Reaction Viewer
在 VS Code 1.84.1 及以上版本中并排比较、对齐和播放分子轨迹。
Compare, align, and play molecular trajectories side by side in VS Code 1.84.1 or later.
中文 · English
中文
Reaction Viewer 是一个 VS Code 扩展，用于通过 3Dmol.js 并排查看和比较 1–3 个 XYZ 或文本格式的 TRJ 分子轨迹。查看器所需资源均包含在扩展中，运行时无需联网。
功能
- 从资源管理器选择 1–3 个
.xyz / .trj 文件，右键打开；也可以从命令面板运行 Reaction Viewer: Open Molecular Comparison。
- 使用球棍模型并排显示多个 3Dmol.js 视图。
- 联动旋转、平移和缩放：操作任意面板，其他面板会同步视角。
- Center XYZ：逐帧移除每个结构的几何中心偏移。
- Kabsch align：根据第一帧的原子顺序，将所有选中轨迹刚性对齐到第一个文件，并将变换应用到全部帧。
- 多帧轨迹共享播放、帧滑块和播放速度控制。
- 根据元素和距离推测金属–配体接触，并用分离清晰的彩色虚线显示；工具栏提供 Strict、Normal 和 Wide 三档距离阈值，关闭 Metal contacts 会真正隐藏这些接触。
- 当文件名为
reactant.xyz、transition_state.xyz 和 product.xyz 时，自动启用反应模式，显示能量曲线、正逆反应能垒、反应能和反应中心。
金属–配体接触基于元素类型与共价半径缩放距离进行启发式推测，并在轨迹中使用滞回来减少阈值附近的闪烁。普通 XYZ 不包含键级、电荷或配位信息，因此虚线表示推测的接触，而不是对配位键类型的确定结论。默认 Normal 适用于常见过渡金属配合物；使用 Strict 可减少误判，使用 Wide 可显示较长的离子接触。氢接触和金属–金属接触不会被归入此类。
安装与使用
- 在 VS Code 中打开扩展视图。
- 从右上角
… 菜单选择 Install from VSIX...，然后选择生成的 .vsix 文件。
- 在资源管理器中选择最多三个
.xyz 或 .trj 文件并右键。
- 选择 Reaction Viewer: Open Molecular Comparison。
也可以先打开文件所在工作区，再从命令面板执行同名命令并选择轨迹文件。
反应能与反应中心
在三个反应文件的 XYZ 注释行中分别提供能量，例如：
energy=-100.123456 hartree
支持 hartree / Ha / a.u.、eV、kcal/mol 和 kJ/mol。可换算的能量统一显示为相对 kcal/mol。如果不提供单位，则三个值都必须无单位，能量曲线会使用通用能量单位。
反应中心通过原子顺序比较反应物与产物中基于距离推测的连接关系，包括非金属共价候选和金属–配体接触。显示采用三级聚焦：核心原子和键保留元素原色并略微放大，2.5 Å 内的局部环境中度淡化，其余结构高度淡化；核心原子外使用低饱和金色线框光环标记。过渡态中的部分成键使用元素原色虚线表示，不使用额外的键改色。三个文件必须包含相同的原子，并保持相同顺序。
支持的轨迹格式
.xyz 和 .trj 当前均按多帧 XYZ 文本解析：
3
frame 1
O 0.000 0.000 0.000
H 0.958 0.000 0.000
H -0.240 0.927 0.000
3
frame 2
...
每一帧必须具有相同的原子数量和元素顺序。二进制 TRJ 需要对应格式的拓扑和解析器，目前不支持。
开发与打包
npm install
npm test
npm run compile
npx @vscode/vsce package
在 VS Code 中打开项目目录并按 F5，即可启动 Extension Development Host 进行调试。
English
Reaction Viewer is a VS Code 1.84.1+ extension for viewing and comparing one to three XYZ or text-based TRJ molecular trajectories side by side with 3Dmol.js. All viewer assets are bundled with the extension, so no network connection is required at runtime.
Features
- Select 1–3
.xyz / .trj files in the Explorer and open them from the context menu, or run Reaction Viewer: Open Molecular Comparison from the Command Palette.
- Compare structures in side-by-side 3Dmol.js stick-and-sphere viewers.
- Linked rotation, pan, and zoom: manipulate any panel and the others follow.
- Center XYZ removes each frame's centroid independently.
- Kabsch align rigidly aligns every selected trajectory to the first file using the atom order in the first frame, then applies the transform to all frames.
- Shared playback, frame scrubbing, and speed controls for multi-frame trajectories.
- Inferred metal–ligand contacts shown as clearly separated, element-colored dashed lines; Strict, Normal, and Wide distance ranges are available, and disabling Metal contacts hides them completely.
- Automatic reaction mode for files named
reactant.xyz, transition_state.xyz, and product.xyz, including an energy profile, forward and reverse barriers, reaction energy, and reaction-center highlighting.
Metal–ligand contacts are inferred heuristically from element types and covalent-radius-scaled distances, with trajectory hysteresis to reduce flicker near a cutoff. Plain XYZ data has no bond order, charge, or coordination metadata, so a dashed line represents an inferred contact rather than a definitive bond classification. The default Normal range works well for common transition-metal complexes; use Strict to reduce false positives or Wide for longer ionic contacts. Hydrogen and metal–metal contacts are not included in this category.
Install and use
- Open the Extensions view in VS Code.
- Choose Install from VSIX... from the
… menu, then select the generated .vsix file.
- Select up to three
.xyz or .trj files in the Explorer and right-click.
- Choose Reaction Viewer: Open Molecular Comparison.
Alternatively, open the containing workspace, run the same command from the Command Palette, and select the trajectory files.
Reaction energies and centers
Put an energy on the XYZ comment line of all three reaction files, for example:
energy=-100.123456 hartree
Accepted units are hartree / Ha / a.u., eV, kcal/mol, and kJ/mol. Convertible values are reported as relative kcal/mol. If no unit is supplied, all three values must be unitless and the profile is shown in generic energy units.
The reaction center is inferred by comparing distance-based connectivity in the reactant and product using atom order, including both nonmetal covalent candidates and metal–ligand contacts. A three-level focus keeps core atoms and bonds at their normal element colors and slightly enlarged, shows the local environment within 2.5 Å at medium opacity, and strongly fades distant context. Low-saturation gold wireframe halos mark the core atoms. Partial transition-state bonds use element-colored dashed lines without bond recoloring. All three files must contain the same atoms in the same order.
Both .xyz and .trj are currently parsed as multi-frame XYZ text:
3
frame 1
O 0.000 0.000 0.000
H 0.958 0.000 0.000
H -0.240 0.927 0.000
3
frame 2
...
Every frame must contain the same number of atoms in the same element order. Binary TRJ variants require a format-specific topology and parser and are not currently supported.
Develop and package
npm install
npm test
npm run compile
npx @vscode/vsce package
Open this folder in VS Code and press F5 to start an Extension Development Host.
