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I have three dimension coordinate information of protein object. The task is to project protein onto three dimension grid (in such a way its special arrangement will be restored), so that I can perform processing further. The three dimension coordinate information is available in pdb (PROTEIN DATA BANK) file and be defined as follows:

ATOM  C x  y  z

where "ATOM" represents a tag and "C" represent carbon atom and x,y,and, z are three dimension coordinates of carbon atom.

For example:

ATOM   C   5.84714  27.90645  31.85267          
ATOM   O   5.84216  27.92345  31.85267   

       :

       :

       :

ATOM   N       x       y        z

I tried to store this information in three dimension grid, but fails because if you see atom "C" and "O" they have approximately similar coordinates. Due to this, they will store in same cell of three dimension grid.

I scaled the coordinate by factor of 10^i, it works but taking huge amount of time in processing.

Please help me out from this issue!!

Thanks in advance

marc_s
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Aman Agarwal
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    What exactly is your issue? And what have you tried at least? – Axois Aug 15 '19 at 12:33
  • if multiplying by constant is too slow than I am afraid any processing will be even worse.... unless you are coding this wrong. Anyway [python] tag hinds of python usage which is slow on its own (unless using build in functions/packages that are coded in faster compiler/language) try to code this in C++ instead... Why do you need grid? cant you find the aligning orientation from current coordinates? Do you have an example of what pattern you look for or simple example of molecule and its orientation wanted ... I got the feeling this should be relatively easy using proper math – Spektre Aug 16 '19 at 07:16
  • Grid is required to detect cavities on the protein surface. To know about cavity please see the following image (https://www.google.com/search?q=image+cavity+protein&source=lnms&tbm=isch&sa=X&ved=0ahUKEwjTr8jkl4fkAhUK7nMBHZl9BzkQ_AUIESgB&biw=1600&bih=789#imgrc=YC4LE9HMmVkiqM:) – Aman Agarwal Aug 16 '19 at 10:37
  • @AmanAgarwal looks like this [Finding holes in 2d point sets?](https://stackoverflow.com/a/21884021/2521214) ported to 3D – Spektre Aug 16 '19 at 17:03

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