adding support for HETATM in caprieval

[VGPReys]

Checklist

• Tests added for the new code
• Documentation added for the code changes
• Modifications / enhancements are reflected on the haddock3 user-manual
• CHANGELOG.md is updated to incorporate new changes
• Does not break licensing
• Does not add any dependencies, if it does please add a thorough explanation

Summary of the Pull Request

Adding support to use HETATM from reference file in caprieval module.
This is performed by using an additional parameter: keep_hetatm (default false) in the module allowing to keep HETATM from the input reference file.

Related Issue

Closes #1271

[VGPReys]

And do we want the default to be false?

I have no idea.

• Default true: easier to test a reference structure that contains HETATM(s)
• Default false: easy to get rid of most of the undesired things from a PDB file (water, ions, ...)

[amjjbonvin]

The yaml file used "considered" - may-be better to use the same terminology in the code