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Updated Mol_analysis.py + README with new -nomkndx option#24

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pablosanchezizquierdo wants to merge 1 commit intomasterfrom
fix22_updating_multiple_chain_option_to_python3
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Updated Mol_analysis.py + README with new -nomkndx option#24
pablosanchezizquierdo wants to merge 1 commit intomasterfrom
fix22_updating_multiple_chain_option_to_python3

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Fixed the script to be able to take multiple chains as input + added an option to input custom index

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