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 = []
