Fix for Minor Issues with PDB <--> OxDNA Conversion

[Lucandia]

Hi,

Thank you so much for integrating the full conversion feature for PDB <--> OxDNA in oat—it's fantastic!

I tested the conversion by converting some oxDNA files to PDB and back. While the conversion from oxDNA to PDB worked flawlessly, I encountered issues with the conversion from PDB to oxDNA, particularly for single strands. After investigating, I identified the following problems:

1. The conversion from oxDNA to PDB does not add the "END" identifier at the end of the PDB file.
2. When the one_file_per_strand flag is set to True, the oxDNA to PDB conversion saves each strand with the strand.id of the previous strand.
3. If the 'TER' identifier is present but the 'END' identifier is missing, the PDB to oxDNA conversion function does not include the last system in the output. For example, it doesn't add the last system in PDB files generated with oxDNA to PDB (which miss the 'END' identifier).

I have addressed all these issues with minor changes to the code.

Looking forward to your feedback!

Best,
Luca

[lorenzo-rovigatti]

I'm not in charge of oat so I won't comment on the code, but while we wait for Erik's checks I want to thank you for contributing!