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Selection

Philip Loche requested to merge selection into develop

Closes #22 (closed)

This PR unifies the selection command for all modules on the command line level. On the python level the user is now able to pass a selected AtomGroup. Some of our module can handle several AtomGroups and some only a single. To deal with this fact I introduced a child class MultiGroupAnalysisBase for multiple groups and SingleGroupAnalysisBase for Single groups. I currently adjusted only the density script but I will also adjust the others during the next days/weeks...

Since the selection now takes places outside the modules we can not take the selection string as a header for our outputfiles. For now I wrote a simple function called atomgroup_header(AtomGroup). It will take a AtomGroup and returns a string containing number of atoms and residues. Though, I'm not very happy with this... If you more clever ideas tell me.

Edited by Philip Loche

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