Expected network degree for move set MS1

The set of programs described in the article
  1. Clote P. Expected degree of RNA secondary structure networks. J Comput Chem. 2015 Jan 15;36(2):103-17. doi: 10.1002/jcc.23776. Epub 2014 Nov 7
are available here: MS1 code

These programs compute the expected network degree (expected number of neighbors) for the directed graph G = (V,E) , where V is the set of all secondary structures of a given RNA sequence, and E is the set of directed edges s → t, where structure t is obtained from s by an element of move set MS1 consisting of base pair additions and removals.

Expected network degree for move set MS2

The set of programs described in the article
  1. P. Clote, A. Bayegan. Network properties of the ensemble of RNA structures. submitted, 25 June 2015.
are available here: MS2 code

These programs compute the expected network degree (expected number of neighbors) for the directed graph G = (V,E) , where V is the set of all secondary structures of a given RNA sequence, and E is the set of directed edges s → t, where structure t is obtained from s by an element of move set MS2 consisting of base pair additions, removals, and shifts, The algorithm is not a simple extension of the algorithm for MS1, but requires entirely new concepts and is surprisingly complex.

Some data and Python code

Here is the data used (from both PDB and Rfam), along with code to compute contact order, and to approximate the distribution of network degree by sampling:
  1. DATA
  2. Rfam Data
  3. PDB Data