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我正在从事生物项目。
我有.pdb（蛋白质数据库）文件，其中包含有关分子的信息。

我想找出.pdb文件中分子的以下内容：

  1. 分子质量。
  2. H键供体。
  3. H键受体。
  4. 日志P。
  5. 折射率。

python中是否有任何模块可以处理.pdb文件以找到这个？
如果没有，那么任何人都可以让我知道我该怎么做？

我发现了一些类似的模块sequtils，protienparam但他们不做这样的事情。
我已经先研究然后发布，所以，请不要投反对票。
请评论，如果你仍然反对你为什么这样做。

提前致谢。

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3 回答 3

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PDBXMLfile还输出一个PDBML可以使用xml解析库轻松解析的文件

http://pdbml.pdb.org/
于 2013-02-13T02:12:48.667 回答
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A pdb file can contain pretty much anything. A lot of projects allows you to parse them. Some specific to biology and pdb files, other less specific but that will allow you to do more (setup calculations, measure distances, angles, etc.).

I think you got downvoted because these projects are numerous: you are not the only one wanting to do that so the chances that something perfectly fitting your needs exists are really high.

That said, if you just want to parse pdb files for this specific need, just do it yourself:

  • Open the files with a text editor.
  • Identify where the relevant data are (keywords, etc.).
  • Make a Python function that opens the file and look for the keywords.
  • Extract the figures from the file.
  • Done.

This can be done with a short script written in less than 10 minutes (other reason why downvoting).

于 2013-02-06T09:51:57.850 回答
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我不知道它是否符合您的需求，但Biopython看起来可能会有所帮助。

于 2013-02-06T09:43:09.373 回答