rules to RECAP class for …
JonasSchaub Dec 10, 2024
c564d90
WIP, adjusts amide and ester rules and tests them individually; both …
JonasSchaub Dec 10, 2024
73f9fed
WIP, splits amine rule into secondary and tertiary amine rules, add m…
JonasSchaub Dec 11, 2024
4423556
WIP, just re-organizes todos
JonasSchaub Dec 11, 2024
980a743
Merge branch 'production' into recap-integration
JonasSchaub Dec 12, 2024
7fa5c9c
WIP, makes the amide rule even more restrictive
JonasSchaub Dec 16, 2024
3a5c45e
WIP, makes ester and amine rules more restrictive
JonasSchaub Dec 16, 2024
0a01942
WIP, reorders tests
JonasSchaub Dec 16, 2024
ab65e85
WIP, adds succinimide test to cyclic tertiary amine test
JonasSchaub Dec 16, 2024
2d9f2d5
WIP, makes amide more restrictive by excluding structures with N havi…
JonasSchaub Dec 18, 2024
66b0f4a
WIP, makes amide, ester, amine more restrictive (no multi-bonds to ca…
JonasSchaub Dec 18, 2024
33d4be4
WIP, overhauls the ether cleavage rule
JonasSchaub Dec 19, 2024
4380968
WIP, reworks the olefin cleavage rule
JonasSchaub Dec 19, 2024
5e8edcb
WIP, reworks the quaternary nitrogen rule
JonasSchaub Dec 20, 2024
de9c4e3
WIP, reworks aromatic nitrogen to aliphatic carbon rule
JonasSchaub Dec 20, 2024
9069fe8
WIP, reworks lactam rule but still needs to be tested and commented
JonasSchaub Dec 20, 2024
45c98d8
WIP, adds more tests for the lactam rule
JonasSchaub Jan 7, 2025
f91de94
WIP, solves the aromatic lactam not recognised issue
JonasSchaub Jan 8, 2025
6fde908
WIP, reworks the aromatic carbon to aromatic carbon rule and tests it
JonasSchaub Jan 8, 2025
270665b
Merge branch 'production' into recap-integration
JonasSchaub Jan 9, 2025
caeb702
updates copyright in new files
JonasSchaub Jan 9, 2025
eb94d03
switches to official CDK 2.10 release
JonasSchaub Jan 10, 2025
dbfa7c4
adds todo
JonasSchaub Feb 10, 2025
068e4f1
adjusts all the SMIRKS codes again, according to the developed and re…
JonasSchaub Feb 20, 2025
124d063
Merge branch 'production' into recap-integration
JonasSchaub Feb 27, 2025
8bdd8db
adds cdk-smarts as dependency and fixes import
JonasSchaub Feb 27, 2025
60977f2
extends some tests, fixes minor bug in cyclic tertiary amine, adds mo…
JonasSchaub Feb 27, 2025
547817c
extends some tests
JonasSchaub Feb 27, 2025
ee67665
Merge branch 'production' into recap-integration
JonasSchaub Mar 17, 2025
ff662b1
Merge branch 'production' into recap-integration
JonasSchaub Jul 3, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions build.gradle
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@ dependencies {
implementation group: 'org.openscience.cdk', name: 'cdk-interfaces', version: cdkVersion
implementation group: 'org.openscience.cdk', name: 'cdk-ioformats', version: cdkVersion
implementation group: 'org.openscience.cdk', name: 'cdk-smiles', version: cdkVersion
implementation group: 'org.openscience.cdk', name: 'cdk-smarts', version: cdkVersion
implementation group: 'org.openscience.cdk', name: 'cdk-inchi', version: cdkVersion
implementation group: 'org.openscience.cdk', name: 'cdk-standard', version: cdkVersion
implementation group: 'org.openscience.cdk', name: 'cdk-valencycheck', version: cdkVersion
Expand Down
Loading
Loading