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

Fix multiple issues related to strand generation, also reduce timestep to 100fs if coarse_local_twist==True

Added fill_sequence parameter to SegmentModel.set_sequence and to the mrdna and enrgmd scripts, with default value 'T', since that is most common for origami. Thanks to Elija Feigl for recommending the change.

Connections between ssDNA and dsDNA should now always be of the type 'sscrossover', never 'intrahelical'

The latter could result in bonds between the end of dsDNA and ssDNA
from forming if the dsDNA end was also bound to another helix, but
this may remain an issue for three-way dsDNA junctions.

Added box_type=orthogonal and CUDA_DEVICE={gpu} to oxDNA input file; thanks to Elija Feigl for bringing the issue to our attention

Ensure no duplicate bonds in ENM, logging violations; thanks to Elija Feigl for bringing duplicate bonds to our attention

Updated ENM to avoid situation where network is applied to single-stranded DNA at end of double-stranded helix

Fixed two small bugs, one involving use of is for string comparison, the other involving an incorrect function call when a restraint is added to the system with only one argument