Use graph methods to compute location of bead in _other_ segments for better performance; update some development logger messages

Make generate_bead_model use one_bead_per_monomer=True by default with max 1 bead per nt and bp, otherwise False

Elija Feigl authored 3 years ago and cmaffeo2 committed 3 years ago

Switch to static package build: replace setup.py with setup.cfg and pyproject.toml; update MANIFEST.in; remove mrdna/RELEASE-VERSION from .gitignore

Add mrdna/arbdmodel/resources to MANIFEST; shold have been done with commit 455420b8; thanks to Elija Feigl for catching this oversight!

Use average persistence length of parent segments in model.simulate(), rather than object returned _get_parent(), which can be 'model'; thanks to Elija Feigl

Fix --crossover-to--intrahelical-cutoff option to mrdna script broken in commit af4b5e33; thanks to Elija Feigl for catching the error

Revert "Add mrdna.simulate.multiresolution_simulation(...,center_object = True,...) to center objects at each step during multiresolution simulations, avoiding drift to locations where PDB format cannot be used"

This reverts commit 0fdd92dc.

Add mrdna.simulate.multiresolution_simulation(...,center_object = True,...) to center objects at each step during multiresolution simulations, avoiding drift to locations where PDB format cannot be used

Added option to specify custom persistence length to mrdna script for first 25% of coarse simulation

Expose enrg_md_steps option in mrdna and enrgmd scripts and in mrdna.simulate.multiresolution_simulation(); thanks to Elija Feigl for the suggestion

Make correct use of "gpu" option in SegmentModel.simulate_oxdna(); thanks to Elija Feigl catching the issue