Pinyili2

New Features:

• scadnano Support:

Integrated support for scadnano, enabling users to read in model from scadnano designs.

• Pandas-Compatible List Reading:

Added functionality to read in model in pd.DataFrame format and retrieve its own DataFrame.

Enhancements:

• oxDNA Bonds and Base Pairing Localization:

Implemented the ability to locate oxDNA bonds and analyze base-pairing behavior using the virt2nuc file (generated by tacoxDNA.

• Cadnano Data Retrieval for oxDNA Generation:

Enhanced the system to retrieve relevant caDNAno information, facilitating the generation of oxDNA structures.

assigned to @pinyili2

added 1 commit

• 43805028 - Fix bug handling insertions and skips at strand ends; handle multiple...

Compare with previous version

marked this merge request as ready

added 1 commit

• 6aa4baad - Delete segmentmodel_from_oxdna.py.bak

Compare with previous version

added 6 commits

• 23d3df48 - 1 commit from branch master
• db5c5712 - Segmend.connect_ends(...) will not make a crossover for '5prime' locations
• 3dee5868 - Merge branch 'master' into pinyili2
• 537868ea - Fix segment orientation and coordinate splines for new cadnano reader
• d6069d75 - Order of double-stranded segment creation and ds-segment direction should...
• a5677aa8 - Merge remote-tracking branch 'refs/remotes/origin/pinyili2' into pinyili2

Compare with previous version

added 1 commit

• 6f01c8d2 - Draft routine for updating reader list coordinates and orientations

Compare with previous version

added 2 commits

• e68eab9b - 1 commit from branch master
• ee4032a6 - Merge branch 'master' into pinyili2

Compare with previous version

added 1 commit

• bf407268 - remove oxlibs

Compare with previous version

added 2 commits

• a900a88a - Fix bug when in new model_from_lists option when setting default nucleotide_rank
• eab065f0 - Add cadnano vhelix and z_idx information via callbacks in new list-based reader

Compare with previous version

added 1 commit

• 45445532 - rename oxdna reader

Compare with previous version

added 1 commit

• f6a1810f - init

Compare with previous version

mentioned in commit 3b257147

merged