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Created with Raphaël 2.2.05Dec12Nov22Oct842119Sep18131027Aug26242322212017161413876542130Jul2526Mar1Dec22Nov161429Oct2627Jul20191011May13Feb1Nov31Oct18Feb729Nov29Oct2827252128Sep13Jul20May5Mar210Feb7Dec320Aug28Jul10Jun522Apr18Mar95328Feb2524211918128724Jan227212Dec618Nov31Oct927Sep26255427Aug201310Jul10May30Apr8525Mar21158Feb129Jan19321Dec189215Nov417Oct129Sep282725232221201918171514131110765429Aug2824212017131023Jul2018171613106328Jun1514139Apr754130Mar27232221202128Feb2621Dec2017Oct18Sep31Aug30112124Jul2018131211107629Jun2827261514138131May2910Apr754329Mar2726128Feb262423222120191716153add segPrevent PointParticle (or other Child objects) from looking up explicitly excluded methods such as __hash__ and __copy__ from ParticleType; Add ParticleType __copy__ and __deepcopy__ methods that return to ensure types do not change upon copying a group or modelFix typomake assign bead type competitable with arbdmodelsegment model fixesmake mrdna competitable with current arbdmodelMerge branch 'pinyili2' of gitlab.engr.illinois.edu:tbgl/tools/mrdna into pinyili2add arbd model to branchaddaddaadd arbd model to branchgeneralized fwd helix directionsset angle to 180Remove some unused codeFix matrix transpose in new quaterion_from_matrix routineAdd explicitly_unstacked argument to oxDNA reader to ensure we get terminal_crossover connectionsMerge branch 'pinyili2' of gitlab.engr.illinois.edu:tbgl/tools/mrdna into pinyili2add 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 pinyili2