Tool:rna-pdb-tools - idea of Python library with utils (small linux-cmd-like programs) for RNA structures

Question

[mmagnus]

Hi,

I guess we all have gone through it. How to convert one "PDB format" into another "PDB format". You do CHARMM, you get some output, you want to do something else and you need to change to use it as an input to another program.

There can not be one converter/parser for all. Sometimes you need to convert CHARMM PDB files into ROSETTA-like. What to do?

For me it seems to be very useful to work with the library of functions, and then take what I need for a particular case as set of operations (like, --rosetta2generic). This project at github is pretty new, although it used some functions for a few years now.

You can use the functions as library, you can use the program (just a simple example) to run it in the console:

$ ./yapdb_parser.py  -h
usage: yapdb_parser [-h] [-r] [-c] [--getchain GETCHAIN] [--getseq]
                    [--rosetta2generic] [--getrnapuzzle]
                    file

positional arguments:
  file                 file

optional arguments:
  -h, --help           show this help message and exit
  -r, --report         get report
  -c, --clean          get clean structure
  --getchain GETCHAIN  get chain, .e.g A
  --getseq             get seq
  --rosetta2generic    convert ROSETTA-like format to generic pdb
  --getrnapuzzle       get RNApuzzle ready

Why I think it might be interesting for some of you:

• you see input & output files at github -- is this what you want to get?
• it's tested via Travis! -- it (should) always works as you just want!
• you miss a converter you would like to have? Just Do It Yourself - compose your converter/parser from LEGO brick-like functions, see --rosetta2generic)

I share it with you, maybe someone will find it useful.

It would be fun if anyone could contribute with one functions. We will see how it goes.

It useful for me right now. I used the project as a parser for our new RNA-protein & DNA-protein docking method (http://iimcb.genesilico.pl/NPDock/ ).

Join the project, comment, clone, pull, enjoy! If you have any comments, then you are well welcome.

I hope someone will find it useful.

Magnus

https://github.com/m4rx9/rna-pdb-tools

[João Rodrigues]

Great coincidence, both of us posting a similar set of tools at the same time. I'll have a look at yours, might be useful for us. Thanks for the README tip!

Answer 1

[mmagnus]

Hi, yes, yes, I have seen it. I even thought that you posted your tools when you had seen that I posted something analogous (which is very interesting!).

I uploaded a collection of script that I used for 2-3 years. First, I called it yapdb_parser.py (yet another PDB parser) and then I realized why I created my scripts, it is not reallly yet another parser. My scripts:

1. .. are customized to work with RNA structures, that's way very often PDB parsers downloaded from the Internet do not work as we want to (e.g. get sequence).
2. I wanted to create a library of functions and a simple "framework" (yapdb_parser.py) to compose your own parser/converters. I think it is the reason why there are some many pdb parsing tools. We all need very often to do something that might be used only for very specific application. Thus, a nice library it is a way to go (at least this is what I think).
3. I uploaded input and output files so every commit I test what will be the impact of the changes on files. I can easily spot if my change mess up some files. I think this is my Test Driven Development approach to keep the software trustful all the time.

Yeah, If you have time please take a look at my code. It would be nice if at some point the problem of PDB parsing/convert will be fun, not a pain :-)

[João Rodrigues]

Why didn't you rely on a more established library like Biopython? That has the parser already and you can write on top of it. From the top of my head, a get sequence should work there too.

Converting between formats is good, but the problem is the correspondence of atoms/types between force fields for example. Do you convert this or just the coordinate information?

Answer 2

[mmagnus]

This is what I wanted to accomplish, make a toolbox to analyze structures and simulations of RNA (https://github.com/mmagnus/rna-pdb-tools) . Now the toolbox is recognized by the field (http://ahsoka.u-strasbg.fr/rnapuzzles/) and got a nice documentation (http://rna-pdb-tools.rtfd.io). It's open & free to everyone! :-)

Answer 3

[mmagnus]

And now we have more docs, so you can learn more about the package. http://rna-pdb-tools.readthedocs.io/en/latest/