def test_length():
backbone = parser.parse("data/glut1.pdb")
dssp = dssp_mod.DSSP(backbone)
list_helices = dssp.get_ca()
for helix in list_helices:
orig, axis = axis_mod.principal_axis(helix)
len = length_mod.length_helix(helix, axis, orig)
print(len)
def test():
backbone = parser.parse("data/glut1.pdb")
dssp = dssp_mod.DSSP(backbone)
test_print(dssp)
#print("\n *********** GET CAS TEST *********** \n")
# test_get_ca(dssp)
print("\n *********** GET HELICES TEST *********** \n")
test_get_helices(dssp)
def test_parse():
# Test for static molecule
backbone = parser.parse("data/glut1.pdb")
print("#a_carbon: ", len(backbone["alpha_carbon"]))
print("#carbon: ", len(backbone["carbon"]))
print("#hydrogen: ", len(backbone["hydrogen"]))
print("#nitrogen: ", len(backbone["nitrogen"]))
print("#nitrogen: ", len(backbone["oxygen"]))
print("#res: ", len(backbone["res_number_list"]))
# Test for trajectory file
backbones = parser.parse("data/TSPO_traj.pdb")
backbone = backbones[2]
print(len(backbones))
print("#a_carbon: ", len(backbone["alpha_carbon"]))
print("#carbon: ", len(backbone["carbon"]))
print("#hydrogen: ", len(backbone["hydrogen"]))
print("#nitrogen: ", len(backbone["nitrogen"]))
print("#nitrogen: ", len(backbone["oxygen"]))
print("#res: ", len(backbone["res_number_list"]))
def test_hbonds():
backbone = parser.parse("data/glut1.pdb")
hbonds = dssp_mod.find_hbonds(backbone)
print("#hbond", len(hbonds))
print("example of hbond: ", hbonds[0])
def test_com():
filename = "data/TSPO_traj.pdb"
backbones = parser.parse(filename)
com.showGraphMassCenters(filename, True)