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.

mrdna/readers/__init__.py

 ## TODO: make module this package conform to a single style for input/output
 
-def read_cadnano(json_file, sequence=None, fill_sequence='T', **model_parameters):
+def read_cadnano_legacy(json_file, sequence=None, fill_sequence='T', **model_parameters):
     from .cadnano_segments import read_json_file
     from .cadnano_segments import read_model as model_from_cadnano_json
 
     data = read_json_file(json_file)
     return model_from_cadnano_json(data, sequence, fill_sequence, **model_parameters)
 
-def read_cadnano_input(json_file,sequence=None,**model_parameters):
+def read_cadnano(json_file,sequence=None,**model_parameters):
     from .segmentmodel_from_cadnano import mrdna_model_from_cadnano
     
     return mrdna_model_from_cadnano(json_file,seq=sequence,**model_parameters)