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Structure Library: check, reorganise, π-ligands, navigation

Aberta
  • Algo errado?
#327 0 comentários 0 reações 0 responsáveis Ver no GitHub

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Avaliação

Dificuldade
5/5
Tempo estimado
Mais de uma semana
Facilidade para iniciantes
18/100
Tipo de issue
Refatoração
Clareza
Razoavelmente clara
Status de atividade
Ativa
Stack de tecnologia
linux, macos
Domínio
data, desktop-dev, documentation, testing

Direção de pesquisa

This is a multi-part maintainer plan, not a single task: start by reading the structure files under the SimpleStructures and Ligands folders, and the two found-so-far fixes (2fa576a1, e36bc6aa), to see the file format. The first deliverable is the validation script over all 338 files, run as a test, whose findings are reported before any repair. Done means each listed category is covered and the findings are documented; the layout, ligand split, and navigation changes depend on #325 and should be coordinated with the maintainers first.

Escrita pelo modelo de indexação a partir do texto da issue.

Descrição

Collected from testing on 2026-10-14. One job, after #321 item 9.

1. Check every structure. A validation script over all 338 files, run as a test: bond lengths against covalent radii (missing or extra bonds), valences, overlapping atoms, charge against formula, stray nubs. Found so far by hand: ferrocene bonded Fe to one ring only (fixed in 2fa576a1), NoConverge (a PNNL test case, removed in e36bc6aa). The script's findings are listed before anything is repaired.

2. Layout. The "2" folders (Miscellaneous2, Simple_arenes2, Simple_heterocyclic_compounds2) are alphabetical halves, not topics; Miscellaneous is a mix; ferrocene sits under arenes. Proposed for SimpleStructures: small molecules and solvents; hydrocarbons; alcohols, ethers and carbonyls; acids; arenes; heterocycles; organometallics; natural products (alkaloids, steroids, hormones, vitamins). Teaching: diatomics plus the VSEPR set (SF4, ClF3, PF5, ...). Amino acids, DNA, RNA unchanged.

3. Duplicates and names. Ethene/Ethylene, Acetylene/Ethyne; NH3 and H2O both in Miscellaneous2 and Ligands. Names: Methanole → Methanol, Maleinic_Acid → Maleic acid, h2o, n_Butyric_Acid, Dimethylsulfoxide spelling.

4. Ligands split in two.

  • "Ligands (σ-donors)": a nub on each donor atom (bipy, acac, en, phen, PPh3, PMe3, CO, CN⁻, NH3, H2O, pyridine, oxalate), with abbreviations in the names.
  • New "π-ligands", no nubs, η in each name: Cp⁻ (η5), Cp*⁻ (η5), indenyl⁻ (η5/η3), benzene, hexamethylbenzene, p-cymene (η6), C7H7⁺ (η7), COT²⁻ (η8), allyl⁻ (η3), 1,3-butadiene (η4), ethene (η2), acetylene and diphenylacetylene (η2), COD and NBD (2 × η2), dba (η2). Each with a test that it attaches with that hapticity (#325).
  • Check first that Greek letters and superscripts in folder and file names display on Linux, Windows and macOS; otherwise ASCII ("Pi ligands", "eta5").

5. Hapticity rule extension (#325). A picked atom in a planar conjugated sp2 chain bonds the whole chain (allyl η3, butadiene η4); isolated C=C stay η2 (COD, NBD: two attachments, one nub each).

6. Navigation. The Structure Library's drop-down lists only the top-level categories: inside SimpleStructures/Simple_arenes it offers RNA, DNA etc., not the other SimpleStructures subfolders. Replace with a tree (folders expandable) or a two-level choice, and add a search field matching names and abbreviations (Cp, acac, bipy, COD).

7. Help: update pages that name library folders (Molecules for teaching).

Linguagem predominante
C
Estrelas
10
Forks
8
Merge médio
21min
PRs com merge (30d)
1

Preparar o ambiente

Este projeto não oferece contêiner de desenvolvimento, Dockerfile nem guia de contribuição, então a configuração fica por sua conta: comece pelo README e veja nosso guia da primeira contribuição para os passos gerais.

Primeiros passos

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