add complete coverage and deprecated destroy pmb object

[pm-blanco]

Closes #58, with this PR we reach full effective coverage of pyMBE. The lines that show as uncovered in the coverage report are due to the two versions of espresso that we currently support and are in reality covered when the testsuite runs with the development version. This issue will be solved once we update our dependency to the newer release of Espresso.

Added

• Case-specific methods to delete particles, residues and molecules in pyMBE: delete_particle_in_system, delete_residue_in_system, delete_molecule_in_system.

Removed

• pmb.destroy_pmb_object has been deprecated in favor of case-specific deletion methods.
• pmb.create_pmb_object has been deprecated in favor of case-specific creation methods.

[1234somesh]

I like the overall structure of the new case specific delete functions instead of the destroy_pmb_objects.
The newly defined function pmb._clean_ids_in_df_row, takes only 1 row at a time to delete rows from the dataframe. This fits the current requirement. We might think about generaliing this to delete multiple rows.

[pm-blanco]

@1234somesh thank you very much for your careful review, it has been very useful. I have solved your comments, if you think that the PR is ready for merging then I think we are ready to close this PR.

[1234somesh]

I aprrove the new changes. Using case-specific delete methods instead of destroy_pmb_object reduces confusion and give better control for the user when deleting pyMBE objects. Moreover, these methods are analogous to existing create_particles/residues/molecules methods, so it make sense to have them.