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

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#327 0 則留言 0 個 reaction 已指派 0 人 在 GitHub 檢視

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評估

難度
5/5
預估耗時
一週以上
新手友好度
18/100
Issue 類型
重構
描述清晰度
基本清楚
活躍度
活躍
技術堆疊
linux, macos
領域
data, desktop-dev, documentation, testing

研究方向

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.

由索引模型根據 Issue 內容生成。

描述

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).

主要語言
C
星號
10
分支
8
平均合併
2 小時 34 分鐘
30 天內合併 PR
3

環境準備

這個專案沒有提供開發容器、Dockerfile 或貢獻指南，環境需要你自己搭建：先看它的 README，通用步驟見我們的新手貢獻指南。

從這裡開始

  1. 先讀完整個 Issue，再讀專案的貢獻指南。
  2. 在 Issue 下留言說明你要接手 —— 這能避免兩個人做同樣的事。
  3. Fork 儲存庫，在一個分支上完成修改。
  4. 送出 Pull Request，並在描述裡引用這個 Issue 編號。

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