Fixed chain auto-capitalisation issue

[OWissett]

109

Problem: Some PDB files contain two occurrences of the same chain ID, e.g., B and b. The library automatically capitalizes change IDs, this leads to a chain ID conflict which is not possible to resolve simply.

Solution: Remove the functionality which automatically capitalizes the values.

Notes:

• This may lead to breaking changes for users who assume automatic captialisation.
• Maybe this should be handled by a feature flag or an option being passed to the PDB open function, which allows for the selection of whether to use automatic capitalisation.

[douweschulte]

Looks good to me (also see reaction on the issue itself). One small refactor though, maybe it would be better to rename prepare_identifier -> prepare_identifier_uppercase, and prepare_identifier_case_sensitive -> prepare_identifier. I think that captures the gist of it a bit better. But feel free to disagree.

[OWissett]

Sounds fine to me. I will fix those in a bit

[OWissett]

This functionality could be linked with the builder solution I suggest in #113

[OWissett]

Addressed naming suggestoins