def read_dssp(dssp_file): try: dssp, keys = BP.make_dssp_dict(dssp_file) except(PDBException): print("SKIPPING THIS protein: pdb exception occurred for %s" % dssp_file) return return dssp, keys
def read_dssp(dssp_file): try: dssp, keys = BP.make_dssp_dict(dssp_file) except (PDBException): print("SKIPPING THIS protein: pdb exception occurred for %s" % dssp_file) return return dssp, keys
from Bio import PDB from collections import Counter if __name__ == '__main__': db = sys.argv[1] # Path to db. dssp_dir = sys.argv[2] # Path to dir with DSSP output files. conn = sqlite3.connect(db) c = conn.cursor() query = "SELECT BEST_MODEL FROM BEST_MODELS;" c.execute(query) bestModels = [str(i[0]) for i in c.fetchall()] for bestModel in bestModels: dssp_file = os.path.join(dssp_dir, bestModel + '.dssp') d, keys = PDB.make_dssp_dict(dssp_file) ss_list = [] aa_list = [] cys_set = { "C", "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z" } helix_set = {"H", "G", "I"} beta_set = {"B", "E"} loop_set = {"T", "S"} helix_res = [] beta_res = [] loop_res = []