Code Box Files

Here I save various small programs and scripts for later use.  There
is no unifying theme to this, simply an effort to keep code to
re-use it later.

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[11.02.14] code-box v0.1
* atom-neighbors: VK: Added distances to different chains. This fixes
the dist to waters in another chain and contacts between ASU.
* atom-neighbors: VK: Added license information.
* binbox: VK - Added license information
* atomdist: VK - Added license information

[11.02.09]
* atom-neighbors: VK: Fixed processing if chain field is empty.

[11.02.07]
* atom-neighbors: VK: Added auto creation of the output filename.

[11.01.14]
* atom-neighbors: VK: Added an option for the protein chain.

[11.01.14]
* atom-neighbors: VK: Print polar argument into the file.

[11.01.13]
* atom-neighbors: VK: Added a flag to search for carboxylic groups.

[11.01.13]: New script added - atom-neighbors.py
* atom-neighbors - Atom Neighbors
This program calculates the distances to all of the atoms
that are around a specific atom within a sphere of a specified radius.
The program reads in a PDB file and outputs a file with Residue type,
residue ID, atom type, distance to the center atom, and atom element.

The output filename is created from the input filename.
If the input file has no chain ID, do not pass any chain option

[10.12.21]: New script added - binbox.py
* binbox - v1.0 Lipid Membrane Thickness Calculation
This program calculates distance between to lipid layers.
It does so by binning the lipids two layers of bins, one
for the top lipid layer and one for the bottom.  It then
averages the Z-coordinate in each bin and finally
calculates the distance between the average Z coordinate
between the top bin and the bottom bin.
                    
The program can process multiple files with lipid
coordinates.  With each new file, it will add the
lipids to the same set of bins as for the previous
file.  Once all the files are read, the z-coordinate in
each bin is averaged.  Finally the thickness is calculated
for each (bin-X,bin-Y) coordinate by calculating the 
difference between the average z-coordinates in the top
and bottom bins.

[10.10.29]: New script added - atomdist.py
* atomdist - v0.1
Given two data files, calculate distances between atoms in file1
and atoms in file2.  This script assumes that both files have identical
structure, so that line 1 of file 1 corresponds to the same atom on line 1 of
file 2.  The calculated distances are saved to the output file