Code

Add AO indices#100

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mcocdawc wants to merge 70 commits intomaintroyvvgroup/quemb:mainfrom add_AO_indicestroyvvgroup/quemb:add_AO_indicesCopy head branch name to clipboard

+847-232

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Commits on Jan 24, 2025

• Implemented the chemical fragmentation based on Van der Waals radii

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• finished hydrogen

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• better documentation

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• finished doc strings

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• better names

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• increase radius by 20 % and freeze all datastructures

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Commits on Jan 25, 2025

• change van der waals scaling

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• disable caching

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• get rid of caching

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• corrected grammar

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Commits on Jan 26, 2025

• unify the usage of the term "motif"

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• further clarification in comment

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• added test for agreement with autogen

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• started AO index structure

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• represent fragments as Sequence[OrderedSet[...]]

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• adjusted the tests of fragmented structure to the sequence format

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Commits on Jan 27, 2025

• fix doc build problems

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• return motifs in order

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• remove AO index stuff, comes later

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• fix missing index

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• add back in the FragmentedMolecule

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• fix wrong link for DOC

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• Merge branch 'chemical_fragmentation' into add_AO_indices

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• introduced SeqOverFrag and SeqOverAtom

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• small reformatting

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• added frag_idx_per_edge (formerly known as center :D)

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Commits on Jan 28, 2025

• added known to fail test for bug

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• check for not isclose in failing test

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• renamed test file

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• cleaned up comments

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• fixed typing issues (very strange)

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• fixed small setting issue

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• updated test files

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• mark known-to-fail test as known-to-fail

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• use Mapping instead of dict; better AOidx type

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• correctly implemented other_rel_AO_per_edge_per_frag

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• Update src/quemb/molbe/chemfrag.py

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• consistently renamed site -> motif and adressed Minsik's comment

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• put missing comment why ruamel is ignored

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• allow more fine-grained control over van der waals radii

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• add easy manipulation of van der waals radii

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• Merge branch 'chemical_fragmentation' of github.com:troyvvgroup/quemb into chemical_fragmentation

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Commits on Jan 29, 2025

• finished van der Waals modification

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• ensure that H are not shared among motifs

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• ignore missing link to Number

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• fix doc

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• fixed bug

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• finished

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• Merge branch 'chemical_fragmentation' into add_AO_indices

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• Merge branch 'main' of github.com:troyvvgroup/quemb into add_AO_indices

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• renamed fragpart components to match autogen names

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• fixed typo edgsites -> edgesites

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• fixed docstring variable names of autogen

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• successfully implemented restrict_key

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Commits on Jan 30, 2025

• finished all existing variables

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• fixed ordering for tests

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• make order explicit in documentation

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• Merge branch 'main' of github.com:troyvvgroup/quemb into add_AO_indices

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• reintroduced hlist_atom and add_center_atom to fragpart

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• nearly finished, but get wrong mypy errors

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• declare as ordered set instead of sequence

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• declare autogen matching types as list, not sequence

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• expose chemfrag to fragpart

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• added test for BE calculation

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• added BE3 test for chemgen as well

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• fixed doc

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• added missing reason to pytest skipif

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Commits on Jan 31, 2025

• actually allow BEn n > 9

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Commits on Feb 3, 2025

• Merge branch 'main' of github.com:troyvvgroup/quemb into add_AO_indices

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• fix issues from main merge

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