# **************************************************************************
# DESCRIPTION:
# Scripts developed under IRENE project.

# AUTHOR:
# Martin Hediger, Copenhagen University
# 
# USAGE:
# Documented in tutorial_screening.pdf
#
# NOTE:
# The scripts belong to one of the two categories:
# - Data production is related to all steps required for setting up
#   and carrying out calculations using the MOPAC program.
# - Data processing is concerned with the steps to analyse the data
#   produced.
# The scripts are described roughly in order of usage. Caution is required
# in the usage of the scripts because they
# a) Could potentially overwrite CPU costly output
# b) In some cases require adjustment of keywords which are required
#    for parsing input.
# ..........................................................................

# **************************************************************************
# Scripts Data Production
- 'seq_files.py'          : Generate back bone sequence files.
- 'vsc.py'                : V-ariant s-ide c-hain file generation from PyMOL. Point
                            mutations are entered in this script.
- 'vsc-bcx.py'            : VSC modified to generate all side chains at selected positions.
- 'vsc-ext.py'            : VSC extended, get all positions within selection,
                            generate all or defined mutants at these positions.
- 'vsc-set.py'            : VSC used to prepare mutant sets (mutations depending on
                            current 'resn')
- 'avf.py'                : A-ssemble V-ariant F-iles.
- 'cha2scf.sh'            : Charge to scf calculation transfer.
- 'fix.py'                : Script to constrain side chains.
- 'intcat.sh'             : Interpolate between two structures, concatenate frames.
- 'intcha.sh'             : Interpolate between two structures and write keyword for
                            MOPAC charge determination.  
- 'scf2opt.sh'            : Write MOPAC input for optimization based on SCF output.
- 'opt2spe.sh'            : Transfer structure data from optimization to MOPAC
                            SPE input file.
- 'cat_arc2pdb.py'        : Writes PDB file with interpolation frames from MOPAC output
                            for viewing in PyMOL (see also 'del_PDB_header.sh')
- 'int_arc2mop.py'        : Writes MOPAC interpolation input
- 'del_MOPAC_header.sh'   : Removes MOPAC header in '.arc' files
- 'del_PDB_header.sh'     : Removes 'HEADER', 'TER' and 'END' records in PDB files
                            (required prior to using 'cat_arc2pdb.py')
- 'fix_reacting_atoms.py' : Set optimization flags for two atoms to '+0'
- 'check-charge-double.py': Compare predicted and computed charge for double mutants

# Scripts Data Processing
- 'profiles.py'     : Extract heat of formation from MOPAC output files
                      and write a file for each unique mutant.
- 'ext_rest_barrier': Extract barriers.
- 'plots.py'        : Write gnuplot files for plotting blocks
                      related of mutants.
- 'vec.py'          : Script used in order to analyze partial Hessian
                      vibrational analysis.
# ..........................................................................