def test_solv_water_free(tmp_path):
mol_free = FreeEner('DEN', f'{tmp_path}/indene_water_solv')
mol_free.water_box_from_SMILE('C1C=Cc2ccccc12')
start_coor = pdb_manip.Coor(mol_free.gmxsys.coor_file)
assert start_coor.num == 1625
# To avoid domain decomposition errors:
# Use only one proc
mol_free.gmxsys.nt = 1
mol_free.equilibrate_solvent_box(em_steps=100,
dt=0.002,
prod_time=0.02,
short_steps=500)
delta_coul = 0.5
coul_list = np.arange(0, 1 + delta_coul, delta_coul)
vdw_coul = 0.5
vdw_list = np.arange(0, 1 + vdw_coul, vdw_coul)
mol_free.run(lambda_coul_list=coul_list,
lambda_vdw_list=vdw_list,
em_steps=100,
nvt_time=0.1,
npt_time=0.1,
prod_time=0.1,
temp_groups='System')
dg_solv, dg_std_solv = mol_free.get_free_ener()
print(dg_solv, dg_std_solv)
assert ((10 < dg_solv) and (dg_solv < 30))
def test_solv_oct(tmp_path):
mol_free = FreeEner('DEN', f'{tmp_path}/indene_oct_solv')
mol_free.octanol_box_from_SMILE('C1C=Cc2ccccc12')
start_coor = pdb_manip.Coor(mol_free.gmxsys.coor_file)
assert start_coor.num == 1502
mol_free.gmxsys.nt = 1
mol_free.equilibrate_solvent_box(em_steps=100,
dt=0.002,
prod_time=0.02,
short_steps=500)
def test_symetry_corr(smile, dg):
assert FreeEner.symmetry_correction(smile) == pytest.approx(dg, rel=1e-3)
def test_free_bind(tmp_path):
dna_free = FreeEner('DAP', f'{tmp_path}/1D30_solv')
dna_free.prepare_complex_pdb(PDB_1D30,
'NC(=N)c1ccc(cc1)c2[nH]c3cc(ccc3c2)C(N)=N')
start_coor = pdb_manip.Coor(dna_free.gmxsys.coor_file)
assert start_coor.num == 20973
dna_free.equilibrate_complex(em_steps=100,
HA_time=0.001,
CA_time=0.002,
CA_LOW_time=0.02,
dt=0.002,
dt_HA=0.001,
temp=300,
receptor_grp='DNA',
short_steps=500)
dna_free.compute_add_intermol_from_traj(ref_coor=None, rec_group='DNA')
dg_rest_water = dna_free.get_water_restr()
print(dg_rest_water)
assert ((5.5 < dg_rest_water) and (dg_rest_water < 9.5))
dna_free.plot_intermol_restr()
delta_restr = 0.5
restr_list = np.arange(0, 1 + delta_restr, delta_restr)
delta_coul = 0.5
coul_list = np.arange(0, 1 + delta_coul, delta_coul)
vdw_coul = 0.5
vdw_list = np.arange(0, 1 + vdw_coul, vdw_coul)
dna_free.run(lambda_restr_list=restr_list,
lambda_coul_list=coul_list,
lambda_vdw_list=vdw_list,
em_steps=50,
nvt_time=0.05,
npt_time=0.05,
prod_time=0.25,
temp_groups='System')
dna_free.extend_lambda_prod(prod_time=0.5)
dg_bind, dg_std_bind = dna_free.get_free_ener()
print(dg_bind, dg_std_bind)
assert ((0 < dg_bind) and (dg_bind < 200))
# Need to think about using alchemlyb as a dependance or not
dna_free.plot_convergence(dt=0.25, graph_out=f'{tmp_path}/alchem.png')
dna_free.compute_convergence_gbar(dt=0.25)
dna_free.plot_convergence_graph(graph_out=f'{tmp_path}/bar.png')
def test_is_palindrome(smile, dg):
assert FreeEner.symmetry_correction(smile) == pytest.approx(dg, rel=1e-3)