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Created with Raphaël 2.2.022Apr18Mar95328Feb2524211918128724Jan227212Dec618Nov31Oct927Sep26255427Aug201310Jul10May30Apr8525Mar21158Feb129Jan19321Dec189215Nov417Oct129Sep282725232221201918171514131110765429Aug2824212017131023Jul2018171613106328Jun1514139Apr754130Mar27232221202128Feb2621Dec2017Oct18Sep31Aug30112124Jul2018131211107629Jun2827261514138131May2910Apr754329Mar2726128Feb262423222120191716153Added routines for writing atomic bp restraints and for changing debye lengthUpdated routines for removing DNA to optionally allow removing locations as wellAdded option for assigning hj equilibrium angleMade an option for specifying a frame range for readAvgArbdCoords1.0a1.0aFixed version script so it changes directories to version.__file__Slightly updated routine for circular DNA in case beads overlapFixed edge case with model_from_lists when circular helices have crossovers near their 'ends'Minor bug fix: Segment.rotate() provides numpy array of quaternions instead of listImproved atomic pdb basepair assignment by making distance metric symmetric and by assigning basepairs in order of quality of fitVarious changes to make it easy to run circular structuresOption and commands to convert crossovers into intrahelicalMade minimum automatic dimensions 1000Added easy commands for ignoring long bonds during coarse-simulationFixed SegmentModel.count_crossovers() to include terminal_crossover connectionsDeprecated SingleStrandedDNA.connect_5endFixed small things broken by mergeMerge remote-tracking branch 'mrdna/master'Merge branch 'dev'Sync with arbdmodel 4784882; syntax changes have not yet been propogated to SegmentModelAdded routines for obtaining a bounding box for a nanostructureSegmentModel.clear_strands() works for merged modelsFixed angle potential spring constant; didn't have a significant effect on persistence lengthAdded deprecated dummy modules for mrdna modules that have moved into arbdmodelSpeed up model construction using lookup table for twist spring constantsReordered A/B in minimizeRmsd() to be consistent with supplied arguments; does not affect return valuesImproved performance for segmentmodel._getParent()Shift segment occupancies when extending segmentmodelAdded mrdna messageAdded routines for getting bounding boxMade spring constant for twist between adjacent crossovers draw from a series of "springs":0.5a0.5aImproved potentials around crossoversAdded nonbonded exclusions between beads participating in crossovers within 3 bp of the crossoverDistance between beads is now calculated more accuratelyFixed sign error in geometric term for HarmonicBondFixed swapped origin/dimensionsFixed bug introduced in commit 47b578f where ArbdModel.__init__ arguments were incorrectly provided by SegmentModel.__init__Fix from Will Kaufhold to add_nick routine when on_fwd_strand==FalseOptionally run enrg-md simulationsSet origin of arbd box using structure in mrdna scriptmrdna script now recognizes list files for model creation