如何将分子存储在记忆体中？ [英] How to store molecules in memory?

问题描述

我想将分子存储在记忆体中。这些可以是简单的分子：

 甲烷（CH4）
 CH债券长度：108.7 pm 
 HH角度：109度
  

而且更复杂的分子，如扑热息痛（C8H9NO2）：

如何将分子存储在记忆，包括所有的债券长度和角度？

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一个好主意，将atom-struct存储在数组中？还是有更好的方法？

解决方案

它看起来像某种图形数据结构：

• 一个分子有一组原子


• 原子由债券链接：
  
  
  
  
  • 债券可以是双倍，单一或三倍
  
  
  • 债券的长度
  
  
  • 债券有一个角度
  
  


• 这是一个循环图（例如，问题中的例子有一个交替的单键和双键）


• 它不是一个有向图（如果两个原子相互抵触，那么你接近债券就不重要）

通常，您将图形存储为一个节点数（原子）和边缘数组（bond）。节点和边缘都是指向结构体的指针。

节点（atom）将存储元素。

边缘（债券）将存储以下字段：

• 一个指向节点的指针


• 债券类型（双/单）


• 债券长度和角度

既然是您的数据结构不是有向图，您的数据结构将考虑A和B之间的边缘等于B和A之间的边。也就是说，对于给定的原子对，您会希望边缘数组包含来自A的边到B，从不从B到A。

I want to store molecules in memory. These can be simple molecules:

Methane (CH4)
C-H bond-length: 108.7 pm
H-H angle: 109 degrees

But also more complex molecules, like paracetamol (C8H9NO2):

How can I store molecules in memory, including all bond-lengths and angles?

---

A good idea to store atom-structs in an array? Or is there a better way?

解决方案

It looks like some kind of graph data structure:

• A molecule has a set of atoms
• Atoms are linked by bonds:
  • A bond can be double, single or tripple
  • A bond has a length
  • A bond has an angle
• It's a cyclic graph (for instance, the example in the question has a ring of alternating single and double bonds)
• It's not a directed graph (if two atoms are bonded, it doesn't matter from which end you approach the bond)

Typically you'd store a graph as an array of nodes (atoms) and an array of edges (bonds). Nodes and edges would both be pointers to structs.

A node (atom) would store the element.

An edge (bond) would store the following fields:

• A pair of pointers to nodes
• The type of bond (double/single)
• The bond length and angle

Since it's not a directed graph, your data structure would consider an edge between A and B to be equivalent to an edge between B and A. That is, for a given pair of atoms, you'd expect your edge array to contain an edge from A to B and never from B to A.

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