Manually changing chain orientation (flex mode)

[ljubica-milovic]

Background

Automatic antisense strand creation described in this ticket: #5678.
This ticket's aim is to allow the user to manually create antisense or antisense-like chains through connecting bases via hydrogen bonds (introducing H-bonds: #5403), and changing the orientation of one chain manually.

Requirements

1. Valid selection (only flex mode) must include only one whole backbone that has at least one sugar that is connected to a base via R3(s)-R1(b)and those bases. All other side connected monomers cannot be selected

2 Right clicking on any selected monomer should give the user the option to "Flip Chain Orientation".

2.1. If the selection is not valid, but within the selected monomers there is a sugar connected to a base (R3-R1), the option should appear but be disabled.

3. The logic for flipping the selected monomers is the same as doing a "Horizontal Flip" and "Vertical flip" (from molecules mode) one after the other.

Monomer coordinates should be recalculated it relation to the center of all the monomers both vertically and horizontally.

4. Monomer numbering should stay the same on the flipped chain.

If the left-most monomer used to be 1 it should still stay 1 regardless of the fact that that monomer is now the right-most.

5. The terminal indicators should be changed from N to C (or the reversed) and from 5' to 3' (or the reversed) and they should be placed next to the new left-most amino-acid/sugar.

6. If the original backbone chain did not have the property "Antisense" assigned to it, upon flipping the chain it should be assigned to it, and if it did, then it should be removed.

UX

TBD

Examples

Note: These are just examples to get the idea across, there are some mistakes - numbers are in the wrong position etc.

Example 1

Original chain:

"Flipped" chain:

Example 2

Original chain:

"Flipped" chain:

Example 3

Original chain:

"Flipped" chain:

Example 4

Original chain:

"Flipped" chain:

Example 5

Original canvas:

"Flip" the selected chain: