Where does BioPython store information related to various chemical molecules?
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11 days ago
user366312 ▴ 10

If we reconstruct a protein from a PDB file, is it enough to have a PDB file, or do we need more info external to the PDB?

Take, for example, the BioPython framework. If any info is needed external to the PDB files, where does this framework store them?

Can I open and check to see those files?

protein pdb python biopython • 813 views
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What do you mean by 'reconstruct'? Biopython is fundamentally just a parser, and PDB files are just text files. If the PDB file doesn't contain the information, biopython can't really know it (unless you invoke some other processing tool which then stores that info in the PDB spec).

There are some 'plugins' of sorts that allow you to view PDB structures, but these are generally separate tools that biopython just happens to expose an API for.

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Reconstruct means I want to read PDB files and create an abstract data type of protein that will mimic the real-world protein excluding H-bonds.

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Perhaps I'm being a bit slow here, but I don't think that really answers the question. Mimic in what way? Biopython already has an object model (an abstraction of data) which captures features of the protein from the PDB (chain IDs, hetero atoms, ligands and so on as relevant).

You can represent it however you like, it just comes down to what you want to do with it as to which is the 'correct' way.

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I don't care. Those websites are not owned by Biostar. So, either answer or stop policing.

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As long as you follow bad etiquette, I'll keep pointing it out. The next time you cross-post, your post on biostars will be removed and your account will be suspended.

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I really don't care. You are not answering my questions. So, you are not helping me. You are just abusing me while policing. You are doing this for fun.

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Besides, this website is the least useful one. Whenever I post a question, I either don't get an answer or get irrelevant answers. Most of the answers posted in this forum are totally useless.

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For example, three answers posted in this thread are totally useless.

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OK, goodbye

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11 days ago
Jiyao Wang ▴ 280

I am not sure about BioPython. But here is the JavaScript function to determine covalent bonds "hasCovalentBond()" at https://github.com/ncbi/icn3d/blob/master/src/utils/utilsCls.js. The covalent radii of atoms "this.covalentRadii" are at https://github.com/ncbi/icn3d/blob/master/src/utils/parasCls.js.

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Suppose I want to read PDB files and create an abstract data type of protein that mimics real-world protein, excluding H-bonds.

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The data structure depends on which viewer you want to use.

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11 days ago

To get more information on a protein go to uniprot:

https://www.uniprot.org/

Then here is the European Protein Database

https://www.ebi.ac.uk/pdbe/

These databases store information, whereas BioPython helps parse and process the information.

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