- <init>
Create a new layout refiner for the provided molecule.
- backupCoords
Backup the coordinates of atoms (idxs) in the stack to the provided destination.
- bend
Bend select atoms around a provided pivot by the specified amount (r).
- bendOrStretch
Resolves conflicts either by bending bonds or stretching bonds in the shortest
path between an overl
- findCongestedPairs
Find all pairs of un-bonded atoms that are congested.
- haveCrossingBonds
Check if any of the bonds adjacent to u, v (not bonded) are crossing.
- invert
Special case congestion minimisation, rotate terminals bonds around ring systems
so they are inside
- isCrossed
Check if two bonds are crossing.
- isOdd
- macroCycleInversion
- makeAtmBndQueues
Internal - makes atom (seq) and bond priority queues for resolving overlap. Only
(acyclic - but not
- numFixedMoved