https://gitlab.engr.illinois.edu/tbgl/tools/arbdmodel

https://gitlab.engr.illinois.edu/tbgl/tools/arbdmodel

https://gitlab.engr.illinois.edu/tbgl/tools/arbdmodel

Added test to check that model_from_basepair_stack_3prime works with circular ssDNA; removed warnings and made function work with lists instead of numpy arrays

Fixed polygon_mesh reader so that it works with user-generated .ma files, not just autogenerated ones

find_stacks routine moved to segmentmodel_from_lists using only coordinates and transforms; generate stacks automatically if None

kept old find_stacks routine in segmentmodel_from_pdb as find_stacks_mdanalysis

1) Passthrough of mrdna.segmentmodel arguments
2) Improved input validation
3) Stacks are removed unless stack[bp[stack]] == stack
4) Cleaner code for assigning ends of terminally-connected "segments"

Eliminated numpy log(0) error message when writing bond potentials, which is caught anyway by .isnan

Prepared code structure in potential section so that dsDNA and ssDNA are treated using separate defs

Reduced timestep of high resolution simulations from 50 to 40 fs because of instability in some systems