Introduction :
==============

This directory contains a set of utility Python programs for easy manipulation
of "xyz" formatted files.

The XYZ format :
================

It is used in Quantum Chemistry to represent the structure of molecules in 3D.
For more details, see : http:https://en.wikipedia.org/wiki/XYZ_file_format

details of the format :
|-------------------------------------------------------------|
|<number of atoms> (N for example)                            | <- line 1
|Any comment you want                                         | <- line 2
|atom_symbol_1  x_coordinate_1  y_coordinate_1  z_coordinate_1| <- line 3 and
|atom_symbol_2  x_coordinate_2  y_coordinate_2  z_coordinate_2|    beyond
|...                                                          |
|atom_symbol_N  x_coordinate_N  y_coordinate_N  z_coordinate_N|
|-------------------------------------------------------------|

The atomic coordinates are generally given in Angstroms.

Content of the directory :
==========================

- rotate_atomic_positions.py
- translate_atomic_positions.py
- sort_atomic_positions.py
- duplicate_atomic_positions.py

The names of the programs are pretty self-explanatory. Each program reads an xy
z  formatted file, and then manipulates the atomic coordinates according to the
type of operation selected (translation, rotation, sorting, duplication).  When
all the coordinates have been updated, an output file is created with the first
2 lines matching  perfectly  the ones  in the original file, and the subsequent
lines containing the updated coordinates (except  for the duplication operation
where the program writes a new comment line  to indicate  how the original cell
has been duplicated).

The ouput file names are respectively :
- <seedname>_duplicated for "duplicate_atomic_positions.py"
- <seedname>_sorted     for "sort_atomic_positions.py"
- <seedname>_translated for "translate_atomic_positions.py"
- <seedname>_rotated    for "rotate_atomic_positions.py"
where seedname is the original name of the file the program is reading.

All the programs use a set of command line options. For details just type :
|$my_prompt> python <name_of_the_program.py> [ENTER]
This will print the "help" menu of the program.

The "duplicate_atomic_positions.py" program is interactive in that the user has
to answer some questions before the program can duplicate the coordinates. 

Dependencies :
==============

Some programs in this directory need a working version of Numpy.