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Created with Raphaël 2.2.02Oct119Sep18131027Aug26242322212017161413876542130Jul2526Mar1Dec22Nov161429Oct2627Jul20191011May13Feb1Nov31Oct18Feb729Nov29Oct2827252128Sep13Jul20May5Mar210Feb7Dec320Aug28Jul10Jun522Apr18Mar95328Feb2524211918128724Jan227212Dec618Nov31Oct927Sep26255427Aug201310Jul10May30Apr8525Mar21158Feb129Jan19321Dec189215Nov417Oct129Sep282725232221201918171514131110765429Aug2824212017131023Jul2018171613106328Jun1514139Apr754130Mar27232221202128Feb2621Dec2017Oct18Sep31Aug30112124Jul2018131211107629Jun2827261514138131May2910Apr754329Mar2726128Feb262423222120191716153add arbdmodeladdaddacompatibility to arbd modeladdfix oxdna dataframe writing bugMerge branch 'pinyili2'Merge remote-tracking branch 'refs/remotes/origin/master'Merge remote-tracking branch 'refs/remotes/origin/pinyili2' into pinyili2remove ipynbMerge branch 'pinyili2' into 'master'initrename oxdna readerMake new cadnano reader a bit fasterMerge branch 'master' into pinyili2Add utility for converting crossovers to types other than intrahelicalUse graph methods to compute location of bead in _other_ segments for better performance; update some development logger messagesAdd cadnano vhelix and z_idx information via callbacks in new list-based readerFix bug when in new model_from_lists option when setting default nucleotide_rankremove oxlibsMerge branch 'master' into pinyili2Make generate_bead_model use one_bead_per_monomer=True by default with max 1 bead per nt and bp, otherwise FalseDraft routine for updating reader list coordinates and orientationsMerge remote-tracking branch 'refs/remotes/origin/pinyili2' into pinyili2Order of double-stranded segment creation and ds-segment direction should match original cadnano reader.Fix segment orientation and coordinate splines for new cadnano readerDelete segmentmodel_from_oxdna.py.bakMerge branch 'master' into pinyili2Segmend.connect_ends(...) will not make a crossover for '5prime' locationsFix bug handling insertions and skips at strand ends; handle multiple consecutive skips; in model_from_lists, convert terminal_crossover dsDNA-dsDNA connections to intrahelical when nearby crossovers exist between the two segmentsrename oxdna_pinyi to oxdnamodify bakremove dot filesremove testsmodify git ignoreremove baksremove nfsfix some bugsset one bead per mono back to False