Implement PropertyTransition abstract class

[#49843371]

It allows to smoothly change property over desired time period.
Add PropertyTransition tests

[#49843371]
Implement AtomTransition class and support it in MD2D modeler

[#49843371]
Add AtomTransition tests

[#49843371]
Use new atom transitions in genetic engine

[#49656281]

So, now it's possible to smoothly move all amino acids to the right,
code is simpler and some issues are gone (like huge slowdown of engine
when new tRNA was being added).
Remove old, ugly method of real-time based transitions in MD2D model

[#49843371]
Implement custom force in MD2D engine pushing amino acids above ribosome

[#49656281]

Instead of using negative gravity.
TODO: such feature should be moved to a separate, MD2D engine plugin.
Add CML file for quantum-collision
Support delay in property transition

[#49843371]
Add atomTransition() to MD2D Scripting API

[#49843371]
Add new interactive presenting atomTransition()

[#49843371]

Note that this model is created completely by hand. Empty model is
used, as a fake properties set.

So, it's visible that we can easily support undefined / null model URL
(and then use just {} as model properties set).
Try to fix issue with invisible tRNA on Safari

[#49656281]
QD: Fix conversion from Classic MW energy levels (which are in eV)
quantum interactive: fix nm/fs->m/s conversion

1nm/fs = 1e6 m/s; we were using 1e5. This was covered up by incorrect energy level conversion.
QD: clarify "precalculateVelocities"
Fix DNA translation edge cases when there are 0-2 non-STOP codons
[#49657325]
Make sure that whole mRNA is moved away at the end of translation

[#49657325]
Optimize rendering of tRNAs (keep max 3 tRNA in DOM)

[#49917027]
Add photons table to QD metadata; create on plugin creation

[#48675225]
Pass md2d to QD plugin, so we have access to engine props

We need model dimensions for photons, and plugin should have
access to md2d api anyway.

Also move plugin declaration after main model property initializations
(though still before creation of atoms).

[#48675225]