Cli score fix

[mgiulini]

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Closes #782 and Closes #781 by

• adding a type check and conversion on the variable input dictionary
• copying the input pdb file to a temporary file that will be deleted immediately after use

Additionally I moved the test file for cli score (hard to maintain without CNS and prone to garbage generation) to the integration tests, thus requiring CNS to run

[VGPReys]

in the future, a new flag parameter (--keep-hydrogens) to fix the hydrogens during the topoaa step should be added enabling both non-variability in the integration tests and unchanged hydrogen positions of the structures.

[amjjbonvin]

in the future, a new flag parameter (--keep-hydrogens) to fix the hydrogens during the topoaa step should be added enabling both non-variability in the integration tests and unchanged hydrogen positions of the structures.

Probably not needed as I found the cause of the "energetic instability" in the rebuild process... Will create a separate issue for this