def test_zinc_finger(tmp_path):
gmx.show_log()
##################################
# ## Create the topologie: ###
##################################
prot = gmx.GmxSys(name='1jd4', coor_file=PDB_1JD4)
prot.prepare_top(out_folder=os.path.join(tmp_path, 'top_DIAP1'),
vsite='hydrogens',
ignore_ZN=False)
top_coor = pdb_manip.Coor(prot.coor_file)
assert top_coor.num == 3292
prot.switch_ion_octa_dummy()
top_coor = pdb_manip.Coor(prot.coor_file)
assert top_coor.num == 3304
prot.solvate_add_ions(out_folder=os.path.join(tmp_path, 'top_sys'),
maxwarn=3)
prot.em(out_folder=os.path.join(tmp_path, 'em_DIAP1'),
nsteps=10,
constraints='none')
em_coor = pdb_manip.Coor(prot.coor_file)
assert em_coor.num == 56366
ener_pd = prot.get_ener(['Potential'])
assert ener_pd['Potential'].values[-1] < -155000
def test_set_protonate_amber(tmp_path):
gmx.show_log()
##########################################
# ## Create the topologie at PH 4.0 ###
##########################################
res_prot_dict = {
'GLH': {
'res_num': [9, 24, 31, 57]
},
'ASH': {
'res_num': [3, 70]
},
'HIP': {
'res_num': [28, 35]
},
'HID': {
'res_num': [175]
},
'HIE': {
'res_num': [214]
}
}
prot = gmx.GmxSys(name='1RXZ_ph4', coor_file=PDB_1RXZ)
prot.prepare_top(out_folder=os.path.join(tmp_path, 'top_1RXZ_ph4'),
ph=7.0,
res_prot_dict=res_prot_dict,
ff="amber99sb-ildn")
top_coor = pdb_manip.Coor(prot.coor_file)
assert top_coor.num == 4081
top_1RXZ = gmx.TopSys(prot.top_file)
assert top_1RXZ.charge() == -4
def test_cys_bond_charmm(tmp_path):
gmx.show_log()
##################################
# ## Create the topologie: ###
##################################
prot = gmx.GmxSys(name='1dpx', coor_file=PDB_1DPX)
prot.prepare_top(out_folder=os.path.join(tmp_path, 'top_DISU'),
vsite='hydrogens',
ignore_ZN=False)
top_coor = pdb_manip.Coor(prot.coor_file)
assert top_coor.num == 2096
prot.solvate_add_ions(out_folder=os.path.join(tmp_path, 'top_sys'),
maxwarn=3)
prot.em(out_folder=os.path.join(tmp_path, 'em_DISU'),
nsteps=10,
constraints='none')
em_coor = pdb_manip.Coor(prot.coor_file)
assert em_coor.num == 27086
cystein_s_index = em_coor.get_index_selection({
'name': ['SG'],
'res_name': ['CYS']
})
distance = pdb_manip.Coor.atom_dist(em_coor.atom_dict[cystein_s_index[0]],
em_coor.atom_dict[cystein_s_index[-1]])
assert distance < 2.1
def test_insert_ethanol(tmp_path):
gmx.show_log()
##################################
# ## Create the topologie: ###
##################################
prot = gmx.GmxSys(name='1y0m', coor_file=PDB_1Y0M)
prot.prepare_top(out_folder=os.path.join(tmp_path, 'top_SH3'))
top_coor = pdb_manip.Coor(prot.coor_file)
assert top_coor.num == 996
prot.solvate_add_ions(out_folder=os.path.join(tmp_path, 'top_sys'))
prot.em(out_folder=os.path.join(tmp_path, 'em_SH3'),
nsteps=10,
constraints='none')
em_coor = pdb_manip.Coor(prot.coor_file)
assert em_coor.num == 15383
ener_pd = prot.get_ener(['Potential'])
assert ener_pd['Potential'].values[-1] < -155000
###################################
# ### Create Ethanol system ###
###################################
smile = 'CCO'
eth_pdb = os.path.join(tmp_path, 'ethanol.pdb')
charge = ambertools.smile_to_pdb(smile, eth_pdb, 'ETH')
assert charge == 0
eth_sys = gmx.GmxSys(name='ETH', coor_file=eth_pdb)
eth_sys.prepare_top_ligand(out_folder=os.path.join(tmp_path, 'eth_top'),
ff='amber99sb-ildn',
include_mol={'ETH': smile})
eth_sys.create_box(name=None, dist=0.5)
####################################################
# # Insert 4 copy of ethanol in the SH3 system: ###
####################################################
prot.insert_mol_sys(mol_gromacs=eth_sys,
mol_num=10,
new_name='SH3_ETH',
out_folder=os.path.join(tmp_path, 'top_ETH_SH3'))
################################
# ## Minimize the system ###
################################
prot.em_2_steps(out_folder=os.path.join(tmp_path, 'em_ETH_SH3'),
no_constr_nsteps=10,
constr_nsteps=10)
prot_lig_coor = pdb_manip.Coor(prot.coor_file)
assert 15300 < prot_lig_coor.num < 15518
prot.display_history()
def test_insert_peptide_vsite(tmp_path):
gmx.show_log()
##################################
# ## Create the topologie: ###
##################################
prot = gmx.GmxSys(name='1y0m', coor_file=PDB_1Y0M)
prot.prepare_top(out_folder=os.path.join(tmp_path, 'top_SH3'),
vsite='hydrogens')
top_coor = pdb_manip.Coor(prot.coor_file)
assert top_coor.num == 1064
prot.solvate_add_ions(out_folder=os.path.join(tmp_path, 'top_sys'))
prot.em(out_folder=os.path.join(tmp_path, 'em_SH3'),
nsteps=10,
constraints='none')
em_coor = pdb_manip.Coor(prot.coor_file)
assert em_coor.num == 15337
ener_pd = prot.get_ener(['Potential'])
assert ener_pd['Potential'].values[-1] < -155000
###################################
# ## Create a DD peptide ###
###################################
pep = gmx.GmxSys(name='DD')
pep.create_peptide(sequence='DD',
out_folder=os.path.join(tmp_path, 'top_DD'),
em_nsteps=10,
equi_nsteps=0,
vsite='hydrogens')
####################################################
# # Insert 4 copy of ethanol in the SH3 system: ###
####################################################
prot.insert_mol_sys(mol_gromacs=pep,
mol_num=10,
new_name='SH3_DD',
out_folder=os.path.join(tmp_path, 'top_DD_SH3'))
################################
# ## Minimize the system ###
################################
prot.em_2_steps(out_folder=os.path.join(tmp_path, 'em_DD_SH3'),
no_constr_nsteps=10,
constr_nsteps=10)
prot_lig_coor = pdb_manip.Coor(prot.coor_file)
assert 15300 < prot_lig_coor.num < 15518
prot.display_history()
def test_protonate_ph4_7_amber(tmp_path):
gmx.show_log()
##########################################
# ## Create the topologie at PH 4.0 ###
##########################################
prot = gmx.GmxSys(name='1RXZ_ph4', coor_file=PDB_1RXZ)
prot.prepare_top(out_folder=os.path.join(tmp_path, 'top_1RXZ_ph4'),
ph=4.0,
ff="amber99sb-ildn")
top_coor = pdb_manip.Coor(prot.coor_file)
top_1RXZ = gmx.TopSys(prot.top_file)
if (version.parse(pdb2pqr.__version__) < version.parse("3.5")):
assert top_coor.num == 4107
assert top_1RXZ.charge() == 22
else:
assert top_coor.num == 4106
assert top_1RXZ.charge() == 21
##########################################
# ## Create the topologie at PH 7.0 ###
##########################################
prot = gmx.GmxSys(name='1RXZ_ph7', coor_file=PDB_1RXZ)
prot.prepare_top(out_folder=os.path.join(tmp_path, 'top_1RXZ_ph7'),
ph=7.0,
ff="amber99sb-ildn")
top_coor = pdb_manip.Coor(prot.coor_file)
assert top_coor.num == 4073
top_1RXZ = gmx.TopSys(prot.top_file)
assert top_1RXZ.charge() == -12
##########################################
# ## Create the topologie at PH 10.0 ###
##########################################
# Remark: Amber allow lysine unprotonated
prot = gmx.GmxSys(name='1RXZ_ph10', coor_file=PDB_1RXZ)
prot.prepare_top(out_folder=os.path.join(tmp_path, 'top_1RXZ_ph10'),
ph=10.0,
ff="amber99sb-ildn")
top_coor = pdb_manip.Coor(prot.coor_file)
assert top_coor.num == 4071
top_1RXZ = gmx.TopSys(prot.top_file)
assert top_1RXZ.charge() == -14
def test_insert_peptide_vsite(tmp_path):
# Gromacs verions >= 2021 support cyclic peptides
gmx.show_log()
cyclic_pep = gmx.GmxSys(name='5vav', coor_file=PDB_5VAV)
top_coor = pdb_manip.Multi_Coor(cyclic_pep.coor_file)
assert top_coor.coor_list[0].num == 209
cyclic_pep.cyclic_peptide_top(
out_folder=os.path.join(tmp_path, 'cyclic/top'))
top_coor = pdb_manip.Coor(cyclic_pep.coor_file)
assert top_coor.num == 209
cyclic_top = gmx.TopSys(cyclic_pep.top_file)
assert cyclic_top.prot_res_num() == 14
cyclic_top.display()
cyclic_pep.em(out_folder=os.path.join(tmp_path, 'cyclic/em/'),
nsteps=10,
create_box_flag=True)
cyclic_amber_pep = gmx.GmxSys(name='5vav_amber', coor_file=PDB_5VAV)
top_coor = pdb_manip.Coor(cyclic_pep.coor_file)
assert top_coor.num == 209
cyclic_amber_pep.cyclic_peptide_top(out_folder=os.path.join(
tmp_path, 'cyclic/top'),
ff='amber99sb-ildn')
top_coor = pdb_manip.Coor(cyclic_pep.coor_file)
assert top_coor.num == 209
cyclic_amber_top = gmx.TopSys(cyclic_amber_pep.top_file)
print(cyclic_amber_top.charge())
cyclic_amber_pep.em(out_folder=os.path.join(tmp_path, 'cyclic/em/'),
nsteps=10,
create_box_flag=True)
def test_protonate_ph4_7_12_charmm(tmp_path):
gmx.show_log()
##########################################
# ## Create the topologie at PH 4.0 ###
##########################################
prot = gmx.GmxSys(name='1RXZ_ph4', coor_file=PDB_1RXZ)
prot.prepare_top(out_folder=os.path.join(tmp_path, 'top_1RXZ_ph4'), ph=4.0)
top_coor = pdb_manip.Coor(prot.coor_file)
assert top_coor.num == 4108
top_1RXZ = gmx.TopSys(prot.top_file)
assert top_1RXZ.charge() == 23
##########################################
# ## Create the topologie at PH 7.0 ###
##########################################
prot = gmx.GmxSys(name='1RXZ_ph7', coor_file=PDB_1RXZ)
prot.prepare_top(out_folder=os.path.join(tmp_path, 'top_1RXZ_ph7'), ph=7.0)
top_coor = pdb_manip.Coor(prot.coor_file)
assert top_coor.num == 4073
top_1RXZ = gmx.TopSys(prot.top_file)
assert top_1RXZ.charge() == -12
##########################################
# ## Create the topologie at PH 10.0 ###
##########################################
# Remark: Charmm doesn't allow lysine unprotonated
prot = gmx.GmxSys(name='1RXZ_ph10', coor_file=PDB_1RXZ)
prot.prepare_top(out_folder=os.path.join(tmp_path, 'top_1RXZ_ph10'),
ph=10.0)
top_coor = pdb_manip.Coor(prot.coor_file)
assert top_coor.num == 4073
top_1RXZ = gmx.TopSys(prot.top_file)
assert top_1RXZ.charge() == -12
