Yu Zeyun, Holst Michael J, Cheng Yuhui, McCammon J Andrew
Department of Mathematics, University of California, San Diego, La Jolla, CA 92093, United States.
J Mol Graph Model. 2008 Jun;26(8):1370-80. doi: 10.1016/j.jmgm.2008.01.007. Epub 2008 Feb 7.
We describe a chain of algorithms for molecular surface and volumetric mesh generation. We take as inputs the centers and radii of all atoms of a molecule and the toolchain outputs both triangular and tetrahedral meshes that can be used for molecular shape modeling and simulation. Experiments on a number of molecules are demonstrated, showing that our methods possess several desirable properties: feature-preservation, local adaptivity, high quality, and smoothness (for surface meshes). We also demonstrate an example of molecular simulation using the finite element method and the meshes generated by our method. The approaches presented and their implementations are also applicable to other types of inputs such as 3D scalar volumes and triangular surface meshes with low quality, and hence can be used for generation/improvement of meshes in a broad range of applications.
我们描述了一系列用于分子表面和体网格生成的算法。我们将分子中所有原子的中心和半径作为输入，该工具链输出可用于分子形状建模和模拟的三角形和四面体网格。展示了对多个分子的实验，表明我们的方法具有几个理想的特性：特征保留、局部适应性、高质量和平滑性（对于表面网格）。我们还展示了一个使用有限元方法和我们生成的网格进行分子模拟的示例。所提出的方法及其实现也适用于其他类型的输入，例如低质量的3D标量体积和三角形表面网格，因此可用于广泛应用中的网格生成/改进。
