Use the real nucleotide numbers from the pdb file instead of re-numbering them to start from 1
Add the seq_dict keyword to the graph structure to describe the identity of the nucleotide at a particular position
Removed print statements
Load a particular chain
Mark and add missing nucleotides
Removed some debug statements and added the average_atom_positions.py script
Print pseudoatoms when calculating the average positions
Visualize only certain cg elements (constraints)
removed print statements, used seq_dict in junction_virtual_atom_distance, and reverted to the old virtual atom method
Use a mapping to point to the residues ids as specified in the pdb file.
Fix the define residue_num_iterator
Fixed bug with get_node_from_res..., the collapsing of stems with degenerate loops, and intermediate dirs set to None
Bug in extract_subchain
Bug in bg.define_range_iterator
Fixed a bug in define_residue_num_iterator when asking for seq_ids
Added iterate_over_seq_id_range
Removed seq_dict since it's been superceded by seq_ids
Include the chain id in the cg name
Added the ConformationStats structure
Load a bulgegraph from a dotbracket string