Use one-based indexing in final PDB output#6
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Instead of propagating the internal zero-based indexing using in DODO, this commit updates the indexing of atoms and residues to standard one-based indexing right before writing
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Description
Instead of propagating the internal zero-based indexing used internally by DODO, this commit updates the indexing of atoms and residues to standard one-based indexing right before writing the output PDB file. It is a minimal patch for #5 .
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