Add support for trajectories of part of the system to new analysis framework - Redmine #1861

Currently the new analysis framework can only read trajectory files of all atoms in the tpr. Convert could produce a tpr of a subgroup, but that is messy (#1667).
Allowing reading of trajectories of part of the system should not be much work, since that just requires one extra selection with the xtc group and an index translation.

(from redmine: issue id 1861, created on 2015-11-25 by berkhess, closed on 2016-04-05)

Relations:
- relates #1667 (closed)
Changesets:
- Revision 12c07b72 by Teemu Murtola on 2016-01-10T12:25:09Z:

Support arbitrary subset trajectories in poscalc.*

- Make low-level selection code work with trajectories that contain an
  arbitrary subset of the topology atoms, instead of just the first N.
- Add an entry to t_trxframe to represent such trajectories.
- Add some basic tests.  Negative cases crash with an assert, so not
  tested (should get caught higher up).

This should cover all of selection evaluation, but various consistency
checks need to be adjusted as well (will be done in a child change).

Related to #1861.

Change-Id: I727c79a38e39fb9142976875ab3311e7b1172a55

Revision 4239f345 by Teemu Murtola on 2016-01-10T13:33:53Z:

Support frames with atom subsets in selections

- Instead of just computing the highest atom index required for
  evaluating the selections, compute all the atom indices.
- Use these to check that the input frame actually contains the
  necessary atoms.
- Add basic tests for one positive and a few negative cases.

Part of #1861.

Change-Id: If4c2d031f638f56d81ca4c7844dffa242f863af8

Revision 4ee73c88 by Teemu Murtola on 2016-01-10T16:19:44Z:

Support trajectory analysis with any atom subset

Make tools written for the new C++ analysis framework support analyzing
trajectories that contain an arbitrary subset of atoms.

Part of #1861.

Change-Id: I4a658e953f6f4e3d2ec1151c9c4d405c2e888780