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Connectivity_graph_dev #5

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@Niolon Niolon commented Apr 30, 2025 •
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  • Add a new growing mechanism for completing molecular fragments without growing polymeric structures infinitely

@Niolon Niolon self-assigned this Apr 30, 2025
@Niolon Niolon linked an issue May 1, 2025 that may be closed by this pull request
Extend symmetry growing along bonds to complete fragments #8
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3 tasks
Niolon added 30 commits June 20, 2025 10:45
@Niolon
Update symbols to match current modes
f771f2e
@Niolon
Extent testing in dev file
9f5d038
@Niolon
Make sure bonds always have a symmetry in valid format
45c8341
@Niolon
make the atom position key safely unique
79eef8a
@Niolon
Remove edge case, where multicharacter symOp Labels could lead to a w…
4174ded 
…rong label
@Niolon
Remove profiling file
e08d17f
@Niolon
Fix grow-fragment to not create lots of non-sensical bonds in high-sy…
521e214 
…mmetry cases
@Niolon
Add tests for SymmetryGrower
ae81122
@Niolon
Add a display of the unit cell when growing the cell
833a449
@Niolon
work on grow-cell (non-working intermediate step)
a7c9ff2
@Niolon
remove tests from pre-commit to allow for more atomic commits
f8d6765
@Niolon
Outlines of new growCell to limit recomputation and too large growth
a0fad8f
@Niolon
some bugfixing
bd1f1c7
@Niolon
Adapt growFragment tests to differnt function output
bf39c9c
@Niolon
Adapt SymmetryGrower and its tests to special position output from gr…
f1e04b7 
…owFragment
@Niolon
clean up the dev.js file used for timing growCell and growFragment
bdc4ee5
@Niolon
remove unused imports and definitions in cell3d.js
db66393
@Niolon
do not used combined symm elements in growCell.js (is actually slower…
731162b 
… not faster)
@Niolon
working implementation
47e4d6b
@Niolon
Add tests for grow-cell base functions. Remove non-sensical edge case
a8bfbb7
@Niolon
update husky configuration to not merge when eslint makes changes
abb58bd
@Niolon
eslint changes
726610a
@Niolon
Add tests for growAtomsInGroup
7aa3389
@Niolon
Add Bond tests, fix bond behaviour
c79dd45
@Niolon
More tests and fixes in External Bond growing
6a59d8f
@Niolon
give clear names to cell box and arrow parameters
e37fec2
@Niolon
Fix interaction of HydrogenFilter with growCell where base atom might…
a090c50 
… be moved/renamed
@Niolon
Extend problem structure collection to modifiers
fe1cc4d
@Niolon
Fix cell3d test
1f33338
@Niolon
Do not move acceptor
6b2612d
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Extend symmetry growing along bonds to complete fragments

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