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(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)
+def read_scadnano(sc_file, **model_parameters):
+    from .segmentmodel_from_scadnano import mrdna_model_from_scadnano
+    return mrdna_model_from_scadnano(sc_file, **model_parameters)
+
 def read_vhelix(maya_file, **model_parameters):
     from .polygon_mesh import parse_maya_file, convert_maya_bases_to_segment_model
 
@@ -28,12 +36,16 @@ def read_list(infile,**model_parameters):
     from .segmentmodel_from_lists import model_from_basepair_stack_3prime
     return model_from_basepair_stack_3prime(coords, bp, stack, three_prime)
 
+def read_pandas(df,coordinate_col="r",bp_col="bp",stack_col="stack",three_prime_col="threeprime",
+                        seq_col="seq",orientation_col="orientation"):
+    from .segmentmodel_from_lists import model_from_pandas
+    return model_from_pandas(df,coordinate_col,bp_col,stack_col,three_prime_col,
+                        seq_col,orientation_col)
 
 def read_atomic_pdb(pdb_file, **model_parameters):
     from .segmentmodel_from_pdb import SegmentModelFromPdb
     return SegmentModelFromPdb(pdb_file)
 
-def read_oxdna(coordinate_file, topology_file, idealized_coordinate_file=None, **model_parameters):
-    """ Idealized coordinate file: coordinates for detecting stacks and base pairs, defaults to coordinate_file """ 
+def read_oxdna(coordinate_file, topology_file, virt2nuc=None, **model_parameters):
     from .segmentmodel_from_oxdna import mrdna_model_from_oxdna
-    return mrdna_model_from_oxdna(coordinate_file, topology_file, idealized_coordinate_file, **model_parameters)
+    return mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc, **model_parameters)