Eliminate mdtraj-specific public API for SystemBuilder about yank HOT 14 CLOSED

We can use mdtraj under the hood, but it should be encapsulated and hidden inside of each class that uses it.

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Can you give examples of which things you think should be private?

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• Return the positions in mdtraj format
• Return the mdtraj object
• Set the mdtraj object

Still working my way through the rest of the code.

I'm making changes as I go, so hold off on changes now. I'm not addressing this issue---just reformatting the docstrings and whitespace as I understand the code.

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I agree with the point 1 and 3, but I think that the ability to output an mdtraj object is a highly useful public-facing function. For example, it allows us to dump coordinates to an array of file formats.

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I'd prefer to stick to OpenMM-only interfaces for this release. We can go mdtraj-crazy in the next one, but we should support mdtraj for everything then. I just don't want inconsistent interfaces.

(For example, right now, ComplexSystemBuilder has a coordinates_as_quantity property, an openmm_positions, and a positions property, which all return different things.)

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(By contrast, the other SystemBuilder objects lack coordinates_as_quantity, have have the two other properties.)

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This was totally fine for a first pass, of course! But it's making it more difficult to debug.

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Do openmm and mdtraj use different Topology formats?

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They are slightly different, as we have made some enhancements to facilitate various things. There is a function traj.top.to_openmm() that gives you a pure-openmm version.

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Also, is the only way to create an MDTraj object to read from disk? We have the positions in memory and an OpenMM Topology object, why would we need to write to disk and then read again?

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That should be possible.

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top_mdtraj = md.Topology.from_openmm(top)
traj = md.Trajectory(xyz, top_mdtraj)

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Thanks!

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To my knowledge this is done.

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