Add basic measurement functions

 * Add utilities to measure distances, angles and dihedral angles.
Update objects

 * Add `Atom.bonded` property.
 * Update `Selection` internals.
Add function to find hydrogen bonds
Performance upgrade

Major improvement
 * Use trick to get Atom's coordinates faster.
 * Prevent unnecessary updates of Selection.
Minor improvements
 * Define __slots__ for Atom.
 * Use more explicit imports.
 * Add debug message to loader.
Add assertion for almost equal sequences
Update `Loader`

 * Use `Molecule` instead of parameter file.
 * Use `step` parameter to stride trajectory.
 * Use `chunk` parameter to define number of frames loaded at once.
Pepify

 * Do not reuse atomsel in `Atom.pick`. If selection is coordinate
   based, the atomsel may not point to single atom.
 * Clean the code.