def feature(chain):
#initialize dict of dict
samples = dict()
#calculate exposure for entire chain
hse_cn = ExposureCN(chain)
#assign exposure for each residue to dictionary
for residue in hse_cn:
exposure = residue[1]
res_index = residue[0].get_id()[1]
samples[res_index] = {"res_access": exposure}
return samples
def test_ExposureCN(self):
"""HSExposureCN."""
_ = ExposureCN(self.model, self.radius)
residues = self.a_residues
self.assertEqual(0, len(residues[0].xtra))
self.assertEqual(1, len(residues[1].xtra))
self.assertEqual(25, residues[1].xtra["EXP_CN"])
self.assertEqual(1, len(residues[2].xtra))
self.assertEqual(28, residues[2].xtra["EXP_CN"])
self.assertEqual(1, len(residues[3].xtra))
self.assertEqual(29, residues[3].xtra["EXP_CN"])
# ...
self.assertEqual(1, len(residues[-2].xtra))
self.assertEqual(48, residues[-2].xtra["EXP_CN"])
self.assertEqual(1, len(residues[-1].xtra))
self.assertEqual(38, residues[-1].xtra["EXP_CN"])
if args.exp[0] == "H" and args.exp[3] == "A":
hse = HSExposureCA(m, RADIUS)
if args.exp[-1] == "D":
k = "EXP_HSE_A_D"
else:
k = "EXP_HSE_A_U"
elif args.exp[0] == "H" and args.exp[3] == "B":
hse = HSExposureCB(m, RADIUS)
# hse.write_pymol_script()
if args.exp[-1] == "D":
k = "EXP_HSE_B_U"
else:
k = "EXP_HSE_B_D"
elif args.exp == "CN":
hse = ExposureCN(m, RADIUS)
k = "EXP_CN"
elif args.exp == "ANGLE":
hse = HSExposureCA(m, RADIUS)
k = "EXP_CB_PCB_ANGLE"
format = "%4.1f"
elif args.exp == "DSSPR":
d = DSSP(m, args.pdbfile, dssp=args.dssp)
k = "EXP_DSSP_RASA"
format = "%.4f"
elif args.exp == "DSSPA":
d = DSSP(m, args.pdbfile, dssp=args.dssp)
k = "EXP_DSSP_ASA"
elif args.exp == "RD":
d = ResidueDepth(m, args.pdbfile, msms_exec=args.msms)
k = "EXP_RD"