diff --git a/.github/ISSUE_TEMPLATE/feature-request.yml b/.github/ISSUE_TEMPLATE/feature-request.yml index 6f59e41..fb93aef 100644 --- a/.github/ISSUE_TEMPLATE/feature-request.yml +++ b/.github/ISSUE_TEMPLATE/feature-request.yml @@ -13,5 +13,3 @@ body: id: rationale attributes: label: Why is this needed? - validations: - required: true diff --git a/.github/ISSUE_TEMPLATE/support.yml b/.github/ISSUE_TEMPLATE/support.yml new file mode 100644 index 0000000..c64abc3 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/support.yml @@ -0,0 +1,10 @@ +name: Support +description: Finding support on how to use the plugin +labels: ['support'] +body: + - type: textarea + id: problem + attributes: + label: What do you need to help with? + validations: + required: true diff --git a/.gitignore b/.gitignore index 8f8e5c4..2eeedeb 100644 --- a/.gitignore +++ b/.gitignore @@ -23,3 +23,6 @@ data.json # previous builds .versions + +# plugin asset +rdkit/ diff --git a/LICENSE b/LICENSE index ab123e3..f91e984 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2023 Chiyu Liang +Copyright (c) 2023-2024 Chiyu Liang Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README-ZH.md b/README-ZH.md index f215e6a..f00a31b 100644 --- a/README-ZH.md +++ b/README-ZH.md @@ -1,34 +1,40 @@ # Obsidian Chem -![Obsidian Downloads](https://img.shields.io/badge/dynamic/json?logo=obsidian&color=%23483699&label=downloads&query=%24%5B%22chem%22%5D.downloads&url=https%3A%2F%2Fraw.githubusercontent.com%2Fobsidianmd%2Fobsidian-releases%2Fmaster%2Fcommunity-plugin-stats.json) +![Obsidian Downloads](https://img.shields.io/badge/dynamic/json?logo=obsidian&color=%23483699&label=downloads&query=%24%5B%22chem%22%5D.downloads&url=https%3A%2F%2Fraw.githubusercontent.com%2Fobsidianmd%2Fobsidian-releases%2Fmaster%2Fcommunity-plugin-stats.json) ![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC) [English](README.md) | [简体中文](README-ZH.md) -**Chem** 是一个旨在提升化学相关笔记记录体验的 [Obsidian.md](https://obsidian.md/) 插件。目前，本插件能够将您笔记中的SMILES字符串渲染为化学结构式。（基于 [Smiles Drawer](https://github.com/reymond-group/smilesDrawer)） +**Chem** 是一个旨在提升化学相关笔记记录体验的 [Obsidian.md](https://obsidian.md/) 插件。目前，本插件能够将您笔记中的SMILES字符串渲染为化学结构式。（基于 [Smiles Drawer](https://github.com/reymond-group/smilesDrawer) 与 [RDKit.js](https://github.com/rdkit/rdkit-js)） > [!Note] -> 最新插件版本: 0.3.0 -> 文档版本: 0.3.0 +> 最新插件版本: 0.4.1 +> 文档版本: 0.4.1 ## 功能介绍 -### 渲染 SMILES 字符串为化学结构式 +### 将 SMILES 字符串渲染为化学结构式 + +#### 代码块渲染 如图所示，本插件能够识别语言被标记为 `smiles` 的代码块，并将其中的 SMILES 字符串逐行转化为化学结构式。得益于 SMILES 的纯文本特性，数据能够持久保存，该功能将得到稳定支持；此外，由于 SMILES 是一个通用标准，即使本插件换用了其他化学信息学工具包，SMILES 字符串仍能够被正确解析和渲染 ![渲染 SMILES 字符串](https://github.com/Acylation/obsidian-chem/assets/73122375/a9f9a440-dc66-4689-ab1a-1ef265242778) -### 设置结构图像大小和样式主题 +#### 行内渲染 + +行内渲染功能可以在插件设置页中启用。具有特定前缀的代码行将被 Chem 插件识别、解析。默认的语法格式是 `$smiles=C1=CC=CC=C1`，前缀同样可以在插件设置页中调整 + +#### 设置结构图像大小和样式主题 您可以在插件设置页面调整化学结构式的尺寸比例，或指定图像大小，并分别调整浅色模式/深色模式下对应的结构式颜色主题。插件设置发生更改，或浅色/深色模式切换后，图像样式会自动更新 ![设置大小和样式主题](https://github.com/Acylation/obsidian-chem/assets/73122375/fde8d0a4-2c9c-458c-b357-78952480b755) -### 复制、导出图像 +#### 复制、导出图像 复制功能位于结构图像的右键菜单。图像均以 `png` 格式导出，并能直接粘贴到笔记中，作为文件保存入附件文件夹，也可以以图片形式粘贴到微信、PowerPoint 等其他软件中。导出比例、透明/有背景色、颜色主题等可以灵活配置。 -### 在代码块中调用 Dataview +#### 在代码块中调用 Dataview 在插件设置中启用`解析 Dataview`功能后，`smiles` 代码块将逐行被 Dataview 解析，解析结果用于渲染结构图像。内联 Dataview 查询式 (Queries) 和内联 DataviewJS 的启用、前缀等设置与 Dataview 插件本体保持一致。 @@ -36,9 +42,9 @@ > [!Warning] > 本功能依赖 Dataview 插件本体，若要使用本功能，请确保您已安装并启用 Dataview 插件 -> +> > 运行 DataviewJS 需要调用 `eval()` 函数，具有一定的风险。请确保您输入/粘贴的代码是受信任的 -> +> > 若您希望在启用 Dataview 查询式 (Queries) 时禁用 DataviewJS，请在 Dataview 插件设置中禁用 `Enable JavaScript Queries` 或 `Enable Inline JavaScript Queries` 选项 ## SMILES 介绍 @@ -53,7 +59,9 @@ SMILES 使用 ASCII 字符串表示化学结构的特性与 Obsidian 的纯文 ### 如何生成 SMILES 字符串？ - 对于简单结构，您在初步学习 SMILES 知识后即可手动输入。对于复杂结构，您可以使用 ChemDraw，[ChemDrawJS](https://chemdrawdirect.perkinelmer.cloud/js/sample/index.html#)，[MarvinJS](https://marvinjs-demo.chemaxon.com/latest/index.html) 或 [Ketcher](https://lifescience.opensource.epam.com/KetcherDemoSA/index.html) 等**结构编辑器**先行绘制，再导出 SMILES 字符串。您也可以使用 [Open Bable](http://openbabel.org/wiki/Main_Page)，[JOELib](https://sourceforge.net/projects/joelib/) 或 [Chemical Translation Service](https://cts.fiehnlab.ucdavis.edu/) 等**化学语言转换工具**/**化学数据库**，将化合物名称、CAS 号、*.mol 文件等转化为 SMILES 格式 +对于简单结构，您在初步学习 SMILES 知识后即可手动输入。对于复杂结构，您可以使用 ChemDraw，[ChemDrawJS](https://chemdrawdirect.perkinelmer.cloud/js/sample/index.html#)，[MarvinJS](https://marvinjs-demo.chemaxon.com/latest/index.html) 或 [Ketcher](https://lifescience.opensource.epam.com/KetcherDemoSA/index.html) 等**结构编辑器**先行绘制，再导出 SMILES 字符串。您可以使用 [Obsidian Ketcher](https://github.com/yuleicul/obsidian-ketcher) 插件在 Obsidian 中直接绘制化学结构，并导出 SMILES 字符串。 + +您也可以使用 [Open Babel](https://openbabel.org/)，[JOELib](https://sourceforge.net/projects/joelib/) 或 [Chemical Translation Service](https://cts.fiehnlab.ucdavis.edu/) 等**化学语言转换工具**/**化学数据库**，将化合物名称、CAS 号、`*.mol` 文件等转化为 SMILES 格式 ## 安装步骤 @@ -68,6 +76,9 @@ SMILES 使用 ASCII 字符串表示化学结构的特性与 Obsidian 的纯文 2. 将上述文件复制到您本地的笔记库的插件路径，如 `[yourvault]/.obsidian/plugins/chem/`。您可能需要自行新建 `chem` 这个文件夹 3. 打开/重启 Obsidian 或刷新插件列表，您将看到 `Chem` 插件，点击启用，安装完成！ +> [!Note] +> 若您希望使用 `RDKit.js` 作为渲染器，插件会访问 [release](https://github.com/Acylation/obsidian-chem/releases/latest) 页面，尝试下载 `RDKit_minimal` 和 `RDKit_minimal.wasm` 两个文件。若您无法连接到 GitHub，请在 [release](https://github.com/Acylation/obsidian-chem/releases/latest) 页面中手动下载它们，并放在 `[yourvault]/.obsidian/plugins/chem/rdkit/` 路径下，以供插件识别、加载 + ## 插件定位 我希望本插件能够提升化学相关笔记的记录体验。例如，您可能希望在电子实验记录中记下您今天合成的化合物的结构式，或者您想创建有机化学反应的 Anki 卡片等等。下面是一些我认为本插件可以提供的功能： @@ -100,7 +111,7 @@ SMILES 使用 ASCII 字符串表示化学结构的特性与 Obsidian 的纯文 ## 致谢 -本插件依赖 [Smiles Drawer](https://github.com/reymond-group/smilesDrawer) 实现 SMILES 字符串的解析以及结构式绘制的功能，导入这个包的例子来源于 [Mathpix](https://github.com/Mathpix/mathpix-markdown-it)。在此向这些杰出的工作表示感谢! +本插件依赖 [Smiles Drawer](https://github.com/reymond-group/smilesDrawer) 和 [RDKit.js](https://github.com/rdkit/rdkit-js) 实现 SMILES 字符串的解析以及结构式绘制的功能。[Mathpix](https://github.com/Mathpix/mathpix-markdown-it) 展示了导入 Smiles Drawer 包以及使用代码块语法的实例。向这些杰出的工作表示感谢! 在整个开发过程中，官方[开发者文档](https://docs.obsidian.md/Plugins/Getting+started/Build+a+plugin)提供了非常详细的指引，感谢 [@marcusolsson](https://github.com/marcusolsson) 的早期非官方文档，以及对官方开发者文档整理工作的领导! diff --git a/README.md b/README.md index 35f4c78..40ccc01 100644 --- a/README.md +++ b/README.md @@ -1,47 +1,53 @@ # Obsidian Chem -![Obsidian Downloads](https://img.shields.io/badge/dynamic/json?logo=obsidian&color=%23483699&label=downloads&query=%24%5B%22chem%22%5D.downloads&url=https%3A%2F%2Fraw.githubusercontent.com%2Fobsidianmd%2Fobsidian-releases%2Fmaster%2Fcommunity-plugin-stats.json) +![Obsidian Downloads](https://img.shields.io/badge/dynamic/json?logo=obsidian&color=%23483699&label=downloads&query=%24%5B%22chem%22%5D.downloads&url=https%3A%2F%2Fraw.githubusercontent.com%2Fobsidianmd%2Fobsidian-releases%2Fmaster%2Fcommunity-plugin-stats.json) ![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC) [简体中文](README-ZH.md) | [English](README.md) -**Chem** is a plugin for [Obsidian.md](https://obsidian.md/) providing chemistry support. It allows you to insert chemical structures into your notes through code blocks containing SMILES strings (powered by [Smiles Drawer](https://github.com/reymond-group/smilesDrawer)). +**Chem** is a plugin for [Obsidian.md](https://obsidian.md/) providing chemistry support. It allows you to insert chemical structures into your notes through code blocks containing SMILES strings (powered by [Smiles Drawer](https://github.com/reymond-group/smilesDrawer) & [RDKit.js](https://github.com/rdkit/rdkit-js)). > [!Note] -> Latest release: 0.3.0 -> Document version: 0.3.0 +> Latest release: 0.4.1 +> Document version: 0.4.1 ## Features & Usage ### Render SMILES Strings as Chemical Structures +#### Render via Code Block + You can use this plugin to render chemical structures from SMILES strings. Just type the SMILES strings in a code block with `smiles` as the language. Each line should contain only one string. The data is stored as plain text, so you won’t lose it. The renderer will always work, even if the plugin changes its cheminfo core. ![Render SMILES strings into structures](https://github.com/Acylation/obsidian-chem/assets/73122375/a9f9a440-dc66-4689-ab1a-1ef265242778) -### Global Sizing and Theming +#### Inline Render + +You can enable inline render feature in plugin settings. Code lines with specified prefix would be recognized. The default syntax is `$smiles=C1=CC=CC=C1` and the prefix is configurable. + +#### Global Sizing and Theming You can adjust the structure scale or the image size and configure light/dark themes of the structure images in the plugin’s settings page. The structures in open notes will be automatically updated when the plugin settings or Obsidian color scheme are changed. ![Configure size and theme](https://github.com/Acylation/obsidian-chem/assets/73122375/fde8d0a4-2c9c-458c-b357-78952480b755) -### Copy & Export +#### Copy & Export The copy feature is accessible through the right-click menu on images. Images are copied in `png` format. Despite common applications, you can also paste the copied image into your note, which will then save the image as a file to your attachment folder. The scale of the export, transparency, and theme can be configured to suit your needs. -### Utilizing Dataview +#### Utilizing Dataview -Inline Dataview queries and DataviewJS rendering can be enabled in the settings tab. Once enabled, lines within the smiles block will be checked and parsed. The return value from this process is used to render chemical structures, providing greater flexibility. The prefix and strategy are fetched directly from the corresponding Dataview plugin settings. +Inline Dataview queries and DataviewJS rendering can be enabled in the settings tab. Once enabled, lines within the smiles block will be checked and parsed. The return values from this process will be used to render chemical structures, providing greater flexibility. The prefix and strategy are fetched directly from the corresponding Dataview plugin settings. ![Dataview lines in smiles block](https://github-production-user-asset-6210df.s3.amazonaws.com/73122375/292734194-d227fdb8-9c8f-4c87-965a-73c0f2445993.png) > [!Warning] > This feature is dependent on the Dataview plugin. Please ensure that you have installed and enabled it. -> -> The execution of DataviewJS is implemented by calling `eval()` at the bottom, which is known to have safety issues.To avoid unintended execution, only trusted code lines should be passed. > -> If you wish to disable DataviewJS rendering, you can toggle off the `Enable JavaScript Queries` or `Enable Inline JavaScript Queries` options through the Dataview plugin settings. +> The execution of DataviewJS is implemented by calling `eval()` at the bottom, which is known to have security issues. To avoid unintended execution, only trusted code lines should be passed. +> +> If you wish to keep inline Dataview queries rendering and only disable DataviewJS, you can toggle off the `Enable JavaScript Queries` or `Enable Inline JavaScript Queries` options through the Dataview plugin settings. ## Introduction on SMILES @@ -55,7 +61,9 @@ Using SMILES strings to represent molecules is easier and more widely supported ### How to Generate SMILES Strings? - For simple structures, you can type them in manually. However, for more complex ones, you may want to use **structure editors**, such as ChemDraw, [ChemDrawJS](https://chemdrawdirect.perkinelmer.cloud/js/sample/index.html#), [MarvinJS](https://marvinjs-demo.chemaxon.com/latest/index.html) and [Ketcher](https://lifescience.opensource.epam.com/KetcherDemoSA/index.html). Also, you can use **translators** like [Open Bable](http://openbabel.org/wiki/Main_Page), [JOELib](https://sourceforge.net/projects/joelib/) and the [Chemical Translation Service](https://cts.fiehnlab.ucdavis.edu/) to convert chemical names, CAS numbers and *.mol files into SMILES strings. +For simple structures, you can type them in manually. However, for more complex ones, you may want to use **structure editors**, such as ChemDraw, [ChemDrawJS](https://chemdrawdirect.perkinelmer.cloud/js/sample/index.html#), [MarvinJS](https://marvinjs-demo.chemaxon.com/latest/index.html) and [Ketcher](https://lifescience.opensource.epam.com/KetcherDemoSA/index.html). There's a Ketcher editor integration plugin [Obsidian Ketcher](https://github.com/yuleicul/obsidian-ketcher) available right in Obsidian. + +Also, you can use **translators** like [Open Babel](https://openbabel.org/), [JOELib](https://sourceforge.net/projects/joelib/) and the [Chemical Translation Service](https://cts.fiehnlab.ucdavis.edu/) to convert chemical names, CAS numbers and `*.mol` files into SMILES strings. ## Installation @@ -71,6 +79,9 @@ You can also follow the steps below to install the plugin manually. 3. Launch/restart Obsidian, or refresh the plugin list, you will see this plugin. 4. In the plugin list, enable `Chem` and enjoy! +> [!Note] +> If you want to utilize `RDKit.js`, Chem plugin would try to fetch `RDKit_minimal` and `RDKit_minimal.wasm` files from [release](https://github.com/Acylation/obsidian-chem/releases/latest). If you have problem connecting GitHub, please download them manully and put them in the directory `[yourvault]/.obsidian/plugins/chem/rdkit/` for recognization and loading. + ## Plugin Scope I have a lot of ideas for this plugin, but my coding skills and resources are limited. I want to make it useful for anyone who needs to take notes on chemistry (such as research records, organic chemistry anki cards, etc.). As examples, here are some of the features I have in mind. @@ -96,11 +107,11 @@ Check out the [roadmap](https://github.com/users/Acylation/projects/6) to see wh `Chem` plugin is now primarily focused on rendering texts into structures. If you want to create complex structures from scratch, the [Ketcher](https://github.com/yuleicul/obsidian-ketcher) plugin has integrated a powerful opensource editor. -[Chemical Structure Renderer](https://github.com/xaya1001/obsidian-Chemical-Structure-Renderer) is a similar plugin, which uses [Ketcher](https://github.com/epam/ketcher), [Indigo](https://github.com/epam/Indigo) online service for parsing and rendering. +[Chemical Structure Renderer](https://github.com/xaya1001/obsidian-Chemical-Structure-Renderer) is a similar plugin of `Chem`, which uses [Ketcher](https://github.com/epam/ketcher), [Indigo](https://github.com/epam/Indigo) online service for parsing and rendering, while `Chem` plugin integrates standalone packages and runs locally. -## Acknowledgement +## Credits -The plugin relies on [Smiles Drawer](https://github.com/reymond-group/smilesDrawer) as the parsing and drawing core, and uses [Mathpix](https://github.com/Mathpix/mathpix-markdown-it) as an example on how to integrate the package. Thank you very much! +The plugin relies on [Smiles Drawer](https://github.com/reymond-group/smilesDrawer) and [RDKit.js](https://github.com/rdkit/rdkit-js) as the parsing and drawing cores, and takes [Mathpix](https://github.com/Mathpix/mathpix-markdown-it) as a good example on integrating Smiles Drawer and use codeblock to decorate the note. Thank you very much! During the whole process of development, I found the [developer documentation](https://docs.obsidian.md/Plugins/Getting+started/Build+a+plugin) super helpful. Massive thanks to [@marcusolsson](https://github.com/marcusolsson) for leading this project! diff --git a/docs/CONTRIBUTING-ZH.md b/docs/CONTRIBUTING-ZH.md index 07ebc5d..d7892e2 100644 --- a/docs/CONTRIBUTING-ZH.md +++ b/docs/CONTRIBUTING-ZH.md @@ -4,7 +4,7 @@ ## 设计原则 -本插件计划提供的功能需要至少满足下列条件中的一条： +本插件计划提供的功能需要满足下列条件中的至少一条： - 助力化学科研笔记，如实验记录、文献阅读笔记、论文大纲撰写等 - 帮助构建与常用化学工具紧密协作的工作流 @@ -23,6 +23,8 @@ - 本仓库提供了 issue 模板，请按照模板指引填写，以提供必要的内容 - 为您需要的功能点赞👍！投票人数更多的功能请求将被优先考虑 +同样欢迎通过 issue 咨询插件使用问题，以及展示您的使用样例！ + ## 提交 PR ### 注意事项 @@ -37,30 +39,30 @@ cd [你的工作文件夹] ``` -> **Note** -> 建议使用一个开发 vault 的配置文件夹作为本插件的工作文件夹。例如 `.obsidian\plugins\)`. +> [!Note] +> 建议使用一个开发 vault 的配置文件夹作为本插件的工作文件夹。例如 `.obsidian\plugins\`. ```cmd git clone https://github.com/Acylation/obsidian-chem.git chem cd chem ``` -> **Note** +> [!Note] > 本插件的 id 是 `chem` 而不是 `obsidian-chem` -### Install dependencies +### 安装依赖 ```cmd npm install ``` -### Developing +### 进行开发 ```cmd npm run dev ``` -> **Note** +> [!Note] > 该命令执行后，将监听源代码的更改，并在保存更改时自动编译出一个新版的`main.js` > 下载并启用 [Hot-Reload](https://github.com/pjeby/hot-reload) 插件以获得流畅的开发体验 @@ -82,9 +84,4 @@ npm run build - 需要针对特定代码提出疑问、提供建议等，请在提交 PR 后使用 GitHub 的 code review 功能 - 您提交的PR将在审核后被合并，或被要求修改 -## 仍有疑问? - -- 如果您有任何疑问，或需要帮助，请在本仓库下的 [Discussions](https://github.com/Acylation/obsidian-chem/discussions) 栏目中发帖询问 -- 若您希望展示您的使用案例，也欢迎前往 [Discussions](https://github.com/Acylation/obsidian-chem/discussions) 栏目 - 感谢您成为本项目的一份子！🙌 diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index d34ef94..6122b94 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -23,6 +23,8 @@ As an Obsidian plugin, this project adheres to the following principles: - When creating a new issue, please follow the templates to provide necessary information. - You can also vote for existing issues by adding a 👍 reaction to show your support. +You are also welcome to raise questions that you came across when using this plugin, or provide awesome showcases through issue! + ## How to submit a pull request ### General @@ -37,7 +39,7 @@ As an Obsidian plugin, this project adheres to the following principles: cd [your-working-folder] ``` -> **Note** +> [!Note] > It is recommended to use the config directory of a dev vault (e.g., .obsidian\plugins\\) as the working directory. ```cmd @@ -45,7 +47,7 @@ git clone https://github.com/Acylation/obsidian-chem.git chem cd chem ``` -> **Note** +> [!Note] > The plugin id in the manifest is `chem` rather than `obsidian-chem`. ### Install dependencies @@ -60,7 +62,7 @@ npm install npm run dev ``` -> **Note** +> [!Note] > This command will listen for changes to the source code and provide a new build when you save changes. > Download and enable the [Hot-Reload](https://github.com/pjeby/hot-reload) plugin to experience a smooth debugging workflow. @@ -82,8 +84,4 @@ npm run build - For raising questions, providing suggestions, or explaining a specific line of code, please use GitHub’s code review feature. - Please wait for a review before your pull request being merged. -## Still have questions? - -- If you still have any questions or need help with using or developing this project, please join our [Discussions](https://github.com/Acylation/obsidian-chem/discussions) right here in the repo. - Thank you for being a part of this project! 🙌 diff --git a/jest.config.js b/jest.config.js new file mode 100644 index 0000000..bdfc5d7 --- /dev/null +++ b/jest.config.js @@ -0,0 +1,7 @@ +module.exports = { + preset: "ts-jest", + testEnvironment: "node", + transform: { + "^.+\\.ts$": "esbuild-jest", + }, +}; diff --git a/manifest.json b/manifest.json index 917f73f..fc32b83 100644 --- a/manifest.json +++ b/manifest.json @@ -1,10 +1,11 @@ { "id": "chem", "name": "Chem", - "version": "0.3.0", + "version": "0.4.0", "minAppVersion": "1.0.0", "description": "Providing chemistry supports. Rendering SMILES strings into chemistry structures.", "author": "Acylation", "authorUrl": "https://github.com/Acylation", + "fundingUrl": "https://ko-fi.com/Acylation", "isDesktopOnly": false } \ No newline at end of file diff --git a/package-lock.json b/package-lock.json index a1e39c1..91a2e62 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,3399 +1,10900 @@ { "name": "chem", - "version": "0.3.0", + "version": "0.4.0", "lockfileVersion": 2, "requires": true, "packages": { "": { "name": "chem", - "version": "0.3.0", + "version": "0.4.0", "license": "MIT", "dependencies": { + "@rdkit/rdkit": "^2023.9.2-1.0.0", "i18next": "^23.4.2", "smiles-drawer": "^2.1.7" }, "devDependencies": { + "@types/jest": "^29.5.12", "@types/node": "^16.11.6", "@typescript-eslint/eslint-plugin": "5.29.0", "@typescript-eslint/parser": "5.29.0", "builtin-modules": "3.3.0", "esbuild": "0.17.3", + "esbuild-jest": "^0.5.0", + "jest": "^29.7.0", "obsidian": "latest", "obsidian-dataview": "^0.5.64", + 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"cliui": "^8.0.1", + "escalade": "^3.1.1", + "get-caller-file": "^2.0.5", + "require-directory": "^2.1.1", + "string-width": "^4.2.3", + "y18n": "^5.0.5", + "yargs-parser": "^21.1.1" + } + }, + "yargs-parser": { + "version": "21.1.1", + "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-21.1.1.tgz", + "integrity": "sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw==", + "dev": true + }, "yocto-queue": { "version": "0.1.0", "resolved": "https://registry.npmmirror.com/yocto-queue/-/yocto-queue-0.1.0.tgz", "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==", - "dev": true, - "peer": true + "dev": true } } } diff --git a/package.json b/package.json index 5fe0a97..4f5f3c2 100644 --- a/package.json +++ b/package.json @@ -1,11 +1,12 @@ { "name": "chem", - "version": "0.3.0", + "version": "0.4.0", "description": "Providing chemistry supports. Rendering SMILES strings into chemistry structures.", "main": "main.js", "scripts": { "dev": "node esbuild.config.mjs", "build": "tsc -noEmit -skipLibCheck && node esbuild.config.mjs production", + "test": "jest --config jest.config.js", "version": "node version-bump.mjs && git add manifest.json versions.json", "lint": "eslint ./src" }, @@ -20,17 +21,22 @@ "author": "Acylation", "license": "MIT", "devDependencies": { + "@types/jest": "^29.5.12", "@types/node": "^16.11.6", "@typescript-eslint/eslint-plugin": "5.29.0", "@typescript-eslint/parser": "5.29.0", "builtin-modules": "3.3.0", "esbuild": "0.17.3", + "esbuild-jest": "^0.5.0", + "jest": "^29.7.0", "obsidian": "latest", "obsidian-dataview": "^0.5.64", + "ts-jest": "^29.1.2", "tslib": "2.4.0", "typescript": "4.7.4" }, "dependencies": { + "@rdkit/rdkit": "^2023.9.2-1.0.0", "i18next": "^23.4.2", "smiles-drawer": "^2.1.7" } diff --git a/src/SmilesBlock.ts b/src/SmilesBlock.ts index ad993c3..ce9b1a2 100644 --- a/src/SmilesBlock.ts +++ b/src/SmilesBlock.ts @@ -1,15 +1,17 @@ +import { gRenderCore } from './global/chemCore'; +import { gDataview, isPluginEnabled, getDataview } from './global/dataview'; +import { addBlock, removeBlock } from './global/blocks'; + +import { ChemPluginSettings } from './settings/base'; +import { convertToSDTheme, getSDBGColor } from './lib/themes/theme'; +import { getCurrentTheme } from './lib/themes/getCurrentTheme'; + import { MarkdownRenderChild, MarkdownPostProcessorContext, Menu, Notice, } from 'obsidian'; -import { gDrawer } from './global/drawer'; - -import { gDataview, isPluginEnabled, getDataview } from './global/dataview'; -import { ChemPluginSettings, DEFAULT_SD_OPTIONS } from './settings/base'; -import { addBlock, removeBlock } from './global/blocks'; - import { i18n } from 'src/lib/i18n'; export class SmilesBlock extends MarkdownRenderChild { @@ -43,15 +45,15 @@ export class SmilesBlock extends MarkdownRenderChild { rows = rows.map((row) => row.trim()); if (rows.length == 1) { - const div = this.el.createDiv({ cls: 'chem-cell' }); - this.renderCell(rows[0], div, this.theme); + const cell = this.el.createDiv({ cls: 'chem-cell' }); + this.renderCell(rows[0], cell); } else { const table = this.el.createDiv({ cls: 'chem-table' }); - const maxWidth = this.settings.options?.width ?? 300; + const maxWidth = this.settings.commonOptions.width ?? 300; - rows.forEach((row) => { + rows.forEach(async (row) => { const cell = table.createDiv({ cls: 'chem-cell' }); - const svgcell = this.renderCell(row, cell, this.theme); + const svgcell = await this.renderCell(row, cell); if (parseFloat(svgcell.style.width) > maxWidth) { const r = parseFloat(svgcell.style.width) / @@ -62,12 +64,11 @@ export class SmilesBlock extends MarkdownRenderChild { }); table.style.gridTemplateColumns = `repeat(auto-fill, minmax(${ - this.settings.options.width?.toString() ?? '300' + this.settings.commonOptions.width?.toString() ?? '300' }px, 1fr)`; } } - // TODO：add test cases private preprocess = async (source: string) => { const dvEl = this.el.createDiv(); this.el.appendChild(dvEl); @@ -75,11 +76,11 @@ export class SmilesBlock extends MarkdownRenderChild { const isDQL = (source: string): boolean => { const prefix = gDataview.settings.inlineQueryPrefix; - return source.startsWith(prefix); + return prefix.length > 0 && source.startsWith(prefix); }; const isDataviewJs = (source: string): boolean => { const prefix = gDataview.settings.inlineJsQueryPrefix; - return source.startsWith(prefix); + return prefix.length > 0 && source.startsWith(prefix); }; const evaluateDQL = (row: string): string => { const prefix = gDataview.settings.inlineQueryPrefix; @@ -92,7 +93,7 @@ export class SmilesBlock extends MarkdownRenderChild { const func = new Function( 'api', - `return eval(\`const dv=api;const dataview = api; ${code}\`)` // await & async exec + `return eval(\`const dv = api; const dataview = api; ${code}\`)` //TODO: await & async exec ); return func(api)?.toString() ?? 'DataviewJS parsing error'; @@ -108,46 +109,22 @@ export class SmilesBlock extends MarkdownRenderChild { return await executeJs(source); } + dvEl.remove(); return source; }; - private renderCell = ( + private renderCell = async ( source: string, target: HTMLElement, - theme: string + theme?: string // theme override for copy&export ) => { - const svg = target.createSvg('svg'); - svg.setAttribute('xmlns', 'http://www.w3.org/2000/svg'); - svg.setAttribute('data-smiles', source); - - const errorCb = ( - error: object & { name: string; message: string }, - container: HTMLDivElement - ) => { - container - .createDiv('error-source') - .setText(i18n.t('errors.source.title', { source })); - container.createEl('br'); - const info = container.createEl('details'); - info.createEl('summary').setText(error.name); - info.createEl('div').setText(error.message); - - container.style.wordBreak = `break-word`; - container.style.userSelect = `text`; - }; + const svg = await gRenderCore.draw(source, theme); + target.appendChild(svg); - gDrawer.draw( - source, - svg, - theme, - null, - (error: object & { name: string; message: string }) => { - target.empty(); - errorCb(error, target.createEl('div')); - } - ); - if (this.settings.options.scale == 0) - svg.style.width = `${this.settings.imgWidth.toString()}px`; + if (this.settings.commonOptions.scale == 0) + svg.style.width = `${ + this.settings.commonOptions.unifiedWidth?.toString() ?? 300 + }px`; return svg; }; @@ -174,11 +151,7 @@ export class SmilesBlock extends MarkdownRenderChild { }; async onload() { - this.theme = - document.body.hasClass('theme-dark') && - !document.body.hasClass('theme-light') - ? this.settings.darkTheme - : this.settings.lightTheme; + this.theme = getCurrentTheme(this.settings); this.render(); this.registerDomEvent(this.el, 'contextmenu', this.handleContextMenu); } @@ -187,12 +160,13 @@ export class SmilesBlock extends MarkdownRenderChild { // Credits to image-toolkit plugin by Sissilab @ GitHub async onCopy(svgString: string, source: string, w: number, h: number) { // Redraw if changing theme - const copyTheme = this.settings.copy.theme; - if (copyTheme !== 'default' && copyTheme !== this.theme) { + let copyTheme = this.settings.copy.theme; + if (copyTheme === 'default') copyTheme = this.theme; + else if (copyTheme !== this.theme) { const div = this.containerEl.createDiv(); div.style.display = 'none'; - const svg = this.renderCell(source, div, copyTheme); + const svg = await this.renderCell(source, div, copyTheme); svgString = svg.outerHTML; svg.remove(); } @@ -223,7 +197,9 @@ export class SmilesBlock extends MarkdownRenderChild { // Apply background color if (!this.settings.copy.transparent) { - ctx.fillStyle = DEFAULT_SD_OPTIONS.themes[copyTheme].BACKGROUND; + copyTheme.contains('rdkit') + ? (ctx.fillStyle = getSDBGColor(copyTheme)) + : (ctx.fillStyle = convertToSDTheme(copyTheme).BACKGROUND); ctx.fillRect(0, 0, canvas.width, canvas.height); } diff --git a/src/SmilesInline.ts b/src/SmilesInline.ts new file mode 100644 index 0000000..65273a3 --- /dev/null +++ b/src/SmilesInline.ts @@ -0,0 +1,285 @@ +/** + Adapted from https://github.com/blacksmithgu/obsidian-dataview/blob/master/src/ui/lp-render.ts + Refered to https://github.com/blacksmithgu/obsidian-dataview/pull/1247 + More upstream from https://github.com/artisticat1/obsidian-latex-suite/blob/main/src/editor_extensions/conceal.ts +*/ + +import { + Decoration, + DecorationSet, + EditorView, + ViewPlugin, + ViewUpdate, + WidgetType, +} from '@codemirror/view'; +import { EditorSelection, Range } from '@codemirror/state'; +import { syntaxTree, tokenClassNodeProp } from '@codemirror/language'; +import { SyntaxNode } from '@lezer/common'; + +import { gRenderCore } from './global/chemCore'; +import { ChemPluginSettings } from './settings/base'; +import { getCurrentTheme } from './lib/themes/getCurrentTheme'; + +import { Component, editorInfoField, editorLivePreviewField } from 'obsidian'; + +function selectionAndRangeOverlap( + selection: EditorSelection, + rangeFrom: number, + rangeTo: number +) { + for (const range of selection.ranges) { + if (range.from <= rangeTo && range.to >= rangeFrom) { + return true; + } + } + return false; +} + +class InlineWidget extends WidgetType { + constructor( + readonly source: string, + private el: HTMLElement, + private view: EditorView + ) { + super(); + } + + eq(other: InlineWidget): boolean { + return other.source === this.source ? true : false; + } + + toDOM(): HTMLElement { + return this.el; + } + + /* Make queries only editable when shift is pressed (or navigated inside with the keyboard + * or the mouse is placed at the end, but that is always possible regardless of this method). + * Mostly useful for links, and makes results selectable. + * If the widgets should always be expandable, make this always return false. + */ + ignoreEvent(event: MouseEvent | Event): boolean { + // instanceof check does not work in pop-out windows, so check it like this + if (event.type === 'mousedown') { + const currentPos = this.view.posAtCoords({ + x: (event as MouseEvent).x, + y: (event as MouseEvent).y, + }); + if ((event as MouseEvent).shiftKey) { + // Set the cursor after the element so that it doesn't select starting from the last cursor position. + if (currentPos) { + const { editor } = this.view.state.field(editorInfoField); + if (editor) { + editor.setCursor(editor.offsetToPos(currentPos)); + } + } + return false; + } + } + return true; + } +} + +// TODO: update these on settings change refer to main.ts +export function inlinePlugin(settings: ChemPluginSettings) { + const renderCell = async ( + source: string, + target: HTMLElement, + theme?: string + ) => { + const svg = await gRenderCore.draw(source, theme); + target.appendChild(svg); + + if (settings.commonOptions.scale == 0) + svg.style.width = `${ + settings.commonOptions.unifiedWidth?.toString() ?? 300 + }px`; + return svg; + }; + + return ViewPlugin.fromClass( + class { + decorations: DecorationSet; + component: Component; + + constructor(view: EditorView) { + this.component = new Component(); + this.component.load(); + this.decorations = this.inlineRender(view) ?? Decoration.none; + } + + update(update: ViewUpdate) { + // only activate in LP and not source mode + if (!update.state.field(editorLivePreviewField)) { + this.decorations = Decoration.none; + return; + } + if (update.docChanged) { + this.decorations = this.decorations.map(update.changes); + this.updateTree(update.view); + } else if (update.selectionSet) { + this.updateTree(update.view); + } else if (update.viewportChanged /*|| update.selectionSet*/) { + this.decorations = + this.inlineRender(update.view) ?? Decoration.none; + } + } + + updateTree(view: EditorView) { + for (const { from, to } of view.visibleRanges) { + syntaxTree(view.state).iterate({ + from, + to, + enter: ({ node }) => { + const { render, isQuery } = this.renderNode( + view, + node + ); + if (!render && isQuery) { + this.removeDeco(node); + return; + } else if (!render) { + return; + } else if (render) { + this.addDeco(node, view); + } + }, + }); + } + } + + removeDeco(node: SyntaxNode) { + this.decorations.between( + node.from - 1, + node.to + 1, + (from, to, value) => { + this.decorations = this.decorations.update({ + filterFrom: from, + filterTo: to, + filter: (from, to, value) => false, + }); + } + ); + } + + addDeco(node: SyntaxNode, view: EditorView) { + const from = node.from - 1; + const to = node.to + 1; + let exists = false; + this.decorations.between(from, to, (from, to, value) => { + exists = true; + }); + if (!exists) { + /** + * In a note embedded in a Canvas, app.workspace.getActiveFile() returns + * the canvas file, not the note file. On the other hand, + * view.state.field(editorInfoField).file returns the note file itself, + * which is more suitable here. + */ + const currentFile = view.state.field(editorInfoField).file; + if (!currentFile) return; + const newDeco = this.renderWidget(node, view)?.value; + if (newDeco) { + this.decorations = this.decorations.update({ + add: [{ from: from, to: to, value: newDeco }], + }); + } + } + } + + // checks whether a node should get rendered/unrendered + renderNode(view: EditorView, node: SyntaxNode) { + const type = node.type; + const tokenProps = type.prop(tokenClassNodeProp); + const props = new Set(tokenProps?.split(' ')); + if (props.has('inline-code') && !props.has('formatting')) { + const start = node.from; + const end = node.to; + const selection = view.state.selection; + if ( + selectionAndRangeOverlap(selection, start - 1, end + 1) + ) { + if (this.isInlineSmiles(view, start, end)) { + return { render: false, isQuery: true }; + } else { + return { render: false, isQuery: false }; + } + } else if (this.isInlineSmiles(view, start, end)) { + return { render: true, isQuery: true }; + } + } + return { render: false, isQuery: false }; + } + + isInlineSmiles(view: EditorView, start: number, end: number) { + if (settings.inlineSmilesPrefix.length > 0) { + const text = view.state.doc.sliceString(start, end); + return text.startsWith(settings.inlineSmilesPrefix); + } else return false; + } + + inlineRender(view: EditorView) { + const currentFile = view.state.field(editorInfoField).file; + if (!currentFile) return; + + const widgets: Range[] = []; + + for (const { from, to } of view.visibleRanges) { + syntaxTree(view.state).iterate({ + from, + to, + enter: ({ node }) => { + if (!this.renderNode(view, node).render) return; + const widget = this.renderWidget(node, view); + if (widget) { + widgets.push(widget); + } + }, + }); + } + return Decoration.set(widgets, true); + } + + renderWidget(node: SyntaxNode, view: EditorView) { + // contains the position of inline code + const start = node.from; + const end = node.to; + // safety net against unclosed inline code + if (view.state.doc.sliceString(end, end + 1) === '\n') { + return; + } + const text = view.state.doc.sliceString(start, end); + const el = createSpan({ + cls: ['smiles', 'chem-cell-inline', 'chem-cell'], + }); + + /* If the query result is predefined text (e.g. in the case of errors), set innerText to it. + * Otherwise, pass on an empty element and fill it in later. + * This is necessary because {@link InlineWidget.toDOM} is synchronous but some rendering + * asynchronous. + */ + let code = ''; + if ( + settings.inlineSmiles && + text.startsWith(settings.inlineSmilesPrefix) + ) { + code = text + .substring(settings.inlineSmilesPrefix.length) + .trim(); + + renderCell(code, el.createDiv(), getCurrentTheme(settings)); + } + + return Decoration.replace({ + widget: new InlineWidget(code, el, view), + inclusive: false, + block: false, + }).range(start - 1, end + 1); + } + + destroy() { + this.component.unload(); + } + }, + { decorations: (v) => v.decorations } + ); +} diff --git a/src/global.d.ts b/src/global.d.ts deleted file mode 100644 index 9ef976f..0000000 --- a/src/global.d.ts +++ /dev/null @@ -1 +0,0 @@ -declare module 'smiles-drawer'; diff --git a/src/global/blocks.ts b/src/global/blocks.ts index 71926eb..8d5d99e 100644 --- a/src/global/blocks.ts +++ b/src/global/blocks.ts @@ -19,12 +19,14 @@ export const removeBlock = (block: SmilesBlock) => { // however, we only want to see the instances refreshed when the file is activated // file info is in the ctx of the block, and activate attribute is in the leaf metadata export const refreshBlocks = () => { + if (!gBlocks) return; gBlocks.forEach((block) => { block.render(); }); }; export const clearBlocks = () => { + if (!gBlocks) return; gBlocks.forEach((block) => { removeBlock(block); }); diff --git a/src/global/chemCore.ts b/src/global/chemCore.ts new file mode 100644 index 0000000..19eba26 --- /dev/null +++ b/src/global/chemCore.ts @@ -0,0 +1,51 @@ +import { ChemPluginSettings } from 'src/settings/base'; + +import type { ChemCore } from 'src/lib/core/ChemCore'; +import SmilesDrawerCore from '../lib/core/smilesDrawerCore'; +import RDKitCore from '../lib/core/rdkitCore'; + +export let gRenderCore: ChemCore; + +export const setCore = async ( + settings: ChemPluginSettings, + onFallback: (error: string) => void +) => { + if (!gRenderCore || settings.core !== gRenderCore.id) { + if (settings.core === 'smiles-drawer') { + gRenderCore = new SmilesDrawerCore(settings); + updateCoreSettings(settings); + } else if (settings.core === 'rdkit') { + try { + gRenderCore = await RDKitCore.init(settings); + updateCoreSettings(settings); + } catch (error) { + onFallback(error); + } + } else { + onFallback(`invalid chem core id. ${settings.core}`); + } + } +}; + +export const setFallbackCore = async (settings: ChemPluginSettings) => { + gRenderCore = new SmilesDrawerCore(settings); + updateCoreSettings(settings); +}; + +export const updateCoreSettings = (settings: ChemPluginSettings) => { + gRenderCore.settings = settings; +}; + +export const clearCore = () => { + const rdkitBundler = document.getElementById('chem-rdkit-bundler'); + if (rdkitBundler) document.body.removeChild(rdkitBundler); + + //@ts-ignore + delete window.RDKit; + //@ts-ignore + delete window.initRDKitModule; + //@ts-ignore + delete window.SmilesDrawer; + //@ts-ignore + delete window.SmiDrawer; +}; diff --git a/src/global/dataview.ts b/src/global/dataview.ts index ba961d2..b7fd04f 100644 --- a/src/global/dataview.ts +++ b/src/global/dataview.ts @@ -6,14 +6,12 @@ export { isPluginEnabled } from 'obsidian-dataview'; export const getDataview = () => { if (isPluginEnabled(app)) { - //@ts-ignore - gDataview = app.plugins.plugins.dataview; + gDataview = app.plugins.getPlugin('dataview'); } else { - gDataview; throw new Error(i18n.t('errors.dataview.title')); } }; export const clearDataview = () => { - gDataview = {}; + gDataview = null; }; diff --git a/src/global/drawer.ts b/src/global/drawer.ts deleted file mode 100644 index 8fa8551..0000000 --- a/src/global/drawer.ts +++ /dev/null @@ -1,12 +0,0 @@ -import { DEFAULT_SD_OPTIONS, SMILES_DRAWER_OPTIONS } from 'src/settings/base'; -import SmilesDrawer from 'smiles-drawer'; - -export let gDrawer = new SmilesDrawer.SmiDrawer(DEFAULT_SD_OPTIONS); - -export const setDrawer = (options: Partial) => { - gDrawer = new SmilesDrawer.SmiDrawer({ ...DEFAULT_SD_OPTIONS, ...options }); -}; - -export const clearDrawer = () => { - gDrawer = {}; -}; diff --git a/src/lib/core/ChemCore.ts b/src/lib/core/ChemCore.ts new file mode 100644 index 0000000..d36c741 --- /dev/null +++ b/src/lib/core/ChemCore.ts @@ -0,0 +1,12 @@ +import { ChemPluginSettings } from 'src/settings/base'; + +export interface ChemCore { + id: string; + settings: ChemPluginSettings; + core: unknown; + + draw: ( + source: string, + theme?: string + ) => Promise; +} diff --git a/src/lib/core/coreFallbackModal.ts b/src/lib/core/coreFallbackModal.ts new file mode 100644 index 0000000..55f37f0 --- /dev/null +++ b/src/lib/core/coreFallbackModal.ts @@ -0,0 +1,50 @@ +import { Modal, App, ButtonComponent } from 'obsidian'; +import { i18n } from 'src/lib/i18n'; + +export class CoreFallbackModal extends Modal { + msg: string; + onConfirm: () => void; + + constructor(app: App, text: string, onConfrim: () => void) { + super(app); + this.msg = text; + this.onConfirm = onConfrim; + } + + onOpen() { + const { contentEl } = this; + + contentEl.createEl('h3', { + text: i18n.t('modals.core-fallback.title'), + }); + + contentEl.createEl('div', { + text: i18n.t('modals.core-fallback.message'), + }); + + contentEl.createEl('br'); + + contentEl.createEl('div', { + text: this.msg, + }); + + const div = contentEl.createDiv(); + div.style.display = 'flex'; + div.style.flex = '1 1 auto'; + div.style.justifyContent = 'flex-end'; + div.style.padding = '3px'; + + new ButtonComponent(div) + .setCta() + .setButtonText(i18n.t('modals.core-fallback.confirm')) + .onClick(() => { + this.close(); + }); + } + + onClose() { + this.onConfirm(); + const { contentEl } = this; + contentEl.empty(); + } +} diff --git a/src/lib/core/rdkitCore.ts b/src/lib/core/rdkitCore.ts new file mode 100644 index 0000000..a034eba --- /dev/null +++ b/src/lib/core/rdkitCore.ts @@ -0,0 +1,233 @@ +import type { ChemCore } from './ChemCore'; + +import { JSMol, RDKitModule, JSReaction } from '@rdkit/rdkit'; +import { ChemPluginSettings } from 'src/settings/base'; +import { DEFAULT_RDKIT_OPTIONS } from 'src/lib/core/rdkitOptions'; +import { convertToRDKitTheme } from 'src/lib/themes/theme'; +import { getCurrentTheme } from 'src/lib/themes/getCurrentTheme'; + +import { normalizePath, requestUrl, Notice } from 'obsidian'; +import { i18n } from '../i18n'; +import { githubAsset } from 'typings/githubAsset'; + +export default class RDKitCore implements ChemCore { + id: 'rdkit'; + settings: ChemPluginSettings; + core: RDKitModule; + + /** + * @private + */ + constructor(settings: ChemPluginSettings, core: RDKitModule) { + this.settings = settings; + this.core = core; + } + + static async init(settings: ChemPluginSettings) { + if (!window.RDKit) { + try { + window.RDKit = await loadRDKit(); + } catch (e) { + try { + window.RDKit = await loadRDKitUnpkg(); + } catch (e) { + throw Error( + "Initializing rdkit failed: Can't fetch resources from unpkg." + ); + } + } + } + return new RDKitCore(settings, window.RDKit); + } + + draw = async ( + source: string, + theme: string = getCurrentTheme(this.settings) + ) => { + let svgstr = ''; + + if (source.includes('>')) { + const rxn = this.core.get_rxn(source); + if (!rxn) return this.logError(source); + svgstr = await this.drawReaction(rxn); + } else { + const mol = this.core.get_mol(source, JSON.stringify({})); + if (!mol) return this.logError(source); + + // https://greglandrum.github.io/rdkit-blog/posts/2024-01-11-using-abbreviations.html + if (this.settings.commonOptions.compactDrawing) + mol.condense_abbreviations(); + + svgstr = await this.drawMolecule(mol, theme); + } + + const container = createDiv(); + container.innerHTML = svgstr; + const svg = container.find('svg') as SVGSVGElement & HTMLElement; + + svg.setAttribute('data-smiles', source); + svg.setAttribute('xmlns', 'http://www.w3.org/2000/svg'); + + const w = svg.width.baseVal.value; + const h = svg.height.baseVal.value; + const r = w / h; + const scale = this.settings.commonOptions.scale ?? 1; + if (this.settings.commonOptions.scale == 0) { + svg.style.width = `${( + this.settings?.commonOptions.unifiedWidth ?? 300 + ).toString()}px`; + svg.style.height = `${( + (this.settings.commonOptions?.unifiedWidth ?? 300) / r + ).toString()}px`; + } else if (w * scale > (this.settings.commonOptions?.width ?? 300)) { + svg.style.width = `${( + this.settings.commonOptions?.width ?? 300 + ).toString()}px`; + svg.style.height = `${( + (this.settings.commonOptions?.width ?? 300) / r + ).toString()}px`; + } else if (w * scale <= (this.settings.commonOptions?.width ?? 300)) { + svg.style.width = `${(w * scale).toString()}px`; + svg.style.height = `${(h * scale).toString()}px`; + } + + return svg; + }; + + private drawReaction = async (rxn: JSReaction) => { + const svgstr = rxn.get_svg_with_highlights( + JSON.stringify({ + width: -1, + height: -1, + }) + ); + return svgstr; + }; + + private drawMolecule = async (mol: JSMol, theme: string) => { + //TODO: AbbrColour -> palette[0] + const palette = convertToRDKitTheme(theme); + const svgstr = mol.get_svg_with_highlights( + JSON.stringify({ + ...DEFAULT_RDKIT_OPTIONS, + ...this.settings.rdkitOptions, + atomColourPalette: palette, + queryColour: palette['6'], + highlightColour: palette['6'], + drawMolsSameScale: true, + width: -1, + height: -1, + addChiralHs: this.settings.commonOptions.explicitHydrogens, + + //https://rdkit.org/docs/cppapi/MolDraw2D_8h_source.html#l00547 + symbolColour: palette['-1'], // the color used for reaction arrows and single-color wedged bonds + legendColour: palette['-1'], + annotationColour: palette['-1'], + variableAttachmentColour: palette['-1'], + }) + ); + return svgstr; + }; + + private logError = (source: string) => { + const div = createDiv(); + div.createDiv('error-source').setText( + i18n.t('errors.source.title', { source }) + ); + div.createEl('br'); + div.createDiv().setText(i18n.t('errors.rdkit.title')); + div.style.wordBreak = `break-word`; + div.style.userSelect = `text`; + return div; + }; +} + +// Credits to fenjalien/obsidian-typst for the idea of loading local wasm by building object url. +// Initialize reference: https://github.com/rdkit/rdkit-js/tree/master/typescript +const loadRDKit = async () => { + const assetPath = normalizePath( + [app.vault.configDir, 'plugins', 'chem', 'rdkit'].join('/') + ); + if (!(await app.vault.adapter.exists(assetPath))) { + await app.vault.adapter.mkdir(assetPath); + } + + const jsPath = [assetPath, 'RDKit_minimal.js'].join('/'); + await checkOrDownload('RDKit_minimal.js'); + + const wasmPath = [assetPath, 'RDKit_minimal.wasm'].join('/'); + await checkOrDownload('RDKit_minimal.wasm'); + + const rdkitBundler = document.body.createEl('script'); + rdkitBundler.type = 'text/javascript'; + rdkitBundler.id = 'chem-rdkit-bundler'; + rdkitBundler.innerHTML = await app.vault.adapter.read(jsPath); + + const getWasmURL = async () => + URL.createObjectURL( + new Blob([await app.vault.adapter.readBinary(wasmPath)], { + type: 'application/wasm', + }) + ); + const url = await getWasmURL(); + const RDKit = await window.initRDKitModule({ + locateFile: () => url, + }); + URL.revokeObjectURL(url); + return RDKit; +}; + +// See https://github.com/rdkit/rdkit-js/issues/160 +const loadRDKitUnpkg = async () => { + const rdkitBundler = document.body.createEl('script'); + new Notice('Fetching RDKit.js from unpkg...'); + + rdkitBundler.innerHTML = await requestUrl( + 'https://unpkg.com/@rdkit/rdkit/dist/RDKit_minimal.js' + ).text; + + const RDKit = await window.initRDKitModule({ + locateFile: () => + 'https://unpkg.com/@rdkit/rdkit/dist/RDKit_minimal.wasm', + }); + new Notice('RDKit.js has been successfully loaded.'); + return RDKit; +}; + +const fetchAsset = async (target: string, localPath: string) => { + const assetInfo = await requestUrl( + `https://api.github.com/repos/acylation/obsidian-chem/releases/tags/${ + app.plugins.getPlugin('chem')?.manifest.version ?? '0.4.0' + }` + ).json; + const asset = assetInfo.assets.find((a: githubAsset) => a.name == target); + if (asset === undefined) throw Error('Could not find the online asset!'); + + const data = await requestUrl({ + url: asset.url, + headers: { Accept: 'application/octet-stream' }, + }).arrayBuffer; + await app.vault.adapter.writeBinary(localPath, data); +}; + +const checkOrDownload = async (target: string) => { + const assetPath = normalizePath( + [app.vault.configDir, 'plugins', 'chem', 'rdkit', target].join('/') + ); + + if (!(await app.vault.adapter.exists(assetPath))) { + new Notice(`Chem: Downloading ${target}!`, 5000); + try { + await fetchAsset(target, assetPath); + new Notice( + `Chem: Resource ${target} successfully downloaded! ✔️`, + 5000 + ); + } catch (error) { + new Notice(`Chem: Failed to fetch ${target}: ${error} ❌`); + throw Error( + `Failed to fetch resource ${target} from GitHub release.` + ); + } + } +}; diff --git a/src/lib/core/rdkitOptions.ts b/src/lib/core/rdkitOptions.ts new file mode 100644 index 0000000..5304166 --- /dev/null +++ b/src/lib/core/rdkitOptions.ts @@ -0,0 +1,43 @@ +/** + * RDKit.js options + * RDKit-js doc: https://www.rdkitjs.com/#drawing-molecules-all-options + * + * RDKit drawing options (upstream) + * https://rdkit.org/docs/cppapi/structRDKit_1_1MolDrawOptions.html + * https://greglandrum.github.io/rdkit-blog/posts/2023-05-26-drawing-options-explained.html + * + * MinimalLib source file + * https://github.com/rdkit/rdkit/blob/master/Code/MinimalLib/minilib.cpp + */ + +import { convertToRDKitTheme } from '../themes/theme'; +import { RGBDecimal } from 'src/lib/themes/helpers'; + +export interface RDKitOptions { + explicitMethyl: boolean; + fixedBondLength: number; + fixedScale: number; + atomColourPalette: Record; // any atom index is a valid palette key + includeRadicals: boolean; + clearBackground: boolean; + addStereoAnnotation: boolean; + annotationColour: RGBDecimal; + singleColourWedgeBonds: boolean; // the color of wedged would be controlled by `symbolColour` + addChiralHs: boolean; +} + +export const DEFAULT_RDKIT_OPTIONS: RDKitOptions = { + explicitMethyl: false, + fixedBondLength: -1, + fixedScale: -1, + atomColourPalette: convertToRDKitTheme('rdkit-default'), + includeRadicals: true, + clearBackground: false, + addStereoAnnotation: false, + annotationColour: [0.63, 0.12, 0.94], // chiral RS annotations + singleColourWedgeBonds: true, // a company option with `symbolColour` + addChiralHs: true, // test case: C1C[C@H]2CCCC[C@H]2CC1 + // wedgeBonds: true, + // wavyBonds: true, + // kekulize: false, +}; diff --git a/src/lib/core/smilesDrawerCore.ts b/src/lib/core/smilesDrawerCore.ts new file mode 100644 index 0000000..d155b4b --- /dev/null +++ b/src/lib/core/smilesDrawerCore.ts @@ -0,0 +1,74 @@ +import type { ChemCore } from './ChemCore'; + +import SmilesDrawer from 'smiles-drawer'; +import { ChemPluginSettings } from 'src/settings/base'; +import { DEFAULT_SD_OPTIONS } from 'src/lib/core/smilesDrawerOptions'; +import { getCurrentTheme } from 'src/lib/themes/getCurrentTheme'; + +import { i18n } from 'src/lib/i18n'; + +export default class SmilesDrawerCore implements ChemCore { + id: 'smiles-drawer'; + settings: ChemPluginSettings; + core: SmilesDrawer.SmiDrawer; + + constructor(settings: ChemPluginSettings) { + this.settings = settings; + this.core = new SmilesDrawer.SmiDrawer( + { + ...DEFAULT_SD_OPTIONS.moleculeOptions, + ...this.settings.smilesDrawerOptions.moleculeOptions, + }, + { + ...DEFAULT_SD_OPTIONS.reactionOptions, + ...this.settings.smilesDrawerOptions.reactionOptions, + } + ); + } + + draw = async ( + source: string, + theme: string = getCurrentTheme(this.settings) + ) => { + const svg = createSvg('svg'); + svg.setAttribute('xmlns', 'http://www.w3.org/2000/svg'); + svg.setAttribute('data-smiles', source); + + const errorDiv = createDiv(); + const errorCb = (error: object & { name: string; message: string }) => { + errorDiv + .createDiv('error-source') + .setText(i18n.t('errors.source.title', { source })); + errorDiv.createEl('br'); + const info = errorDiv.createEl('details'); + info.createEl('summary').setText(error.name); + info.createEl('div').setText(error.message); + + errorDiv.style.wordBreak = `break-word`; + errorDiv.style.userSelect = `text`; + }; + + this.core.draw(source, svg, theme, () => {}, errorCb); + + if (this.settings.commonOptions.scale == 0) + svg.style.width = `${( + this.settings?.commonOptions.unifiedWidth ?? 300 + ).toString()}px`; + else if ( + parseFloat(svg.style.width) > + (this.settings.commonOptions?.width ?? 300) + ) { + const r = + parseFloat(svg.style.width) / parseFloat(svg.style.height); + svg.style.width = `${( + this.settings.commonOptions?.width ?? 300 + ).toString()}px`; + svg.style.height = `${( + (this.settings.commonOptions?.width ?? 300) / r + ).toString()}px`; + } + + if (errorDiv.innerHTML) return errorDiv; + return svg; + }; +} diff --git a/src/lib/core/smilesDrawerOptions.ts b/src/lib/core/smilesDrawerOptions.ts new file mode 100644 index 0000000..cb4454e --- /dev/null +++ b/src/lib/core/smilesDrawerOptions.ts @@ -0,0 +1,115 @@ +import { convertToSDTheme } from 'src/lib/themes/theme'; +import { RDKitThemes } from 'src/lib/themes/rdkitThemes'; +import { SDTheme, SDThemes } from 'src/lib/themes/smilesDrawerThemes'; + +// Smiles-drawer options +// Reference: https://smilesdrawer.surge.sh/playground.html +export interface MoleculeOptions { + width: number; // levelup + height: number; // levelup + scale: number; // levelup + bondThickness: number; + shortBondLength: number; + bondSpacing: number; + atomVisualization: 'default' | 'balls' | 'allballs'; + isomeric: boolean; + debug: boolean; + terminalCarbons: boolean; + explicitHydrogens: boolean; + overlapSensitivity: number; + overlapResolutionIterations: number; + compactDrawing: boolean; + fontFamily: string; + fontSizeLarge: number; + fontSizeSmall: number; + padding: number; + experimentalSSSR: boolean; + kkThreshold: number; + kkInnerThreshold: number; + kkMaxIteration: number; + kkMaxInnerIteration: number; + kkMaxEnergy: number; + themes: Record; +} + +export interface ReactionOptions { + fontSize: number; + fontFamily: string; // comma separated font descriptions. + spacing: number; + plus: { + size: number; + thickness: number; + }; + arrow: { + length: number; + headSize: number; + thickness: number; + margin: number; + }; +} + +export interface SmilesDrawerOptions { + moleculeOptions: Partial; + reactionOptions: Partial; +} + +const collectThemes = () => { + const newThemes: Record = {}; + Object.keys(RDKitThemes).forEach( + (name) => + (newThemes[name] = { + ...SDThemes['light'], // TODO: 0.4.2 check this override + ...convertToSDTheme(name), + }) + ); + + return { + ...SDThemes, + ...newThemes, + }; +}; + +export const DEFAULT_SD_OPTIONS: SmilesDrawerOptions = { + moleculeOptions: { + width: 300, + height: 300, + scale: 1, + bondThickness: 1, + shortBondLength: 0.8, + bondSpacing: 5.1, + atomVisualization: 'default', + isomeric: true, + debug: false, + terminalCarbons: false, + explicitHydrogens: true, + overlapSensitivity: 0.42, + overlapResolutionIterations: 1, + compactDrawing: false, + fontFamily: 'Arial, Helvetica, sans-serif', + fontSizeLarge: 11, + fontSizeSmall: 3, + padding: 2, + experimentalSSSR: true, + kkThreshold: 0.1, + kkInnerThreshold: 0.1, + kkMaxIteration: 20000, + kkMaxInnerIteration: 50, + kkMaxEnergy: 1000000000, + themes: collectThemes(), + }, + reactionOptions: { + fontSize: 9, + fontFamily: 'Arial, Helvetica, sans-serif', + spacing: 10, + plus: { + size: 9, + thickness: 1, + }, + arrow: { + length: 120, + headSize: 6, + thickness: 1, + margin: 3, + }, + }, +}; diff --git a/src/lib/themes/getCurrentTheme.ts b/src/lib/themes/getCurrentTheme.ts new file mode 100644 index 0000000..4c1fe52 --- /dev/null +++ b/src/lib/themes/getCurrentTheme.ts @@ -0,0 +1,8 @@ +import { ChemPluginSettings } from 'src/settings/base'; + +export const getCurrentTheme = (settings: ChemPluginSettings) => { + return document.body.hasClass('theme-dark') && + !document.body.hasClass('theme-light') + ? settings.darkTheme + : settings.lightTheme; +}; diff --git a/src/lib/themes/helpers.test.ts b/src/lib/themes/helpers.test.ts new file mode 100644 index 0000000..43c43bf --- /dev/null +++ b/src/lib/themes/helpers.test.ts @@ -0,0 +1,40 @@ +import { expect, test } from '@jest/globals'; +import { hex2RGB, RGB2hex } from './helpers'; + +test('Convert 6-digit hex color to RGB decimal.', () => { + expect(hex2RGB('#5d6e6a')).toStrictEqual([93 / 255, 110 / 255, 106 / 255]); + expect(hex2RGB('#329c5c')).toStrictEqual([50 / 255, 156 / 255, 92 / 255]); + expect(hex2RGB('#e44f81')).toStrictEqual([228 / 255, 79 / 255, 129 / 255]); + expect(hex2RGB('#761a82')).toStrictEqual([118 / 255, 26 / 255, 130 / 255]); + expect(hex2RGB('#34f7d3')).toStrictEqual([52 / 255, 247 / 255, 211 / 255]); + expect(hex2RGB('#ec5ea8')).toStrictEqual([236 / 255, 94 / 255, 168 / 255]); + expect(hex2RGB('#bb965a')).toStrictEqual([187 / 255, 150 / 255, 90 / 255]); + expect(hex2RGB('#686df3')).toStrictEqual([104 / 255, 109 / 255, 243 / 255]); + expect(hex2RGB('#de35a7')).toStrictEqual([222 / 255, 53 / 255, 167 / 255]); + expect(hex2RGB('#7a46e0')).toStrictEqual([122 / 255, 70 / 255, 224 / 255]); +}); + +test('Convert 3-digit hex color to RGB decimal.', () => { + expect(hex2RGB('#000')).toStrictEqual([0, 0, 0]); + expect(hex2RGB('#fff')).toStrictEqual([1, 1, 1]); + expect(hex2RGB('#c6f')).toStrictEqual([204 / 255, 102 / 255, 1]); +}); + +test('Encode RGB decimal values back to hex string.', () => { + expect('#5d6e6a').toStrictEqual(RGB2hex([93 / 255, 110 / 255, 106 / 255])); + expect('#329c5c').toStrictEqual(RGB2hex([50 / 255, 156 / 255, 92 / 255])); + expect('#e44f81').toStrictEqual(RGB2hex([228 / 255, 79 / 255, 129 / 255])); + expect('#761a82').toStrictEqual(RGB2hex([118 / 255, 26 / 255, 130 / 255])); + expect('#34f7d3').toStrictEqual(RGB2hex([52 / 255, 247 / 255, 211 / 255])); + expect('#ec5ea8').toStrictEqual(RGB2hex([236 / 255, 94 / 255, 168 / 255])); + expect('#bb965a').toStrictEqual(RGB2hex([187 / 255, 150 / 255, 90 / 255])); + expect('#686df3').toStrictEqual(RGB2hex([104 / 255, 109 / 255, 243 / 255])); + expect('#de35a7').toStrictEqual(RGB2hex([222 / 255, 53 / 255, 167 / 255])); + expect('#7a46e0').toStrictEqual(RGB2hex([122 / 255, 70 / 255, 224 / 255])); +}); + +test('Encode will always return 6-digit hex string.', () => { + expect('#000000').toStrictEqual(RGB2hex([0, 0, 0])); + expect('#ffffff').toStrictEqual(RGB2hex([1, 1, 1])); + expect('#cc66ff').toStrictEqual(RGB2hex([204 / 255, 102 / 255, 1])); +}); diff --git a/src/lib/themes/helpers.ts b/src/lib/themes/helpers.ts new file mode 100644 index 0000000..1f09337 --- /dev/null +++ b/src/lib/themes/helpers.ts @@ -0,0 +1,39 @@ +export type RGBDecimal = [number, number, number]; + +/** + * @param {string} hex Hex color leading by char '#' + **/ +export function hex2RGB(hex: string): RGBDecimal { + hex = hex.slice(1); + + // Expand shorthand hex color + if (hex.length === 3) { + hex = hex + .split('') + .map((l) => l.repeat(2)) + .join(''); + } + + const hexInt = parseInt(hex, 16); + const r = (hexInt >> 16) & 255; + const g = (hexInt >> 8) & 255; + const b = hexInt & 255; + + return [r / 255, g / 255, b / 255]; +} + +/** + * @param {RGBDecimal} rgb a number array with each part betweeen 0-1 + **/ +export function RGB2hex(rgb: RGBDecimal): string { + return ( + '#' + + rgb + .map((v) => + Math.round(v * 255) + .toString(16) + .padStart(2, '0') + ) + .join('') + ); +} diff --git a/src/lib/themes/rdkitThemes.ts b/src/lib/themes/rdkitThemes.ts new file mode 100644 index 0000000..12022d8 --- /dev/null +++ b/src/lib/themes/rdkitThemes.ts @@ -0,0 +1,79 @@ +// from https://rdkit.org/docs/cppapi/MolDraw2DHelpers_8h_source.html +// 201 is for hydrogens when atom symbols are not being drawn. + +import { RGBDecimal } from './helpers'; + +export interface RDKitTheme extends Record { + '-1': [number, number, number]; + '0': [number, number, number]; + '6': [number, number, number]; + '7': [number, number, number]; + '8': [number, number, number]; + '9': [number, number, number]; + '15': [number, number, number]; + '16': [number, number, number]; + '17': [number, number, number]; + '35': [number, number, number]; + '53': [number, number, number]; + '201': [number, number, number]; +} + +export const RDKitThemes: Record = { + 'rdkit-default': { + '-1': [0, 0, 0], + '0': [0.1, 0.1, 0.1], + '6': [0.0, 0.0, 0.0], + '7': [0.0, 0.0, 1.0], + '8': [1.0, 0.0, 0.0], + '9': [0.2, 0.8, 0.8], + '15': [1.0, 0.5, 0.0], + '16': [0.8, 0.8, 0.0], + '17': [0.0, 0.802, 0.0], + '35': [0.5, 0.3, 0.1], + '53': [0.63, 0.12, 0.94], + '201': [0.68, 0.85, 0.9], + }, + 'rdkit-avalon': { + '-1': [0, 0, 0], + '0': [0.1, 0.1, 0.1], + '6': [0.0, 0.0, 0.0], + '7': [0.0, 0.0, 1.0], + '8': [1.0, 0.0, 0.0], + '9': [0.0, 0.498, 0.0], + '15': [0.498, 0.0, 0.498], + '16': [0.498, 0.247, 0.0], + '17': [0.0, 0.498, 0.0], + '35': [0.0, 0.498, 0.0], + '53': [0.247, 0.0, 0.498], + '201': [0.68, 0.85, 0.9], + }, + 'rdkit-cdk': { + '-1': [0, 0, 0], + '0': [0.1, 0.1, 0.1], + '6': [0.0, 0.0, 0.0], + '7': [0.188, 0.314, 0.972], + '8': [1.0, 0.051, 0.051], + '9': [0.565, 0.878, 0.314], + '15': [1.0, 0.5, 0.0], + '16': [0.776, 0.776, 0.173], + '17': [0.122, 0.498, 0.122], + '35': [0.651, 0.161, 0.161], + '53': [0.58, 0.0, 0.58], + '5': [1.0, 0.71, 0.71], + '201': [0.68, 0.85, 0.9], + }, + 'rdkit-dark': { + '-1': [0.8, 0.8, 0.8], + '0': [0.9, 0.9, 0.9], + '6': [0.9, 0.9, 0.9], + '7': [0.33, 0.41, 0.92], + '8': [1.0, 0.2, 0.2], + '9': [0.2, 0.8, 0.8], + '15': [1.0, 0.5, 0.0], + '16': [0.8, 0.8, 0.0], + '17': [0.0, 0.802, 0.0], + '35': [0.71, 0.4, 0.07], + '53': [0.89, 0.004, 1], + '201': [0.68, 0.85, 0.9], + }, +}; diff --git a/src/lib/themes/smilesDrawerThemes.ts b/src/lib/themes/smilesDrawerThemes.ts new file mode 100644 index 0000000..a4fb4f9 --- /dev/null +++ b/src/lib/themes/smilesDrawerThemes.ts @@ -0,0 +1,213 @@ +export interface SDTheme extends Record { + C: string; + O: string; + N: string; + F: string; + CL: string; + BR: string; + I: string; + P: string; + S: string; + B: string; + SI: string; + H: string; + BACKGROUND: string; +} + +export const SDThemes: Record = { + dark: { + C: '#fff', + O: '#e74c3c', + N: '#3498db', + F: '#27ae60', + CL: '#16a085', + BR: '#d35400', + I: '#8e44ad', + P: '#d35400', + S: '#f1c40f', + B: '#e67e22', + SI: '#e67e22', + H: '#aaa', + BACKGROUND: '#141414', + }, + light: { + C: '#222', + O: '#e74c3c', + N: '#3498db', + F: '#27ae60', + CL: '#16a085', + BR: '#d35400', + I: '#8e44ad', + P: '#d35400', + S: '#f1c40f', + B: '#e67e22', + SI: '#e67e22', + H: '#666', + BACKGROUND: '#fff', + }, + oldschool: { + C: '#000', + O: '#000', + N: '#000', + F: '#000', + CL: '#000', + BR: '#000', + I: '#000', + P: '#000', + S: '#000', + B: '#000', + SI: '#000', + H: '#000', + BACKGROUND: '#fff', + }, + 'oldschool-dark': { + C: '#fff', + O: '#fff', + N: '#fff', + F: '#fff', + CL: '#fff', + BR: '#fff', + I: '#fff', + P: '#fff', + S: '#fff', + B: '#fff', + SI: '#fff', + H: '#fff', + BACKGROUND: '#000', + }, + solarized: { + C: '#586e75', + O: '#dc322f', + N: '#268bd2', + F: '#859900', + CL: '#16a085', + BR: '#cb4b16', + I: '#6c71c4', + P: '#d33682', + S: '#b58900', + B: '#2aa198', + SI: '#2aa198', + H: '#657b83', + BACKGROUND: '#fff', + }, + 'solarized-dark': { + C: '#93a1a1', + O: '#dc322f', + N: '#268bd2', + F: '#859900', + CL: '#16a085', + BR: '#cb4b16', + I: '#6c71c4', + P: '#d33682', + S: '#b58900', + B: '#2aa198', + SI: '#2aa198', + H: '#839496', + BACKGROUND: '#fff', + }, + matrix: { + C: '#678c61', + O: '#2fc079', + N: '#4f7e7e', + F: '#90d762', + CL: '#82d967', + BR: '#23755a', + I: '#409931', + P: '#c1ff8a', + S: '#faff00', + B: '#50b45a', + SI: '#409931', + H: '#426644', + BACKGROUND: '#fff', + }, + github: { + C: '#24292f', + O: '#cf222e', + N: '#0969da', + F: '#2da44e', + CL: '#6fdd8b', + BR: '#bc4c00', + I: '#8250df', + P: '#bf3989', + S: '#d4a72c', + B: '#fb8f44', + SI: '#bc4c00', + H: '#57606a', + BACKGROUND: '#fff', + }, + carbon: { + C: '#161616', + O: '#da1e28', + N: '#0f62fe', + F: '#198038', + CL: '#007d79', + BR: '#fa4d56', + I: '#8a3ffc', + P: '#ff832b', + S: '#f1c21b', + B: '#8a3800', + SI: '#e67e22', + H: '#525252', + BACKGROUND: '#fff', + }, + cyberpunk: { + C: '#ea00d9', + O: '#ff3131', + N: '#0abdc6', + F: '#00ff9f', + CL: '#00fe00', + BR: '#fe9f20', + I: '#ff00ff', + P: '#fe7f00', + S: '#fcee0c', + B: '#ff00ff', + SI: '#ffffff', + H: '#913cb1', + BACKGROUND: '#fff', + }, + gruvbox: { + C: '#665c54', + O: '#cc241d', + N: '#458588', + F: '#98971a', + CL: '#79740e', + BR: '#d65d0e', + I: '#b16286', + P: '#af3a03', + S: '#d79921', + B: '#689d6a', + SI: '#427b58', + H: '#7c6f64', + BACKGROUND: '#fbf1c7', + }, + 'gruvbox-dark': { + C: '#ebdbb2', + O: '#cc241d', + N: '#458588', + F: '#98971a', + CL: '#b8bb26', + BR: '#d65d0e', + I: '#b16286', + P: '#fe8019', + S: '#d79921', + B: '#8ec07c', + SI: '#83a598', + H: '#bdae93', + BACKGROUND: '#282828', + }, + custom: { + C: '#222', + O: '#e74c3c', + N: '#3498db', + F: '#27ae60', + CL: '#16a085', + BR: '#d35400', + I: '#8e44ad', + P: '#d35400', + S: '#f1c40f', + B: '#e67e22', + SI: '#e67e22', + H: '#666', + BACKGROUND: '#fff', + }, +}; diff --git a/src/lib/themes/theme.test.ts b/src/lib/themes/theme.test.ts new file mode 100644 index 0000000..c01807d --- /dev/null +++ b/src/lib/themes/theme.test.ts @@ -0,0 +1,37 @@ +import { expect, test } from '@jest/globals'; +import { convertToRDKitTheme, convertToSDTheme } from './theme'; + +test('Convert to RDKit theme.', () => { + expect(convertToRDKitTheme('light')).toStrictEqual({ + '-1': [102 / 255, 102 / 255, 102 / 255], + '0': [34 / 255, 34 / 255, 34 / 255], + '6': [34 / 255, 34 / 255, 34 / 255], + '7': [52 / 255, 152 / 255, 219 / 255], + '8': [231 / 255, 76 / 255, 60 / 255], + '9': [39 / 255, 174 / 255, 96 / 255], + '14': [230 / 255, 126 / 255, 34 / 255], + '15': [211 / 255, 84 / 255, 0], + '16': [241 / 255, 196 / 255, 15 / 255], + '17': [22 / 255, 160 / 255, 133 / 255], + '35': [211 / 255, 84 / 255, 0], + '53': [142 / 255, 68 / 255, 173 / 255], + '5': [230 / 255, 126 / 255, 34 / 255], + '201': [102 / 255, 102 / 255, 102 / 255], + }); +}); + +test('Convert to Smiles Drawer format theme.', () => { + expect(convertToSDTheme('rdkit-cdk')).toStrictEqual({ + C: '#000000', + O: '#ff0d0d', + N: '#3050f8', + F: '#90e050', + CL: '#1f7f1f', + BR: '#a62929', + I: '#940094', + P: '#ff8000', + S: '#c6c62c', + B: '#ffb5b5', + BACKGROUND: '#ffffff', + }); +}); diff --git a/src/lib/themes/theme.ts b/src/lib/themes/theme.ts new file mode 100644 index 0000000..6f9e1ac --- /dev/null +++ b/src/lib/themes/theme.ts @@ -0,0 +1,113 @@ +import { RDKitThemes } from './rdkitThemes'; +import { SDTheme, SDThemes } from './smilesDrawerThemes'; + +import { hex2RGB, RGB2hex, type RGBDecimal } from './helpers'; + +export const themeList = { + // from smiles-drawer + light: 'Light', + dark: 'Dark', + oldschool: 'Oldschool', + 'oldschool-dark': 'Oldschool Dark', + solarized: 'Solarized', + 'solarized-dark': 'Solarized Dark', + matrix: 'Matrix', + github: 'GitHub', + carbon: 'Carbon', + cyberpunk: 'Cyberpunk', + gruvbox: 'Gruvbox', + 'gruvbox-dark': 'Gruvbox Dark', + + // from RDKit + 'rdkit-default': 'Light (RDKit)', + 'rdkit-avalon': 'Avalon (RDKit)', + 'rdkit-cdk': 'CDK (RDKit)', + 'rdkit-dark': 'Dark (RDKit)', +}; + +export const convertToSDTheme = ( + name: keyof typeof SDThemes | keyof typeof RDKitThemes +): Record => { + if (Object.keys(SDThemes).includes(name)) { + return SDThemes[name]; + } else if (Object.keys(RDKitThemes).includes(name)) { + const p = RDKitThemes[name]; + const t: Record = {}; + Keys_RD2SD.forEach((v, k) => { + if (p[v]) t[k] = RGB2hex(p[v]); + }); + t['BACKGROUND'] = getSDBGColor(name); + return t; + } + return SDThemes['light']; +}; + +export const convertToRDKitTheme = ( + name: keyof typeof SDThemes | keyof typeof RDKitThemes +): Record => { + if (Object.keys(SDThemes).includes(name)) { + const t = SDThemes[name]; + const p: Record = {}; + Keys_SD2RD.forEach((v, k) => { + p[k] = hex2RGB(t[v]); + }); + return p; + } else if (Object.keys(RDKitThemes).includes(name)) { + return RDKitThemes[name]; + } + return RDKitThemes['rdkit-default']; +}; + +// Get a hexString background color. +export const getSDBGColor = (name: string): string => { + if (Object.keys(SDThemes).includes(name)) { + const t = SDThemes[name]; + return t['BACKGROUND']; + } else if (Object.keys(RDKitThemes).includes(name)) { + return RGB2hex(RDKitThemes[name][6].map((v) => 1 - v) as RGBDecimal); + } + return '#000'; +}; + +// Get a RGBDecimal background color. +export const getRDKitBGColor = (name: string): RGBDecimal => { + if (Object.keys(SDThemes).includes(name)) { + const t = SDThemes[name]; + return hex2RGB(t['BACKGROUND']); + } else if (Object.keys(RDKitThemes).includes(name)) { + return RDKitThemes[name][6].map((v) => 1 - v) as RGBDecimal; + } + return [0, 0, 0]; +}; + +const Keys_RD2SD: Map = new Map([ + ['C', 6], + ['O', 8], + ['N', 7], + ['F', 9], + ['CL', 17], + ['BR', 35], + ['I', 53], + ['P', 15], + ['S', 16], + ['B', 5], + ['SI', 14], + ['H', 1], +]); + +const Keys_SD2RD: Map = new Map([ + [-1, 'H'], + [0, 'C'], + [6, 'C'], + [7, 'N'], + [8, 'O'], + [9, 'F'], + [14, 'SI'], + [15, 'P'], + [16, 'S'], + [17, 'CL'], + [35, 'BR'], + [53, 'I'], + [5, 'B'], + [201, 'H'], +]); diff --git a/src/themeObserver.ts b/src/lib/themes/themeObserver.ts similarity index 100% rename from src/themeObserver.ts rename to src/lib/themes/themeObserver.ts diff --git a/src/lib/translations/en.json b/src/lib/translations/en.json index c65a446..1929f7a 100644 --- a/src/lib/translations/en.json +++ b/src/lib/translations/en.json @@ -6,6 +6,9 @@ }, "dataview": { "title": "Dataview plugin is missing or disabled." + }, + "rdkit": { + "title": "RDKit failed to parse the SMILES." } }, "menus": { @@ -48,6 +51,10 @@ }, "advanced": { "title": "Advanced", + "core": { + "name": "Core configuration", + "description": "Select render core." + }, "compact-drawing": { "name": "Compact drawing", "description": "Linearize simple structures and functional groups." @@ -55,6 +62,10 @@ "terminal-carbons": { "name": "Show terminal carbons", "description": "Explictly draw terminal carbons like methyl or methylene." + }, + "explicit-hydrogen": { + "name": "Explicit hydrogen", + "description": "Enable to show explicit hydrogen." } }, "copy": { @@ -76,8 +87,26 @@ "dataview": { "title": "Dataview", "enable": { - "name": "Inline Dataview", - "description": "Recognize and get return values from Dataview queries and DataviewJS lines as rendering source according to Dataview settings." + "name": "Parse Dataview", + "description": "In smiles block, recognize and get return values from Dataview queries and DataviewJS lines as rendering source according to Dataview settings." + } + }, + "inline": { + "title": "Inline SMILES", + "enable": { + "name": "Enable inline SMILES", + "description": "Render SMILES code lines." + }, + "prefix": { + "name": "Inline SMILES Prefix", + "description": "The prefix to inline SMILES." + } + }, + "modals": { + "core-fallback": { + "title": "Switch core failed", + "confirm": "Confirm", + "message": "Failed to switch to the target package, and will fallback to the default Smiles Drawer core." } } } diff --git a/src/lib/translations/zh-CN.json b/src/lib/translations/zh-CN.json index 474e3a3..93c120f 100644 --- a/src/lib/translations/zh-CN.json +++ b/src/lib/translations/zh-CN.json @@ -6,6 +6,9 @@ }, "dataview": { "title": "Dataview 插件未启用。" + }, + "rdkit": { + "title": "RDKit 无法识别该 SMILES 字符串" } }, "menus": { @@ -18,7 +21,7 @@ "settings": { "scale": { "name": "图像比例", - "description": "调整全局图像比例。该值为 0 时，所有图像将具有相同的大小；若非 0，所有结构将具有相同的键长，但图像尺寸将随结构式的大小变化。", + "description": "调整全局图像比例。该值为 0 时，所有图像将具有相同的大小；若非 0，所有结构将具有相同的键长，图像尺寸将适应结构式的大小。", "tooltip": "恢复默认" }, "unify-bond-length": { @@ -48,6 +51,10 @@ }, "advanced": { "title": "高级", + "core": { + "name": "渲染器", + "description": "选择渲染器。" + }, "compact-drawing": { "name": "紧凑绘制", "description": "简化羧基、硝基、磺酸基等简单官能团的绘制。" @@ -55,10 +62,14 @@ "terminal-carbons": { "name": "端基碳", "description": "显式绘出末端甲基、亚甲基等端基碳。" + }, + "explicit-hydrogen": { + "name": "显式氢", + "description": "启用以绘制显式氢原子。" } }, "copy": { - "title": "复制", + "title": "复制选项", "scale": { "name": "缩放比例", "description": "调整复制所得图像的缩放比例，更大的比例对应更高的分辨率。" @@ -69,16 +80,34 @@ }, "theme": { "name": "颜色主题", - "description": "设置复制所得图像的颜色主题。", + "description": "设置复制所得图像的颜色主题", "default": "跟随 Obsidian" } }, "dataview": { - "title": "Dataview", + "title": "Dataview 集成", "enable": { "name": "解析 Dataview", "description": "根据 Dataview 插件设置，识别并执行 smiles 代码块中的 Dataview 查询式 (Queries) 和 DataviewJS 代码，依查询结果渲染结构。" } + }, + "inline": { + "title": "行内 SMILES 渲染", + "enable": { + "name": "启用行内 SMILES", + "description": "渲染行内代码形式的 SMILES 字符串。" + }, + "prefix": { + "name": "前缀", + "description": "行内 SMILES 的前缀。" + } + } + }, + "modals": { + "core-fallback": { + "title": "切换渲染器失败", + "confirm": "确认", + "message": "切换目标渲染器失败，将回退为默认渲染器 Smiles Drawer。" } } } diff --git a/src/main.ts b/src/main.ts index 9757431..6c47e15 100644 --- a/src/main.ts +++ b/src/main.ts @@ -1,17 +1,15 @@ import { Plugin, MarkdownPostProcessorContext } from 'obsidian'; -import { - DEFAULT_SETTINGS, - ChemPluginSettings, - SETTINGS_VERSION, -} from './settings/base'; +import { ChemPluginSettings, migrateSettings } from './settings/base'; import { ChemSettingTab } from './settings/SettingTab'; -import { updateSettingsVersion } from './settings/update'; + import { SmilesBlock } from './SmilesBlock'; +import { inlinePlugin } from './SmilesInline'; +import { setCore, clearCore, setFallbackCore } from './global/chemCore'; import { setBlocks, clearBlocks } from './global/blocks'; -import { setDrawer, clearDrawer } from './global/drawer'; import { getDataview, clearDataview } from './global/dataview'; -import { setObserver, detachObserver } from './themeObserver'; +import { setObserver, detachObserver } from './lib/themes/themeObserver'; +import { CoreFallbackModal } from './lib/core/coreFallbackModal'; export default class ChemPlugin extends Plugin { settings: ChemPluginSettings; @@ -19,35 +17,37 @@ export default class ChemPlugin extends Plugin { async onload() { await this.loadSettings(); - // this.addRibbonIcon('hexagon', 'This is Chem Plugin', () => {}); - // initialize global variables - setDrawer(this.settings.options); setBlocks(); setObserver(); + setCore(this.settings, (error: string) => { + new CoreFallbackModal(this.app, error, async () => { + this.settings.core = 'smiles-drawer'; + await this.saveSettings(); + await setFallbackCore(this.settings); + }).open(); + }); this.addSettingTab(new ChemSettingTab({ app: this.app, plugin: this })); + + // render modules this.registerMarkdownCodeBlockProcessor('smiles', this.smilesProcessor); + this.registerMarkdownPostProcessor(this.inlineSmilesProcessor); // nested inline render + this.registerEditorExtension(inlinePlugin(this.settings)); // editor extension for patching live-preview inline + this.app.workspace.updateOptions(); // Auto render existing pages when plugin loaded + if (this.settings.dataview) getDataview(); } async onunload() { detachObserver(); clearBlocks(); - clearDrawer(); + clearCore(); clearDataview(); } async loadSettings() { - const candidate = Object.assign({}, await this.loadData()); - if ('version' in candidate && candidate.version == SETTINGS_VERSION) - this.settings = Object.assign({}, DEFAULT_SETTINGS, candidate); - else - this.settings = Object.assign( - {}, - DEFAULT_SETTINGS, - updateSettingsVersion(candidate) - ); + this.settings = migrateSettings(await this.loadData()); } async saveSettings() { @@ -61,4 +61,26 @@ export default class ChemPlugin extends Plugin { ) => { ctx.addChild(new SmilesBlock(el, source, ctx, this.settings)); }; + + //TODO: fix extra br in inline code + inlineSmilesProcessor = ( + el: HTMLElement, + ctx: MarkdownPostProcessorContext + ) => { + //https://docs.obsidian.md/Plugins/Editor/Markdown+post+processing + const inlineCodes = el.findAll('code'); + inlineCodes.forEach((code) => { + const text = code.innerText; + if (text.startsWith(this.settings.inlineSmilesPrefix)) { + const source = text + .substring(this.settings.inlineSmilesPrefix.length) + .trim(); + const container = el.createDiv(); + code.replaceWith(container); + ctx.addChild( + new SmilesBlock(container, source, ctx, this.settings) + ); + } + }); + }; } diff --git a/src/settings/LivePreview.ts b/src/settings/LivePreview.ts index def3eb9..aa69672 100644 --- a/src/settings/LivePreview.ts +++ b/src/settings/LivePreview.ts @@ -1,6 +1,5 @@ -import { ChemPluginSettings } from '../settings/base'; -import { gDrawer } from 'src/global/drawer'; -import { i18n } from 'src/lib/i18n'; +import { ChemPluginSettings } from './base'; +import { gRenderCore } from 'src/global/chemCore'; export class LivePreview { container: HTMLDivElement; @@ -42,9 +41,9 @@ export class LivePreview { this.settings.darkTheme ); - if (this.settings.options.scale == 0) + if (this.settings.commonOptions.scale == 0) this.container.style.gridTemplateColumns = `repeat(auto-fill, minmax(${( - this.settings?.imgWidth ?? 300 + this.settings?.commonOptions.unifiedWidth ?? 300 ).toString()}px, 1fr)`; else this.container.style.gridTemplateColumns = `repeat(auto-fill, minmax(${(lightWidth > @@ -54,74 +53,18 @@ export class LivePreview { ).toString()}px, 1fr)`; }; - updateSettings = (argSettings: ChemPluginSettings) => { - this.settings = argSettings; + updateSettings = (newSettings: ChemPluginSettings) => { + this.settings = newSettings; }; - private renderCell = ( + private renderCell = async ( source: string, target: HTMLElement, - style: string + theme: string ) => { - const svg = target.createSvg('svg'); - svg.setAttribute('xmlns', 'http://www.w3.org/2000/svg'); + const svg = await gRenderCore.draw(source, theme); + target.appendChild(svg); - const errorCb = ( - error: object & { name: string; message: string }, - container: HTMLDivElement - ) => { - container - .createDiv('error-source') - .setText(i18n.t('errors.source.title', { source })); - container.createEl('br'); - const info = container.createEl('details'); - info.createEl('summary').setText(error.name); - info.createEl('div').setText(error.message); - - container.style.wordBreak = `break-word`; - container.style.userSelect = `text`; - container.style.display = `grid`; - container.style.alignContent = `center`; - - if (this.settings.options.scale == 0) - container.style.width = `${( - this.settings?.imgWidth ?? 300 - ).toString()}px`; - else if ( - container.offsetWidth > (this.settings.options?.width ?? 300) - ) { - container.style.width = `${( - this.settings.options?.width ?? 300 - ).toString()}px`; - } - }; - - gDrawer.draw( - source, - svg, - style, - null, - (error: object & { name: string; message: string }) => { - target.empty(); - errorCb(error, target.createEl('div')); - } - ); - if (this.settings.options.scale == 0) - svg.style.width = `${( - this.settings?.imgWidth ?? 300 - ).toString()}px`; - else if ( - parseFloat(svg.style.width) > (this.settings.options?.width ?? 300) - ) { - const r = - parseFloat(svg.style.width) / parseFloat(svg.style.height); - svg.style.width = `${( - this.settings.options?.width ?? 300 - ).toString()}px`; - svg.style.height = `${( - (this.settings.options?.width ?? 300) / r - ).toString()}px`; - } return parseFloat(svg.style.width); }; } diff --git a/src/settings/SettingTab.ts b/src/settings/SettingTab.ts index ad34d5e..fa7c6d6 100644 --- a/src/settings/SettingTab.ts +++ b/src/settings/SettingTab.ts @@ -1,21 +1,18 @@ -import { App, PluginSettingTab, Setting, SliderComponent } from 'obsidian'; - import ChemPlugin from '../main'; +import { DEFAULT_SETTINGS } from './base'; +import { themeList } from '../lib/themes/theme'; import { - DEFAULT_SD_OPTIONS, - SAMPLE_SMILES_1, - SAMPLE_SMILES_2, - themeList, -} from './base'; - -import { setDrawer } from 'src/global/drawer'; + setCore, + updateCoreSettings, + setFallbackCore, +} from 'src/global/chemCore'; import { refreshBlocks } from 'src/global/blocks'; import { clearDataview, getDataview } from 'src/global/dataview'; -import { LivePreview } from './LivePreview'; +import { App, PluginSettingTab, Setting, SliderComponent } from 'obsidian'; import { i18n } from 'src/lib/i18n'; - -// Reference: https://smilesdrawer.surge.sh/playground.html +import { LivePreview } from './LivePreview'; +import { CoreFallbackModal } from '../lib/core/coreFallbackModal'; export class ChemSettingTab extends PluginSettingTab { plugin: ChemPlugin; @@ -25,8 +22,6 @@ export class ChemSettingTab extends PluginSettingTab { this.plugin = plugin; } - //TODO: Caching proposed - display(): void { const { containerEl } = this; @@ -38,39 +33,30 @@ export class ChemSettingTab extends PluginSettingTab { .addExtraButton((button) => { button .setIcon('rotate-ccw') - .setTooltip(i18n.t('settings.scale.description')) + .setTooltip(i18n.t('settings.scale.tooltip')) .onClick(async () => { - this.plugin.settings.options.scale = 1; - scaleSlider.setValue(50); + this.plugin.settings.smilesDrawerOptions.moleculeOptions.scale = 1; + this.plugin.settings.commonOptions.scale = 1; + scaleSlider.setValue(1.0); await this.plugin.saveSettings(); - setDrawer({ - ...DEFAULT_SD_OPTIONS, - ...this.plugin.settings.options, - }); + this.updateCore(); onSettingsChange(); unifyBondLength(); }); }); - const scaleLabel = scaleSetting.controlEl.createDiv('slider-readout'); - scaleLabel.setText( - (this.plugin.settings.options.scale ?? 1.0).toFixed(2).toString() - ); - const scaleSlider = new SliderComponent(scaleSetting.controlEl) - .setValue(50 * (this.plugin.settings.options.scale ?? 1.0)) - .setLimits(0.0, 100, 0.5) + .setValue(this.plugin.settings.commonOptions.scale ?? 1.0) + .setLimits(0.0, 2, 0.01) + .setDynamicTooltip() .onChange(async (value) => { - this.plugin.settings.options.scale = value / 50; - scaleLabel.setText((value / 50).toFixed(2).toString()); + this.plugin.settings.smilesDrawerOptions.moleculeOptions.scale = + value; + this.plugin.settings.commonOptions.scale = value; await this.plugin.saveSettings(); - setDrawer({ - ...DEFAULT_SD_OPTIONS, - ...this.plugin.settings.options, - }); + this.updateCore(); onSettingsChange(); - if (value == 0) unifyImageWidth(); - else unifyBondLength(); + value === 0 ? unifyImageWidth() : unifyBondLength(); }); const widthSettings = new Setting(containerEl); @@ -112,11 +98,11 @@ export class ChemSettingTab extends PluginSettingTab { .setDesc(i18n.t('settings.preview.sample.description')) .addText((text) => text - .setPlaceholder(SAMPLE_SMILES_1) + .setPlaceholder(DEFAULT_SETTINGS.sample1) .setValue(this.plugin.settings.sample1) .onChange(async (value) => { if (value == '') { - value = SAMPLE_SMILES_1; + value = DEFAULT_SETTINGS.sample1; } this.plugin.settings.sample1 = value; await this.plugin.saveSettings(); @@ -125,11 +111,11 @@ export class ChemSettingTab extends PluginSettingTab { ) .addText((text) => text - .setPlaceholder(SAMPLE_SMILES_2) + .setPlaceholder(DEFAULT_SETTINGS.sample2) .setValue(this.plugin.settings.sample2) .onChange(async (value) => { if (value == '') { - value = SAMPLE_SMILES_2; + value = DEFAULT_SETTINGS.sample2; } this.plugin.settings.sample2 = value; await this.plugin.saveSettings(); @@ -142,6 +128,34 @@ export class ChemSettingTab extends PluginSettingTab { new Setting(containerEl) .setName(i18n.t('settings.advanced.title')) .setHeading(); + new Setting(containerEl) + .setName(i18n.t('settings.advanced.core.name')) + .setDesc(i18n.t('settings.advanced.core.description')) + .addDropdown((dropdown) => + dropdown + .addOptions({ + rdkit: 'RDKit.js', + 'smiles-drawer': 'Smiles Drawer', + }) + .setValue(this.plugin.settings.core ?? false) + .onChange(async (value: 'rdkit' | 'smiles-drawer') => { + this.plugin.settings.core = value; + await this.plugin.saveSettings(); + await setCore( + this.plugin.settings, + async (error: string) => { + new CoreFallbackModal(app, error, async () => { + dropdown.setValue('smiles-drawer'); + this.plugin.settings.core = 'smiles-drawer'; + await this.plugin.saveSettings(); + setFallbackCore(this.plugin.settings); + onSettingsChange(); + }).open(); + } + ); + onSettingsChange(); + }) + ); new Setting(containerEl) .setName(i18n.t('settings.advanced.compact-drawing.name')) @@ -149,15 +163,16 @@ export class ChemSettingTab extends PluginSettingTab { .addToggle((toggle) => toggle .setValue( - this.plugin.settings.options?.compactDrawing ?? false + this.plugin.settings.smilesDrawerOptions.moleculeOptions + .compactDrawing ?? false ) .onChange(async (value) => { - this.plugin.settings.options.compactDrawing = value; + this.plugin.settings.smilesDrawerOptions.moleculeOptions.compactDrawing = + value; + this.plugin.settings.commonOptions.compactDrawing = + value; await this.plugin.saveSettings(); - setDrawer({ - ...DEFAULT_SD_OPTIONS, - ...this.plugin.settings.options, - }); + this.updateCore(); onSettingsChange(); }) ); @@ -168,15 +183,38 @@ export class ChemSettingTab extends PluginSettingTab { .addToggle((toggle) => toggle .setValue( - this.plugin.settings.options?.terminalCarbons ?? false + this.plugin.settings.smilesDrawerOptions.moleculeOptions + .terminalCarbons ?? false ) .onChange(async (value) => { - this.plugin.settings.options.terminalCarbons = value; + this.plugin.settings.smilesDrawerOptions.moleculeOptions.terminalCarbons = + value; + this.plugin.settings.rdkitOptions.explicitMethyl = + value; + this.plugin.settings.commonOptions.explicitMethyl = + value; await this.plugin.saveSettings(); - setDrawer({ - ...DEFAULT_SD_OPTIONS, - ...this.plugin.settings.options, - }); + this.updateCore(); + onSettingsChange(); + }) + ); + + new Setting(containerEl) + .setName(i18n.t('settings.advanced.explicit-hydrogen.name')) + .setDesc(i18n.t('settings.advanced.explicit-hydrogen.description')) + .addToggle((toggle) => + toggle + .setValue( + this.plugin.settings.smilesDrawerOptions.moleculeOptions + .explicitHydrogens ?? false + ) + .onChange(async (value) => { + this.plugin.settings.smilesDrawerOptions.moleculeOptions.explicitHydrogens = + value; + this.plugin.settings.commonOptions.explicitHydrogens = + value; + await this.plugin.saveSettings(); + this.updateCore(); onSettingsChange(); }) ); @@ -250,6 +288,36 @@ export class ChemSettingTab extends PluginSettingTab { }); }); + new Setting(containerEl) + .setName(i18n.t('settings.inline.title')) + .setHeading(); + + new Setting(containerEl) + .setName(i18n.t('settings.inline.enable.name')) + .setDesc(i18n.t('settings.inline.enable.description')) + .addToggle((toggle) => { + toggle + .setValue(this.plugin.settings.inlineSmiles) + .onChange(async (value) => { + this.plugin.settings.inlineSmiles = value; + await this.plugin.saveSettings(); + onSettingsChange(); + }); + }); + + new Setting(containerEl) + .setName(i18n.t('settings.inline.prefix.name')) + .setDesc(i18n.t('settings.inline.prefix.description')) + .addText((text) => { + text.setValue(this.plugin.settings.inlineSmilesPrefix).onChange( + async (value) => { + this.plugin.settings.inlineSmilesPrefix = value; + await this.plugin.saveSettings(); + onSettingsChange(); + } + ); + }); + const onSettingsChange = () => { preview.updateSettings(this.plugin.settings); preview.render(); @@ -263,20 +331,19 @@ export class ChemSettingTab extends PluginSettingTab { .addText((text) => text .setValue( - this.plugin.settings.options.width?.toString() ?? + this.plugin.settings.commonOptions.width?.toString() ?? '300' ) .onChange(async (value) => { if (value == '') { value = '300'; } - this.plugin.settings.options.width = + this.plugin.settings.commonOptions.width = + parseInt(value); + this.plugin.settings.smilesDrawerOptions.moleculeOptions.width = parseInt(value); await this.plugin.saveSettings(); - setDrawer({ - ...DEFAULT_SD_OPTIONS, - ...this.plugin.settings.options, - }); + this.updateCore(); onSettingsChange(); }) ); @@ -289,14 +356,16 @@ export class ChemSettingTab extends PluginSettingTab { .setDesc(i18n.t('settings.unify-image-width.description')) .addText((text) => { text.setValue( - this.plugin.settings?.imgWidth.toString() ?? '300' + this.plugin.settings.commonOptions.unifiedWidth?.toString() ?? + '300' ) .setPlaceholder('300') .onChange(async (value) => { if (value == '') { value = '300'; } - this.plugin.settings.imgWidth = parseInt(value); + this.plugin.settings.commonOptions.unifiedWidth = + parseInt(value); await this.plugin.saveSettings(); onSettingsChange(); }); @@ -305,11 +374,17 @@ export class ChemSettingTab extends PluginSettingTab { // Initialize preview.render(); - if ((this.plugin.settings.options?.scale ?? 1) == 0) unifyImageWidth(); + if ( + (this.plugin.settings.smilesDrawerOptions.moleculeOptions.scale ?? + 1) == 0 + ) + unifyImageWidth(); else unifyBondLength(); } hide(): void { refreshBlocks(); } + + updateCore = () => updateCoreSettings(this.plugin.settings); } diff --git a/src/settings/base.ts b/src/settings/base.ts index 0a29ab9..e0f54c5 100644 --- a/src/settings/base.ts +++ b/src/settings/base.ts @@ -1,355 +1,78 @@ -// Global consts -export const SAMPLE_SMILES_1 = 'OC(=O)C(C)=CC1=CC=CC=C1'; -export const SAMPLE_SMILES_2 = - 'OC(C(=O)O[C@H]1C[N+]2(CCCOC3=CC=CC=C3)CCC1CC2)(C1=CC=CS1)C1=CC=CS1'; -export const SETTINGS_VERSION = 'v2'; +import { ChemPluginSettingsV1, DEFAULT_SETTINGS_V1 } from './v1'; +import { ChemPluginSettingsV2, DEFAULT_SETTINGS_V2 } from './v2'; +import { ChemPluginSettingsV3, DEFAULT_SETTINGS_V3 } from './v3'; -// Plugin settings -export interface ChemPluginSettings { - version: string; - darkTheme: string; - lightTheme: string; - sample1: string; - sample2: string; - imgWidth: number; - copy: { - scale: number; - transparent: boolean; - theme: string; - }; - dataview: boolean; - options: Partial; -} +export type ChemPluginSettings = ChemPluginSettingsV3; +export const DEFAULT_SETTINGS = DEFAULT_SETTINGS_V3; +export const SETTINGS_VERSION = 'v3'; -export const DEFAULT_SETTINGS: ChemPluginSettings = { - version: SETTINGS_VERSION, - darkTheme: 'dark', - lightTheme: 'light', - sample1: SAMPLE_SMILES_1, - sample2: SAMPLE_SMILES_2, - imgWidth: 300, - copy: { - scale: 2, - transparent: true, - theme: 'default', - }, - dataview: false, - options: {}, -}; +// const migrate_1_2 = (v1: ChemPluginSettingsV1): ChemPluginSettingsV2 => { +// v1 = { ...DEFAULT_SETTINGS_V1, ...v1 }; +// return { +// ...DEFAULT_SETTINGS_V2, +// darkTheme: v1.darkTheme, +// lightTheme: v1.lightTheme, +// sample1: v1.sample, +// imgWidth: parseInt(v1.width), +// }; +// }; -// Smiles-drawer options -// Reference: https://smilesdrawer.surge.sh/playground.html -export interface SMILES_DRAWER_OPTIONS { - width: number; - height: number; - scale: number; - bondThickness: number; - shortBondLength: number; - bondSpacing: number; - atomVisualization: 'default' | 'balls' | 'allballs'; - isomeric: boolean; - debug: boolean; - terminalCarbons: boolean; - explicitHydrogens: boolean; - overlapSensitivity: number; - overlapResolutionIterations: number; - compactDrawing: boolean; - fontFamily: string; - fontSizeLarge: number; - fontSizeSmall: number; - padding: number; - experimentalSSSR: boolean; - kkThreshold: number; - kkInnerThreshold: number; - kkMaxIteration: number; - kkMaxInnerIteration: number; - kkMaxEnergy: number; - themes: { - [key: string]: { - C: string; - O: string; - N: string; - F: string; - CL: string; - BR: string; - I: string; - P: string; - S: string; - B: string; - SI: string; - H: string; - BACKGROUND: string; - }; +const migrate_1_3 = (v1: ChemPluginSettingsV1): ChemPluginSettingsV3 => { + v1 = { ...DEFAULT_SETTINGS_V1, ...v1 }; + return { + ...DEFAULT_SETTINGS_V3, + darkTheme: v1.darkTheme, + lightTheme: v1.lightTheme, + sample1: v1.sample, + commonOptions: { + ...DEFAULT_SETTINGS_V3.commonOptions, + unifiedWidth: parseInt(v1.width), + }, }; -} +}; -export const DEFAULT_SD_OPTIONS: SMILES_DRAWER_OPTIONS = { - width: 300, - height: 300, - scale: 1.0, - bondThickness: 1, - shortBondLength: 0.8, - bondSpacing: 5.1, - atomVisualization: 'default', - isomeric: true, - debug: false, - terminalCarbons: false, - explicitHydrogens: true, - overlapSensitivity: 0.42, - overlapResolutionIterations: 1, - compactDrawing: false, - fontFamily: 'Arial, Helvetica, sans-serif', - fontSizeLarge: 11, - fontSizeSmall: 3, - padding: 2, - experimentalSSSR: true, - kkThreshold: 0.1, - kkInnerThreshold: 0.1, - kkMaxIteration: 20000, - kkMaxInnerIteration: 50, - kkMaxEnergy: 1000000000, - themes: { - dark: { - C: '#fff', - O: '#e74c3c', - N: '#3498db', - F: '#27ae60', - CL: '#16a085', - BR: '#d35400', - I: '#8e44ad', - P: '#d35400', - S: '#f1c40f', - B: '#e67e22', - SI: '#e67e22', - H: '#aaa', - BACKGROUND: '#141414', - }, - light: { - C: '#222', - O: '#e74c3c', - N: '#3498db', - F: '#27ae60', - CL: '#16a085', - BR: '#d35400', - I: '#8e44ad', - P: '#d35400', - S: '#f1c40f', - B: '#e67e22', - SI: '#e67e22', - H: '#666', - BACKGROUND: '#fff', - }, - oldschool: { - C: '#000', - O: '#000', - N: '#000', - F: '#000', - CL: '#000', - BR: '#000', - I: '#000', - P: '#000', - S: '#000', - B: '#000', - SI: '#000', - H: '#000', - BACKGROUND: '#fff', - }, - 'oldschool-dark': { - C: '#fff', - O: '#fff', - N: '#fff', - F: '#fff', - CL: '#fff', - BR: '#fff', - I: '#fff', - P: '#fff', - S: '#fff', - B: '#fff', - SI: '#fff', - H: '#fff', - BACKGROUND: '#000', - }, - solarized: { - C: '#586e75', - O: '#dc322f', - N: '#268bd2', - F: '#859900', - CL: '#16a085', - BR: '#cb4b16', - I: '#6c71c4', - P: '#d33682', - S: '#b58900', - B: '#2aa198', - SI: '#2aa198', - H: '#657b83', - BACKGROUND: '#fff', - }, - 'solarized-dark': { - C: '#93a1a1', - O: '#dc322f', - N: '#268bd2', - F: '#859900', - CL: '#16a085', - BR: '#cb4b16', - I: '#6c71c4', - P: '#d33682', - S: '#b58900', - B: '#2aa198', - SI: '#2aa198', - H: '#839496', - BACKGROUND: '#fff', +const migrate_2_3 = (v2: ChemPluginSettingsV2): ChemPluginSettingsV3 => { + v2 = { ...DEFAULT_SETTINGS_V2, ...v2 }; + return { + ...DEFAULT_SETTINGS_V3, + darkTheme: v2.darkTheme, + lightTheme: v2.lightTheme, + sample1: v2.sample1, + sample2: v2.sample2, + copy: { + scale: v2.copy.scale, + transparent: v2.copy.transparent, + theme: v2.copy.theme, }, - matrix: { - C: '#678c61', - O: '#2fc079', - N: '#4f7e7e', - F: '#90d762', - CL: '#82d967', - BR: '#23755a', - I: '#409931', - P: '#c1ff8a', - S: '#faff00', - B: '#50b45a', - SI: '#409931', - H: '#426644', - BACKGROUND: '#fff', + dataview: v2.dataview, + inlineSmiles: v2.inlineSmiles, + inlineSmilesPrefix: v2.inlineSmilesPrefix, + commonOptions: { + width: v2.options.width, + scale: v2.options.scale, + unifiedWidth: v2.imgWidth, + compactDrawing: v2.options.compactDrawing, + explicitHydrogens: v2.options.explicitHydrogens, + explicitMethyl: v2.options.terminalCarbons, }, - github: { - C: '#24292f', - O: '#cf222e', - N: '#0969da', - F: '#2da44e', - CL: '#6fdd8b', - BR: '#bc4c00', - I: '#8250df', - P: '#bf3989', - S: '#d4a72c', - B: '#fb8f44', - SI: '#bc4c00', - H: '#57606a', - BACKGROUND: '#fff', + smilesDrawerOptions: { + ...DEFAULT_SETTINGS_V3.smilesDrawerOptions, + moleculeOptions: v2.options, }, - carbon: { - C: '#161616', - O: '#da1e28', - N: '#0f62fe', - F: '#198038', - CL: '#007d79', - BR: '#fa4d56', - I: '#8a3ffc', - P: '#ff832b', - S: '#f1c21b', - B: '#8a3800', - SI: '#e67e22', - H: '#525252', - BACKGROUND: '#fff', + rdkitOptions: { + explicitMethyl: v2.options.terminalCarbons, }, - cyberpunk: { - C: '#ea00d9', - O: '#ff3131', - N: '#0abdc6', - F: '#00ff9f', - CL: '#00fe00', - BR: '#fe9f20', - I: '#ff00ff', - P: '#fe7f00', - S: '#fcee0c', - B: '#ff00ff', - SI: '#ffffff', - H: '#913cb1', - BACKGROUND: '#fff', - }, - gruvbox: { - C: '#665c54', - O: '#cc241d', - N: '#458588', - F: '#98971a', - CL: '#79740e', - BR: '#d65d0e', - I: '#b16286', - P: '#af3a03', - S: '#d79921', - B: '#689d6a', - SI: '#427b58', - H: '#7c6f64', - BACKGROUND: '#fbf1c7', - }, - 'gruvbox-dark': { - C: '#ebdbb2', - O: '#cc241d', - N: '#458588', - F: '#98971a', - CL: '#b8bb26', - BR: '#d65d0e', - I: '#b16286', - P: '#fe8019', - S: '#d79921', - B: '#8ec07c', - SI: '#83a598', - H: '#bdae93', - BACKGROUND: '#282828', - }, - 'catppuccin-dark': { - C: '#cdd6f4', - O: '#f38ba8', - N: '#89b4fa', - F: '#f9e2af', - CL: '#cba6f7', - BR: '#a6e3a1', - I: '#b4befe', - P: '#fab387', - S: '#f5e0dc', - B: '#eba0ac', - SI: '#89dceb', - H: '#94e2d5', - BACKGROUND: '#1e1e2e', - }, - 'catppuccin-light': { - C: '#4c4f69', - O: '#d20f39', - N: '#1e66f5', - F: '#df8e1d', - CL: '#8839ef', - BR: '#40a02b', - I: '#7287fd', - P: '#fe640b', - S: '#dc8a78', - B: '#e64553', - SI: '#04a5e5', - H: '#179299', - BACKGROUND: '#eff1f5', - }, - custom: { - C: '#222', - O: '#e74c3c', - N: '#3498db', - F: '#27ae60', - CL: '#16a085', - BR: '#d35400', - I: '#8e44ad', - P: '#d35400', - S: '#f1c40f', - B: '#e67e22', - SI: '#e67e22', - H: '#666', - BACKGROUND: '#fff', - }, - }, + }; +}; + +const migrate_3_3 = (draft: ChemPluginSettingsV3): ChemPluginSettingsV3 => { + return { ...DEFAULT_SETTINGS, ...draft }; }; -export const themeList = { - light: 'Light', - dark: 'Dark', - oldschool: 'Oldschool', - 'oldschool-dark': 'Oldschool Dark', - solarized: 'Solarized', - 'solarized-dark': 'Solarized Dark', - matrix: 'Matrix', - github: 'GitHub', - carbon: 'Carbon', - cyberpunk: 'Cyberpunk', - gruvbox: 'Gruvbox', - 'gruvbox-dark': 'Gruvbox Dark', - 'catppuccin-light': 'Catppuccin Latte', - 'catppuccin-dark': 'Catppuccin Mocha', +export const migrateSettings = (draft: any): ChemPluginSettingsV3 => { + if (!draft || Object.keys(draft).length === 0) return DEFAULT_SETTINGS; + if (!('version' in draft)) return migrate_1_3(draft); // v1 + else if (draft.version === 'v2') return migrate_2_3(draft); + else if (draft.version === 'v3') return migrate_3_3(draft); // current + return DEFAULT_SETTINGS; // consider branch coverage rate }; diff --git a/src/settings/update.ts b/src/settings/update.ts deleted file mode 100644 index 00511de..0000000 --- a/src/settings/update.ts +++ /dev/null @@ -1,55 +0,0 @@ -interface ChemPluginSettingsV1 { - darkTheme: string; - lightTheme: string; - sample: string; - width: string; -} - -// const DEFAULT_SETTINGS_V1: ChemPluginSettingsV1 = { -// darkTheme: 'dark', -// lightTheme: 'light', -// sample: 'CC(=O)NC1=C-C=C-C=C1-C(=O)O', -// width: '300', -// }; - -interface ChemPluginSettingsV2 { - version: string; - darkTheme: string; - lightTheme: string; - sample1: string; - sample2: string; - imgWidth: number; - copy: { - scale: number; - transparent: boolean; - theme: string; - }; - dataview: boolean; - options: object; -} - -const DEFAULT_SETTINGS_V2: ChemPluginSettingsV2 = { - version: 'v2', - darkTheme: 'dark', - lightTheme: 'light', - sample1: 'OC(=O)C(C)=CC1=CC=CC=C1', - sample2: - 'OC(C(=O)O[C@H]1C[N+]2(CCCOC3=CC=CC=C3)CCC1CC2)(C1=CC=CS1)C1=CC=CS1', - imgWidth: 300, - copy: { - scale: 2, - transparent: true, - theme: 'default', - }, - dataview: false, - options: {}, -}; - -export const updateSettingsVersion = (stale: ChemPluginSettingsV1) => { - const result = { ...DEFAULT_SETTINGS_V2 }; - result.darkTheme = stale.darkTheme; - result.lightTheme = stale.lightTheme; - result.sample1 = stale.sample; - result.imgWidth = parseInt(stale.width); - return result; -}; diff --git a/src/settings/v1.ts b/src/settings/v1.ts new file mode 100644 index 0000000..5df6469 --- /dev/null +++ b/src/settings/v1.ts @@ -0,0 +1,12 @@ +export interface ChemPluginSettingsV1 { + darkTheme: string; + lightTheme: string; + sample: string; + width: string; +} +export const DEFAULT_SETTINGS_V1: ChemPluginSettingsV1 = { + darkTheme: 'dark', + lightTheme: 'light', + sample: 'CC(=O)NC1=C-C=C-C=C1-C(=O)O', + width: '300', +}; diff --git a/src/settings/v2.ts b/src/settings/v2.ts new file mode 100644 index 0000000..1275aec --- /dev/null +++ b/src/settings/v2.ts @@ -0,0 +1,37 @@ +import { MoleculeOptions } from '../lib/core/smilesDrawerOptions'; + +export interface ChemPluginSettingsV2 { + version: string; + darkTheme: string; + lightTheme: string; + sample1: string; + sample2: string; + imgWidth: number; + copy: { + scale: number; + transparent: boolean; + theme: string; + }; + dataview: boolean; + inlineSmiles: boolean; + inlineSmilesPrefix: string; + options: Partial; +} +export const DEFAULT_SETTINGS_V2: ChemPluginSettingsV2 = { + version: 'v2', + darkTheme: 'dark', + lightTheme: 'light', + sample1: 'OC(=O)C(C)=CC1=CC=CC=C1', + sample2: + 'OC(C(=O)O[C@H]1C[N+]2(CCCOC3=CC=CC=C3)CCC1CC2)(C1=CC=CS1)C1=CC=CS1', + imgWidth: 300, + copy: { + scale: 2, + transparent: true, + theme: 'default', + }, + dataview: false, + inlineSmiles: false, + inlineSmilesPrefix: '$smiles=', + options: {}, +}; diff --git a/src/settings/v3.ts b/src/settings/v3.ts new file mode 100644 index 0000000..3db1e3b --- /dev/null +++ b/src/settings/v3.ts @@ -0,0 +1,62 @@ +import { SmilesDrawerOptions } from '../lib/core/smilesDrawerOptions'; +import { RDKitOptions } from '../lib/core/rdkitOptions'; + +export interface ChemPluginSettingsV3 { + version: string; + darkTheme: string; + lightTheme: string; + sample1: string; + sample2: string; + copy: { + scale: number; + transparent: boolean; + theme: string; + }; + dataview: boolean; + inlineSmiles: boolean; + inlineSmilesPrefix: string; + core: 'smiles-drawer' | 'rdkit'; + commonOptions: Partial; + smilesDrawerOptions: SmilesDrawerOptions; + rdkitOptions: Partial; +} + +interface CommonOptions { + width: number; + scale: number; + unifiedWidth: number; + compactDrawing: boolean; + explicitHydrogens: boolean; + explicitMethyl: boolean; +} + +export const DEFAULT_SETTINGS_V3: ChemPluginSettingsV3 = { + version: 'v3', + darkTheme: 'dark', + lightTheme: 'light', + sample1: 'OC(=O)C(C)=CC1=CC=CC=C1', + sample2: + 'OC(C(=O)O[C@H]1C[N+]2(CCCOC3=CC=CC=C3)CCC1CC2)(C1=CC=CS1)C1=CC=CS1', + copy: { + scale: 2, + transparent: true, + theme: 'default', + }, + dataview: false, + inlineSmiles: false, + inlineSmilesPrefix: '$smiles=', + core: 'smiles-drawer', + commonOptions: { + width: 300, + scale: 1, + unifiedWidth: 300, + compactDrawing: false, + explicitHydrogens: false, + explicitMethyl: false, + }, + smilesDrawerOptions: { + moleculeOptions: {}, + reactionOptions: {}, + }, + rdkitOptions: {}, +}; diff --git a/tsconfig.json b/tsconfig.json index b31602c..6203bf1 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -12,6 +12,7 @@ "isolatedModules": true, "strictNullChecks": true, "resolveJsonModule": true, + "allowSyntheticDefaultImports": true, "lib": [ "DOM", "ES5", @@ -21,5 +22,5 @@ }, "include": [ "**/*.ts" - ] + ], } \ No newline at end of file diff --git a/typings/githubAsset.d.ts b/typings/githubAsset.d.ts new file mode 100644 index 0000000..b0f3428 --- /dev/null +++ b/typings/githubAsset.d.ts @@ -0,0 +1,36 @@ +export interface githubAsset { + url: string; + id: number; + node_id: string; + name: string; + label?: null; + uploader: Uploader; + content_type: string; + state: string; + size: number; + download_count: number; + created_at: string; + updated_at: string; + browser_download_url: string; +} + +interface Uploader { + login: string; + id: number; + node_id: string; + avatar_url: string; + gravatar_id: string; + url: string; + html_url: string; + followers_url: string; + following_url: string; + gists_url: string; + starred_url: string; + subscriptions_url: string; + organizations_url: string; + repos_url: string; + events_url: string; + received_events_url: string; + type: string; + site_admin: boolean; +} diff --git a/typings/obsidian.d.ts b/typings/obsidian.d.ts new file mode 100644 index 0000000..fbb9d5e --- /dev/null +++ b/typings/obsidian.d.ts @@ -0,0 +1,13 @@ +import 'obsidian'; +import { Plugin } from 'obsidian'; + +declare module 'obsidian' { + interface App { + plugins: { + getPlugin(name: string): Plugin | null; + plugins: { + [id: string]: Plugin; + }; + }; + } +} diff --git a/typings/rdkit.d.ts b/typings/rdkit.d.ts new file mode 100644 index 0000000..95bfcca --- /dev/null +++ b/typings/rdkit.d.ts @@ -0,0 +1,38 @@ +import '@rdkit/rdkit'; +import { RDKitLoader, RDKitModule } from '@rdkit/rdkit'; + +declare global { + interface Window { + RDKit: RDKitModule; + initRDKitModule: RDKitLoader; + } +} + +declare module '@rdkit/rdkit' { + interface RDKitModule { + get_rxn(source: string): JSReaction; + } + interface JSMol { + add_hs_in_place(): void; + } + interface JSReaction { + draw_to_canvas( + canvas: HTMLCanvasElement, + width: number, + height: number + ): void; + draw_to_canvas_with_highlights( + canvas: HTMLCanvasElement, + details: string + ): void; + draw_to_canvas_with_offset( + canvas: HTMLCanvasElement, + offsetx: number, + offsety: number, + width: number, + height: number + ): void; + get_svg(): string; + get_svg_with_highlights(details: string): string; + } +} diff --git a/typings/smilesDrawer.d.ts b/typings/smilesDrawer.d.ts new file mode 100644 index 0000000..876382c --- /dev/null +++ b/typings/smilesDrawer.d.ts @@ -0,0 +1,75 @@ +declare module 'smiles-drawer' { + class SmiDrawer { + constructor(moleculeOptions?: object, reactionOptions?: object); + static apply( + moleculeOptions?: object, + reactionOptions?: object, + attribute?: string | undefined, + theme?: string, + successCallback?: CallableFunction, + errorCallback?: CallableFunction + ): void; + apply( + attribute?: string, + theme?: string, + successCallback?: CallableFunction, + errorCallback?: CallableFunction + ): void; + draw( + smiles: string, + target: + | HTMLElement + | SVGElement + | HTMLImageElement + | string + | 'svg' + | 'canvas' + | 'img' + | null, + theme?: string, + successCallback?: CallableFunction, + errorCallback?: CallableFunction, + weights?: number[] | object + ): void; + drawMolecule( + smiles: string, + target: + | HTMLElement + | SVGElement + | HTMLImageElement + | string + | 'svg' + | 'canvas' + | 'img' + | null, + theme: string, + weights: number[] | object, + callback: CallableFunction + ): void; + drawReaction( + smiles: string, + target: + | HTMLElement + | SVGElement + | HTMLImageElement + | string + | 'svg' + | 'canvas' + | 'img' + | null, + theme: string, + settings: object, // reaction settings + weights: number[] | object, + callback: CallableFunction + ): void; + svgToCanvas( + svg: SVGElement, + canvas?: HTMLCanvasElement + ): HTMLCanvasElement; + svgToImg(svg: SVGElement, img?: HTMLImageElement): HTMLImageElement; + getDimensions( + element: HTMLImageElement | HTMLCanvasElement | SVGElement, + svg: SVGElement + ): { w: number; h: number }; + } +}