Simple PDB Parser

Here is a very simple reader for Protein Data Bank (PDB) files. (At this stage of the project) Reader can extract xyz-coordinates of C-alpha (CA) atoms from the first (or the only one) model and writes the result into dat-file in format:

<x_firts_atom>    <y_first_atom>    <z_first_atom>
<x_second_atom>   <y_second_atom>   <z_second_atom>

 ...               ...               ...
 
<x_last_atom>     <y_last_atom>     <z_last_atom>

If there are any missing atoms in the model, the program will tell about it and show maps for them both in percents and actual size.

You will be able to rewrite dat-file with only one segment in order to not have any missings.

If there are any CA atoms with the same number, the program automatically takes only the first and ignore all the rest with the same number.

For Whom It Can Be Useful

For people who are not familiar with pdb-format, but want to consider geometry of real experimental proteins (like I do). So they want to have a polymer chain of C-alpha atoms without double sites or any missing sites (then the link length is ~ 3.8 A all the time).

Quick Start

$ git clone https://github.com/Anny-Moon/Simple_PDB_parser
$ cd Simple_PDB_parser/
$ sh compile_script
$ ./pdb-reader

Example: 5dn7

$ ./pdb-reader 5dn7

The output is:

Protein: 5dn7
The first CA atom has number 345.
Missing atoms from 361 to 365 (5 atoms).
Missing atoms from 558 to 562 (5 atoms).
The last CA atom has number  594.
Number of CA atoms in the model: 250.
But there is data only for 240 of them.

***************************************
*      Maps of missing atoms          *
*  atom: .         missing atom: 0    *
***************************************
Percentage: string length = 100 chars.

......00.............................................................................00.............

Actual: string length = number of atoms in model.

................00000................................................................................................................................................................................................00000................................

*****************************************
If you want to rewrite dat-file with only one segment, call
./pdb-reader (without arguments) for instructions.

The program created file results/xyz_5dn7.dat with 240 lines.

Let's concider the maps. They represent the positions and amounts of missing atoms, where 0 stands for missing atom and . for atom from the pdb-file. The first map depicture the percentege picture (so not very precise becouse of rounding). The second one is an actual picture: each char is one char.

Now I want to rewrite the dat-file with one segment in oder to not have missing data there. There are 3 segments there. I will take the largest one, between two missing parts. I can do this by calling the program again but now give the number of the first atom (or any missing atom before the first) in segment as the second argument.

Like this:

$ ./pdb-reader 5dn7 365

or the same:

$ ./pdb-reader 5dn7 366

And the output is:

Protein: 5dn7
Number of CA atoms: 192.

what means that now in results/xyz_5dn7.dat we have 192 lines wich correspond to 192 atoms between the firs and the second missing parts.

If you want to take the first segment (from the first atom to the first missing atom) you always can put second argument is egual to 0:

$ ./pdb-reader 5dn7 0

Note

If you want to have your outpun in file, not on the screen you always can do this:

$ ./pdb-reader 5dn7 > create_and_put_everything_here.dat

Bugs

Since the autor doesn't know all possible formats of notation in PDB, there should be cases when the program will give absurd result. These cases will be fixed when revealed.

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Anna Sinelnikova

Uppsala, 2017