This project contains a list of scripts intended to automate various aspects of structure analysis. 
They are usually called from the command line and accept input from STDIN.
A more detailed description of each program is given here

1) anomalous_around.py 
This program contacts the Periodic Table interface to X-ray absorption edges at the Biomolecular Structure Centre at University of Washington and obtains the F' and F'' values for a particular element around a particular wavelength in Å or an Energy in electron Volt (ev)

for eg.

$ python anomalous_around.py -a Se -w 1.001

Indexed values for Value:12386.0323843, 12300.00 ('-3.071344', '0.5298917') 12400.00 ('-3.383753', '0.5221294') 12500.00 ('-3.863509', '0.5145381')

Documentation:
Usage: anomalous_around.py [options]

Options:
  -h, --help            show this help message and exit
  -a Se, --atom=Se      Atom id for eg. Se
  -e [Energy ev], --energy=[Energy ev]
                        Energy in ev
  -w [wavelength], --wave=[wavelength]
                        Wavelength in A

2) clustal_align_to_pdbfig.py
This program uses a typical pairwise clustal alignment and converts the "*" , ":" , "." and " " line in the  alignment to a numeric value and then replaces the B-factor record in the db file with 100,50,25 or 0 for a fully conserved(*) , Similar(:) , nearly similar (.)  or non-conserved residue

Usage: clustal_align_to_pdbfig.py [options]

Options:
  -h, --help            show this help message and exit
  -i *.pdb, --infile=*.pdb
  -a *.txt with alignment, --alignment=*.txt with alignment



Sample input for this can be a screen copy paste of the alignment or the alignment file itself from a website like the Expasy clustaw site at 
http://www.ebi.ac.uk/Tools/clustalw2/index.html

3)compile_rsmd_to_bfac_column.py
This program transfers the rms-distance between two aligned pdbs as output by coot to the B-factor column on all of the chains in the pdb [smarter version in the works]
Usage: compile_rsmd_to_bfac_column.py [options]

Options:
  -h, --help            show this help message and exit
  -i *.pdb, --infile=*.pdb
                        input file to append bfactors to
  -s *.txt, --screedump=*.txt
                        input file with screen dump after SSM superpose
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