Effective visualization of small molecules is paramount in conveying concepts and results in cheminformatics. Scalable vector graphics (SVG) are preferred for creating such visualizations, as SVGs can be easily altered in post-production and exported to other formats. A wide spectrum of software applications already exist that can visualize molecules, and customize these visualizations, in many ways. However, software packages that can output projected 3D models onto a 2D canvas directly as SVG, while being programmatically accessible from Python, are lacking. Here, we introduce CineMol, which can draw vectorized approximations of three-dimensional small molecule models in seconds, without triangulation or ray tracing, resulting in files of around 50–300 kilobytes per molecule model for compounds with up to 45 heavy atoms. The SVGs outputted by CineMol can be readily modified in popular vector graphics editing software applications. CineMol is written in Python and can be incorporated into any existing Python cheminformatics workflow, as it only depends on native Python libraries. CineMol also provides programmatic access to all its internal states, allowing for per-atom and per-bond-based customization. CineMol’s capacity to programmatically create molecular visualizations suitable for post-production offers researchers and scientists a powerful tool for enhancing the clarity and visual impact of their scientific presentations and publications in cheminformatics, metabolomics, and related scientific disciplines. Scientific contribution We introduce CineMol, a Python-based tool that provides a valuable solution for cheminformatics researchers by enabling the direct generation of high-quality approximations of two-dimensional SVG visualizations from three-dimensional small molecule models, all within a programmable Python framework. CineMol offers a unique combination of speed, efficiency, and accessibility, making it an indispensable tool for researchers in cheminformatics, especially when working with SVG visualizations.

中文翻译：

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CineMol：以编程方式访问的直接 SVG 3D 小分子抽屉


小分子的有效可视化对于传达化学信息学的概念和结果至关重要。可扩展矢量图形 (SVG) 是创建此类可视化效果的首选，因为 SVG 可以在后期制作中轻松更改并导出为其他格式。已经存在多种可以可视化分子并以多种方式定制这些可视化的软件应用程序。然而，目前还缺乏能够将投影 3D 模型以 SVG 形式直接输出到 2D 画布上，同时可以通过 Python 以编程方式访问的软件包。在这里，我们介绍了 CineMol，它可以在几秒钟内绘制三维小分子模型的矢量化近似值，无需三角测量或光线追踪，从而为最多含有 45 个重原子的化合物生成每个分子模型约 50-300 KB 的文件。 CineMol 输出的 SVG 可以在流行的矢量图形编辑软件应用程序中轻松修改。 CineMol 用 Python 编写，可以合并到任何现有的 Python 化学信息学工作流程中，因为它仅依赖于本机 Python 库。 CineMol 还提供对其所有内部状态的编程访问，允许基于每个原子和每个键的定制。 CineMol 能够以编程方式创建适合后期制作的分子可视化，为研究人员和科学家提供了强大的工具，可增强其在化学信息学、代谢组学和相关科学学科中的科学演示和出版物的清晰度和视觉冲击力。 科学贡献 我们推出了 CineMol，这是一种基于 Python 的工具，它能够从三维小分子模型直接生成二维 SVG 可视化的高质量近似值，从而为化学信息学研究人员提供了有价值的解决方案，所有这些都在可编程的 Python 框架内进行。 CineMol 提供了速度、效率和可访问性的独特组合，使其成为化学信息学研究人员不可或缺的工具，尤其是在使用 SVG 可视化时。