def test_smina_rigid(tmp_path, capsys):
# Convert to str to avoid problem with python 3.5
TEST_OUT = str(tmp_path)
# Redirect pdb_manip logs
pdb_manip.show_log()
# Extract center and max_sizer:
lig_coor = pdb_manip.Coor(os.path.join(TEST_PATH, 'lig.pdbqt'))
center_lig = lig_coor.center_of_mass()
max_size = lig_coor.get_max_size()
print("Center coordinates is {:.1f} {:.1f} {:.1f}, maximum dimension"
" is {:.1f} Å".format(*center_lig, max_size))
captured = capsys.readouterr()
assert bool(re.match('Succeed to read file .+/input/lig.pdbqt , 50 '
'atoms found\nDo a rotation of 99.71°\nCenter '
'coordinates is 13.1 22.5 5.5, maximum dimension is '
'18.0 Å\n',
captured.out))
# Create Docking object
test_dock = docking.Docking(
name='test_smina',
rec_pdbqt=os.path.join(TEST_PATH, 'rec.pdbqt'),
lig_pdbqt=os.path.join(TEST_PATH, 'lig.pdbqt'))
out_dock = os.path.join(TEST_OUT, '{}_dock.pdb'.format('test_smina'))
test_dock.run_docking(out_dock,
num_modes=10,
energy_range=1,
exhaustiveness=2,
dock_bin='smina',
center=center_lig,
grid_npts=[max_size + 5] * 3,
seed=1)
captured = capsys.readouterr()
capture_line = captured.out.split('\n')
assert bool(re.match(
("smina --ligand .+lig.pdbqt --receptor .+rec.pdbqt --log "
".+test_smina_dock_log.txt --num_modes 10 --exhaustiveness 2"
" --energy_range 1 --out .+test_smina_dock.pdb "
"--size_x 23.00 --size_y 23.00 --size_z 23.00"
" --center_x 13.08 --center_y 22.52 --center_z 5.54"
" --seed 1"),
capture_line[0]))
rmsd_list = test_dock.compute_dock_rmsd(test_dock.lig_pdbqt)
assert len(rmsd_list) >= 1
assert rmsd_list[0] < 15
assert len(test_dock.affinity) >= 1
assert test_dock.affinity[1]['affinity'] < -10
def test_pdb2pqr_dna(tmp_path):
"""
Check that pdb2pqr produce something with dna
"""
ff = "CHARMM"
pdb_manip.show_log()
##########################################
# ## Compute protonation at PH 4.0 ###
##########################################
out_file = os.path.join(tmp_path, '1D30_charmm_ph4.pqr')
pdb2pqr.compute_pdb2pqr(os.path.join(PDB_1D30), out_file, ff=ff, ph=4.0)
prot_coor = pdb_manip.Coor(out_file)
assert prot_coor.num == 486
def test_prepare_ligand_recetor(tmp_path, capsys):
# Convert to str to avoid problem with python 3.5
TEST_OUT = str(tmp_path)
# Redirect pdb_manip logs
pdb_manip.show_log()
# Read 1hsg.pdb, extract lig.pdb and rec.pdb
coor_1hsg = pdb_manip.Coor(os.path.join(TEST_PATH, '1hsg.pdb'))
captured = capsys.readouterr()
assert bool(
re.match("Succeed to read file .+input/1hsg.pdb , 1686 atoms found\n",
captured.out))
# Extratc Protein:
# Keep only amino acid
rec_coor = coor_1hsg.select_part_dict(
selec_dict={'res_name': pdb_manip.PROTEIN_AA})
out_rec = os.path.join(TEST_OUT, 'rec.pdb')
rec_coor.write_pdb(out_rec)
captured = capsys.readouterr()
assert bool(re.match("Succeed to save file .+rec.pdb\n",
captured.out))
# Extract ligand:
lig_coor = coor_1hsg.select_part_dict(
selec_dict={'res_name': 'MK1'})
out_lig = os.path.join(TEST_OUT, 'lig.pdb')
lig_coor.write_pdb(out_lig)
captured = capsys.readouterr()
assert bool(re.match("Succeed to save file .+lig.pdb\n",
captured.out))
# Extract ligand center of mass and maximum dimension:
center_lig = lig_coor.center_of_mass()
max_size = lig_coor.get_max_size()
print("Center coordinates is {:.1f} {:.1f} {:.1f}, maximum dimension"
" is {:.1f} Å".format(*center_lig, max_size))
captured = capsys.readouterr()
assert bool(re.match('Do a rotation of 99.65°\nCenter coordinates is 13.1'
' 22.5 5.6, maximum dimension is 16.0 Å\n',
captured.out))
# Create Docking object
test_dock = docking.Docking('test',
rec_pdb=out_rec,
lig_pdb=out_lig)
# Prepare receptor
test_dock.prepare_receptor()
captured = capsys.readouterr()
assert bool(re.match(
("python2.+ .+/prepare_receptor4.py -r .+/rec.pdb"
" -A checkhydrogens -o .+/rec.pdbqt\n"),
captured.out))
# Check that receptor is fine
coor_rec = pdb_manip.Coor(test_dock.rec_pdbqt)
print('Protein atom number : {}'.format(coor_rec.select_part_dict(
{'res_name': pdb_manip.PROTEIN_AA}).num))
captured = capsys.readouterr()
assert bool(re.match(
"Succeed to read file .+rec.pdbqt , 1844 atoms found\n"
"Protein atom number : 1844\n",
captured.out))
# Prepare Ligand
test_dock.prepare_ligand(rigid=True)
captured = capsys.readouterr()
assert bool(re.match("python.+ .+prepare_ligand4.py -l lig.pdb -B "
"none -A hydrogens -o lig.pdbqt -Z\n",
captured.out))
# Check that ligand pdbqt is fine
coor_lig = pdb_manip.Coor(test_dock.lig_pdbqt)
print('Protein atom number : {}'.format(coor_lig.select_part_dict(
{'res_name': pdb_manip.PROTEIN_AA}).num))
captured = capsys.readouterr()
assert bool(re.match(
"Succeed to read file .+lig.pdbqt , 50 atoms found\n"
"Protein atom number : 0\n",
captured.out))
def test_autodock_2_rigid(tmp_path, capsys):
# Convert to str to avoid problem with python 3.5
TEST_OUT = str(tmp_path)
# Redirect pdb_manip logs
pdb_manip.show_log()
# Extract center and max_sizer:
lig_coor = pdb_manip.Coor(os.path.join(TEST_PATH, 'lig.pdbqt'))
center_lig = lig_coor.center_of_mass()
max_size = lig_coor.get_max_size()
print("Center coordinates is {:.1f} {:.1f} {:.1f}, maximum dimension"
" is {:.1f} Å".format(*center_lig, max_size))
captured = capsys.readouterr()
assert bool(re.match('Succeed to read file .+/input/lig.pdbqt , 50 '
'atoms found\nDo a rotation of 99.71°\nCenter '
'coordinates is 13.1 22.5 5.5, maximum dimension is '
'18.0 Å\n',
captured.out))
# Create Docking object
test_dock = docking.Docking(
name='test_autodock_2',
rec_pdbqt=os.path.join(TEST_PATH, 'rec.pdbqt'),
lig_pdbqt=os.path.join(TEST_PATH, 'lig.pdbqt'))
out_dock = os.path.join(TEST_OUT, '{}_dock.pdb'.format('test_autodock_2'))
test_dock.run_autodock_docking(out_dock,
num_modes=2,
center=center_lig,
grid_size=[max_size + 5] * 3)
captured = capsys.readouterr()
capture_line = captured.out.split('\n')
assert bool(re.match(
("python2.+ .+prepare_gpf4.py -r rec.pdbqt -l lig.pdbqt -o "
"test_autodock_2_dock.gpf -p npts=62,62,62 -p "
"gridcenter=13.08,22.52,5.54"),
capture_line[0]))
assert bool(re.match(
("autogrid4 -p test_autodock_2_dock.gpf "
"-l test_autodock_2_dock.gpf_log"),
capture_line[1]))
rmsd_list = test_dock.compute_dock_rmsd(test_dock.lig_pdbqt)
assert len(rmsd_list) == 2
assert rmsd_list[0] < 15
assert len(test_dock.affinity) == 2
assert test_dock.affinity[1]['affinity'] < -10
captured = capsys.readouterr()
test_dock.display()
captured = capsys.readouterr()
assert bool(re.match(
("name : test_autodock_2\n"
"lig_pdbqt : .+lig.pdbqt\n"
"rec_pdbqt : .+rec.pdbqt\n"
"dock_pdb : .+test_autodock_2_dock_vmd.pdb\n"
"dock_log : .+test_autodock_2_dock.dlg\n"
"gpf : .+test_autodock_2_dock.gpf\n"
"affinity : {1: .+affinity': -.+}}\n"
),
captured.out))
def test_autodock_rigid(tmp_path, capsys):
# Convert to str to avoid problem with python 3.5
TEST_OUT = str(tmp_path)
# Redirect pdb_manip logs
pdb_manip.show_log()
# Extract center and max_sizer:
lig_coor = pdb_manip.Coor(os.path.join(TEST_PATH, 'lig.pdbqt'))
center_lig = lig_coor.center_of_mass()
max_size = lig_coor.get_max_size()
print("Center coordinates is {:.1f} {:.1f} {:.1f}, maximum dimension"
" is {:.1f} Å".format(*center_lig, max_size))
captured = capsys.readouterr()
assert bool(re.match('Succeed to read file .+/input/lig.pdbqt , 50 '
'atoms found\nDo a rotation of 99.71°\nCenter '
'coordinates is 13.1 22.5 5.5, maximum dimension is '
'18.0 Å\n',
captured.out))
# Create Docking object
test_dock = docking.Docking(
name='test_autodock',
rec_pdbqt=os.path.join(TEST_PATH, 'rec.pdbqt'),
lig_pdbqt=os.path.join(TEST_PATH, 'lig.pdbqt'))
# Prepare Grid
spacing = 0.375
test_dock.prepare_grid(out_folder=TEST_OUT, spacing=spacing,
center=center_lig,
grid_npts=[int(max_size / spacing)] * 3)
captured = capsys.readouterr()
assert bool(re.match(
("python2.+ .+prepare_gpf4.py -r rec.pdbqt -l lig.pdbqt -o "
"test_autodock.gpf -p npts=48,48,48 -p "
"gridcenter=13.08,22.52,5.54\nautogrid4 -p test_autodock.gpf -l "
"test_autodock.gpf_log"),
captured.out))
test_dock.run_autodock(out_folder=TEST_OUT, nrun=1)
rmsd_list = test_dock.compute_dock_rmsd(test_dock.lig_pdbqt)
assert len(rmsd_list) >= 1
assert rmsd_list[0] < 15
captured = capsys.readouterr()
test_dock.display()
captured = capsys.readouterr()
assert bool(re.match(
("name : test_autodock\n"
"lig_pdbqt : .+lig.pdbqt\n"
"rec_pdbqt : .+rec.pdbqt\n"
"dock_pdb : .+test_autodock_vmd.pdb\n"
"dock_log : .+test_autodock.dlg\n"
"gpf : .+test_autodock.gpf\n"
"affinity : {1: .+affinity': -.+}}\n"
),
captured.out))
def test_autodock_cpu(tmp_path, capsys):
# Convert to str to avoid problem with python 3.5
TEST_OUT = str(tmp_path)
# Redirect pdb_manip logs
pdb_manip.show_log()
# Extract center and max_sizer:
lig_coor = pdb_manip.Coor(os.path.join(TEST_PATH, 'lig.pdbqt'))
center_lig = lig_coor.center_of_mass()
max_size = lig_coor.get_max_size()
print("Center coordinates is {:.1f} {:.1f} {:.1f}, maximum dimension"
" is {:.1f} Å".format(*center_lig, max_size))
captured = capsys.readouterr()
assert bool(
re.match(
"File name doesn't finish with .pdb read it as .pdb"
" anyway\n"
'Succeed to read file .+/input/lig.pdbqt , 50 '
'atoms found\nDo a rotation of 99.71°\nCenter '
'coordinates is 13.1 22.5 5.5, maximum dimension is '
'18.0 Å\n', captured.out))
# Create Docking object
test_dock = docking.Docking(name='test_autodock',
rec_pdbqt=os.path.join(TEST_PATH, 'rec.pdbqt'),
lig_pdbqt=os.path.join(TEST_PATH, 'lig.pdbqt'))
# Prepare Grid
spacing = 0.375
test_dock.prepare_grid(out_folder=TEST_OUT,
spacing=spacing,
center=center_lig,
grid_npts=[int(max_size / spacing)] * 3)
captured = capsys.readouterr()
assert bool(
re.match(
("python2.+ .+prepare_gpf4.py -r rec.pdbqt -l lig.pdbqt -o "
"test_autodock.gpf -p npts=48,48,48 -p "
"gridcenter=13.08,22.52,5.54\nautogrid4 -p test_autodock.gpf -l "
"test_autodock.gpf_log"), captured.out))
test_dock.run_autodock_cpu(out_folder=TEST_OUT, nrun=2)
rmsd_list = test_dock.compute_dock_rmsd(test_dock.lig_pdbqt)
assert len(rmsd_list) == 2
assert rmsd_list[0] < 15
assert len(test_dock.affinity) == 2
assert test_dock.affinity[1]['affinity'] < -10
assert bool(test_dock.lig_pdbqt.endswith("lig.pdbqt"))
assert bool(test_dock.rec_pdbqt.endswith("rec.pdbqt"))
assert bool(test_dock.dock_pdb.endswith("test_autodock_vmd.pdb"))
assert bool(test_dock.dock_log.endswith("test_autodock.dlg"))
assert bool(test_dock.gpf.endswith("test_autodock.gpf"))
# Read test_dock.dock_pdb
coor_dock = pdb_manip.Multi_Coor(test_dock.dock_pdb)
assert len(coor_dock.coor_list) == 2
assert len(coor_dock.coor_list[0].atom_dict) == 50
def test_pdb2pqr_ph4_7_12_charmm(tmp_path):
"""
Test pdb2pqr at ph 4, 7 and 12 with the charmm ff.
"""
ff = "CHARMM"
pdb_manip.show_log()
##########################################
# ## Compute protonation at PH 4.0 ###
##########################################
out_file = os.path.join(tmp_path, '4N1M_charmm_ph4.pqr')
pdb2pqr.compute_pdb2pqr(os.path.join(PDB_4N1M), out_file, ff=ff, ph=4.0)
prot_coor = pdb_manip.Coor(out_file)
assert prot_coor.num == 2559
HSD_index = prot_coor.get_index_selection({
'res_name': ['HSD'],
'name': ['CA']
})
HSE_index = prot_coor.get_index_selection({
'res_name': ['HSE'],
'name': ['CA']
})
HSP_index = prot_coor.get_index_selection({
'res_name': ['HSP'],
'name': ['CA']
})
assert len(HSD_index) == 0
assert len(HSE_index) == 0
assert len(HSP_index) == 5
##########################################
# ## Compute protonation at PH 7.0 ###
##########################################
out_file = os.path.join(tmp_path, '4N1M_charmm_ph7.pqr')
pdb2pqr.compute_pdb2pqr(os.path.join(PDB_4N1M), out_file, ff=ff, ph=7.0)
prot_coor = pdb_manip.Coor(out_file)
assert prot_coor.num == 2549
HSD_index = prot_coor.get_index_selection({
'res_name': ['HSD'],
'name': ['CA']
})
HSE_index = prot_coor.get_index_selection({
'res_name': ['HSE'],
'name': ['CA']
})
HSP_index = prot_coor.get_index_selection({
'res_name': ['HSP'],
'name': ['CA']
})
assert len(HSD_index) == 4
assert len(HSE_index) == 0
assert len(HSP_index) == 1
##########################################
# ## Compute protonation at PH 10.0 ###
out_file = os.path.join(tmp_path, '4N1M_charmm_ph10.pqr')
pdb2pqr.compute_pdb2pqr(os.path.join(PDB_4N1M), out_file, ff=ff, ph=10.0)
prot_coor = pdb_manip.Coor(out_file)
assert prot_coor.num == 2548
HSD_index = prot_coor.get_index_selection({
'res_name': ['HSD'],
'name': ['CA']
})
HSE_index = prot_coor.get_index_selection({
'res_name': ['HSE'],
'name': ['CA']
})
HSP_index = prot_coor.get_index_selection({
'res_name': ['HSP'],
'name': ['CA']
})
assert len(HSD_index) == 5
assert len(HSE_index) == 0
assert len(HSP_index) == 0