Skip to content

Exhaustive fragmenter saturation fix and optimization #1

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

Closed
ToLeWeiss wants to merge 47 commits into from
Closed

Exhaustive fragmenter saturation fix and optimization #1

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
47 commits
Select commit Hold shift + click to select a range
66bdb9e
work in progress: implemented the option for the fragmenter to return…
ToLeWeiss Oct 28, 2024
9ad00c9
added tests for unsaturated setting and fixed unsaturated run
ToLeWeiss Oct 28, 2024
db70ad8
work in progress: first copy approaches to fix saturation problem and…
ToLeWeiss Nov 28, 2024
1584523
fix subset generation for case where initial capacity might be negati…
ToLeWeiss Nov 28, 2024
1831ce5
switching to primitive integers because java Lists are indexed by the…
ToLeWeiss Nov 28, 2024
a3f1d35
work in progress: fixed indexing and fix of check for size constraint
ToLeWeiss Nov 28, 2024
49cfd6a
work in progress: switch to primitive int matrices for subset generat…
ToLeWeiss Nov 28, 2024
dc328c8
work in progress: fix size limitation of the subset generation
ToLeWeiss Nov 28, 2024
1677622
work in progress: figuring out why the end atoms are in a different c…
ToLeWeiss Dec 10, 2024
40dfd89
work in progress: fixing for end atoms not in container
ToLeWeiss Dec 13, 2024
c01722e
work in progress: working reimplementation of the exhaustive fragmenter
ToLeWeiss Feb 3, 2025
225a564
work in progress: cleaning up and adding documentation
ToLeWeiss Feb 5, 2025
259eb80
work in progress: cleaning up imports
ToLeWeiss Feb 5, 2025
6ed08bd
work in progress: adding a setter for the maximum tree depth
ToLeWeiss Feb 5, 2025
49536ef
work in progress: refining comments
ToLeWeiss Feb 5, 2025
c2fd014
work in progress: further improvements to comments and more private f…
ToLeWeiss Feb 5, 2025
eaa69e5
Merge branch 'main' into exhaustive_fragmenter
ToLeWeiss Feb 5, 2025
c1596f0
work in progress: first tries to add an saturation option with R-Atoms
ToLeWeiss Apr 6, 2025
f9faed1
work in progress: added tests for pseudo-R-atom saturation and first …
ToLeWeiss Apr 25, 2025
194d446
Merge remote-tracking branch 'origin/main' into exhaustive_fragmenter
ToLeWeiss May 9, 2025
59425df
refactored splitting function to improve saturation and improved docu…
ToLeWeiss May 23, 2025
2ba2fcf
improved tests and documentation
ToLeWeiss Jun 4, 2025
65fef6f
small test documentation fix
ToLeWeiss Jun 4, 2025
53633e7
fixed docs and corrected calculation for HashSet capacity
ToLeWeiss Jun 4, 2025
0fce4ae
WIP fixing issues in documentation and conformities in the code
ToLeWeiss Jul 9, 2025
2e50f4f
implemented comments and improved ring detection and aromaticity copying
ToLeWeiss Jul 23, 2025
33ce575
added null check for input molecule and elaborated on comments
ToLeWeiss Jul 23, 2025
a46401f
Merge branch 'main' into exhaustive_fragmenter
ToLeWeiss Jul 23, 2025
1acf2b1
removed useless comments and imports and added documentation if it is…
ToLeWeiss Aug 4, 2025
829fb47
improved comments and removed dependencies in the test class
ToLeWeiss Aug 14, 2025
0890b0b
implemented test for double bonds, cleaned up code and tests
ToLeWeiss Aug 20, 2025
c7084a5
implemented stereo chemistry copying, a respective test and added mis…
ToLeWeiss Aug 21, 2025
3eeb886
fixed regression in test and fixed wrong maximum tree depth
ToLeWeiss Aug 21, 2025
40a6559
fixed documentation links, added constructor for just saturation and …
ToLeWeiss Sep 3, 2025
d669936
improved comments and code aesthetic for stereo information copying
ToLeWeiss Sep 3, 2025
6302f6c
fixed typo
ToLeWeiss Sep 4, 2025
29781a2
Merge branch 'main' into exhaustive_fragmenter
ToLeWeiss Sep 4, 2025
d6f52e8
added documentation for custom assertion
ToLeWeiss Sep 4, 2025
71da5e6
made param comments more consistent and beginning with lowercase
ToLeWeiss Sep 4, 2025
521afe7
switching to big integers to lift the upper limit of 31 splittable Bo…
ToLeWeiss Sep 17, 2025
e7c5489
cherry picked commit: 71da5e6e4d to revert to integers instead of BigInt
ToLeWeiss Sep 4, 2025
b186c0e
cherry picked hopefully the right commit commit:d6f52e8 to revert to …
ToLeWeiss Sep 4, 2025
6a03305
I finally read the documentation of git cherry-pick and therefore app…
ToLeWeiss Oct 22, 2025
7734d86
Merge remote-tracking branch 'upstream/main' into exhaustive_fragmenter
ToLeWeiss Oct 22, 2025
7abb1f4
adjusted maximum tree depth in the comments to 27
ToLeWeiss Oct 22, 2025
9ca3947
added exception to mitigate the indexing of the fragmentation result …
ToLeWeiss Oct 23, 2025
59e232c
fixed missing value
ToLeWeiss Oct 23, 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
Loading
Loading