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Fixes for hhmakemodel.py #154

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  • Corrected the error 'list index out of range' appearing when using hhmakemodel.py. Fixes issue hhmakemodel.py : list index out of range #135
  • Added and argument to avoid names duplicates in the header of every sequences in the .pir file. This is by default False and does not changes anything when using the script, but is helpful when trying to parse the .pir file in a dictionary for further analyses.
  • Removed the renaming of the chains in the .cif files. This caused modeller to not recognise the chains and not do the modelling.
  • Some typo fixes

- added and option to avoid names duplicates in the header of every sequences in the .pir file
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