pyemap.process_data.calculate_rsa

pyemap.process_data.calculate_rsa(filename, model, node_list, rsa_cutoff)[source]

Returns a list of surface exposed residues as determined by relative solvent accessibility.

Only standard protein residues are currently supported. Non-protein and user specified custom residues cannot be classified as surface exposed using this criteria.

Parameters:

  • filename (str) – Name of pdb file to be analyzed

  • model (Bio.PDB.Model.Model) – Model under analysis

  • node_list (list of str) – List containing which standard residues are included in analysis

  • rsa_cutoff (float) – Cutoff for buried/surface exposed

References

Tien, M. Z.; Meyer, A. G.; Sydykova, D. K.; Spielman, S. J.; Wilke, C. O. PLoS ONE 2013, 8 (11).

Reference for relative solvent accessibility cutoff of 0.05, and for MaxASA values