def save_lightdock_structure(structure):
"""Saves the structure parsed by LightDock"""
log.info("Saving processed structure to PDB file...")
for structure_index, file_name in enumerate(structure.structure_file_names):
moved_file_name = os.path.join(os.path.dirname(file_name),
DEFAULT_LIGHTDOCK_PREFIX % os.path.basename(file_name))
write_pdb_to_file(structure, moved_file_name, structure[structure_index])
log.info("Done.")
def test_write_pdb_to_file(self):
atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPE_l_u.pdb')
protein = Complex(chains)
assert atoms == protein.atoms
write_pdb_to_file(protein, self.test_path + '1PPE_l_u.pdb.parsed', protein.atom_coordinates[0])
assert filecmp.cmp(self.golden_data_path + '1PPE_l_u.pdb.parsed', self.test_path + '1PPE_l_u.pdb.parsed')
def test_null_rotation(self):
protein = Complex(chains=self.chains2)
q = Quaternion()
protein.rotate(q)
write_pdb_to_file(protein, self.test_path + 'rotated.pdb',
protein.atom_coordinates[0])
assert filecmp.cmp(self.golden_data_path + 'two_residues.pdb',
self.test_path + 'rotated.pdb')
def test_write_pdb_to_file(self):
atoms, _, chains = parse_complex_from_file(self.golden_data_path /
'1PPE_l_u.pdb')
protein = Complex(chains)
assert atoms == protein.atoms
write_pdb_to_file(protein, self.test_path / '1PPE_l_u.pdb.parsed',
protein.atom_coordinates[0])
assert filecmp.cmp(self.golden_data_path / '1PPE_l_u.pdb.parsed',
self.test_path / '1PPE_l_u.pdb.parsed')
def save_lightdock_structure(structure):
"""Saves the structure parsed by LightDock"""
log.info("Saving processed structure to PDB file...")
for structure_index, file_name in enumerate(
structure.structure_file_names):
moved_file_name = os.path.join(
os.path.dirname(file_name),
DEFAULT_LIGHTDOCK_PREFIX % os.path.basename(file_name))
write_pdb_to_file(structure, moved_file_name,
structure[structure_index])
log.info("Done.")
def test_parse_pdb_noh(self):
atoms_to_ignore = ['H']
atoms, _, chains = parse_complex_from_file(
self.golden_data_path / '1PPE_lig.pdb.H', atoms_to_ignore)
protein = Complex(chains)
assert atoms == protein.atoms
write_pdb_to_file(protein, self.test_path / 'parsed_1PPE_lig.pdb.H',
protein.atom_coordinates[0])
assert filecmp.cmp(self.golden_data_path / 'parsed_1PPE_lig.pdb.H',
self.test_path / 'parsed_1PPE_lig.pdb.H')
def test_rotation_180_degrees_y_axis_origin_is_0(self):
"""Expected file has been generated with Chimera fixing the rotation to the
center of coordinates and modifying the column of atom name to have the
same padding as the write_pdb_file function.
"""
protein = Complex(chains=self.chains2)
q = Quaternion(0, 0.0, 1.0, 0)
protein.rotate(q)
write_pdb_to_file(protein, self.test_path+'rotated.pdb', protein.atom_coordinates[0])
assert filecmp.cmp(self.golden_data_path+'two_residues_y_180.pdb', self.test_path+'rotated.pdb')
def test_rotation_180_degrees_y_axis_origin_is_0(self):
"""Expected file has been generated with Chimera fixing the rotation to the
center of coordinates and modifying the column of atom name to have the
same padding as the write_pdb_file function.
"""
protein = Complex(chains=self.chains2)
q = Quaternion(0, 0.0, 1.0, 0)
protein.rotate(q)
write_pdb_to_file(protein, self.test_path + 'rotated.pdb',
protein.atom_coordinates[0])
assert filecmp.cmp(self.golden_data_path + 'two_residues_y_180.pdb',
self.test_path + 'rotated.pdb')
def save_lightdock_structure(structure):
"""Saves the structure parsed by LightDock"""
log.info("Saving processed structure to PDB file...")
for structure_index, file_name in enumerate(
structure.structure_file_names):
moved_file_name = Path(file_name).parent / Path(
DEFAULT_LIGHTDOCK_PREFIX % Path(file_name).name)
if moved_file_name.exists():
raise LightDockError(
f"{moved_file_name} already exists, please delete previous setup generated files"
)
write_pdb_to_file(structure, moved_file_name,
structure[structure_index])
log.info("Done.")
def test_rotation_90_degrees_y_axis_90_degrees_x_axis_origin_is_0(self):
"""Expected file has been generated with Chimera fixing the rotation to the
center of coordinates and modifying the column of atom name to have the
same padding as the write_pdb_file function.
"""
protein = Complex(chains=self.chains2)
# Heading 90degrees (Y axis)
q1 = Quaternion(0.7071, 0.0, 0.7071, 0.0)
# Attitude 90degrees (X axis)
q2 = Quaternion(0.7071, 0.0, 0.0, 0.7071)
q = q1 * q2
protein.rotate(q)
write_pdb_to_file(protein, self.test_path / 'rotated.pdb',
protein.atom_coordinates[0])
assert filecmp.cmp(
self.golden_data_path / 'two_residues_y_90_x_90.pdb',
self.test_path / 'rotated.pdb')
def test_null_rotation(self):
protein = Complex(chains=self.chains2)
q = Quaternion()
protein.rotate(q)
write_pdb_to_file(protein, self.test_path+'rotated.pdb', protein.atom_coordinates[0])
assert filecmp.cmp(self.golden_data_path+'two_residues.pdb', self.test_path+'rotated.pdb')
for step in xrange(0, num_steps + 1):
try:
# Parse each stored step file
file_name = 'gso_%d.out' % step
translation, rotation, nm_rec, nm_lig = parse_file(
file_name, glowworm_id)
receptor_pose = receptor.atom_coordinates[0].clone()
ligand_pose = ligand.atom_coordinates[0].clone()
num_rec_nmodes = len(nm_rec)
if num_rec_nmodes:
for i in range(num_rec_nmodes):
receptor_pose.coordinates += nmodes_rec[i] * nm_rec[i]
num_lig_nmodes = len(nm_lig)
if num_lig_nmodes:
for i in range(num_lig_nmodes):
ligand_pose.coordinates += nmodes_lig[i] * nm_lig[i]
# We rotate first, ligand it's at initial position
ligand_pose.rotate(rotation)
ligand_pose.translate(translation)
output_file_name = 'trajectory_%s_step_%s.pdb' % (glowworm_id,
step)
write_pdb_to_file(receptor, output_file_name, receptor_pose)
write_pdb_to_file(ligand, output_file_name, ligand_pose)
log.info("Generated trajectory for step %s" % (step))
except TypeError:
pass
protein_anm.calcModes(n_modes=n_modes)
print('Normal modes calculated')
atoms, residues, chains = parse_complex_from_file(pdb_structure)
lightdock_structures = [{'atoms': atoms, 'residues': residues, 'chains': chains, 'file_name': pdb_structure}]
lightdock_structure = Complex.from_structures(lightdock_structures)
print('Structure read by lightdock')
num_atoms_prody = len(protein.protein)
num_atoms_lightdock = len(atoms)
if num_atoms_prody != num_atoms_lightdock:
raise SystemExit("Number of atoms is different")
protein_anm_ext, protein_all = extendModel(protein_anm, ca_atoms, protein, norm=True)
modes = []
for i in range(n_modes):
nm = protein_anm_ext.getEigvecs()[:, i].reshape((num_atoms_lightdock, 3))
modes.append(nm)
coordinates = lightdock_structure.atom_coordinates[0].coordinates
for i in range(n_modes):
lightdock_structure.atom_coordinates[0].coordinates += modes[i] * factor
output_file = 'anm_' + pdb_structure
write_pdb_to_file(lightdock_structure, output_file, lightdock_structure[0])
print('Structure written to %s' % output_file)
print('Done.')
protein_anm.calcModes(n_modes=n_modes)
print 'Normal modes calculated'
atoms, residues, chains = parse_complex_from_file(pdb_structure)
lightdock_structures = [{'atoms': atoms, 'residues': residues, 'chains': chains, 'file_name': pdb_structure}]
lightdock_structure = Complex.from_structures(lightdock_structures)
print 'Structure read by lightdock'
num_atoms_prody = len(protein.protein)
num_atoms_lightdock = len(atoms)
if num_atoms_prody != num_atoms_lightdock:
raise SystemExit("Number of atoms is different")
protein_anm_ext, protein_all = extendModel(protein_anm, ca_atoms, protein, norm=True)
modes = []
for i in range(n_modes):
nm = protein_anm_ext.getEigvecs()[:, i].reshape((num_atoms_lightdock, 3))
modes.append(nm)
coordinates = lightdock_structure.atom_coordinates[0].coordinates
for i in range(n_modes):
lightdock_structure.atom_coordinates[0].coordinates += modes[i] * factor
output_file = 'anm_' + pdb_structure
write_pdb_to_file(lightdock_structure, output_file, lightdock_structure[0])
print 'Structure written to %s' % output_file
print 'Done.'
# Check NM file for receptor
nm_rec_file = os.path.join(nm_path, DEFAULT_REC_NM_FILE + '.npy')
if os.path.exists(nm_rec_file):
nmodes_rec = read_nmodes(nm_rec_file)
# Check NM file for ligand
nm_lig_file = os.path.join(nm_path, DEFAULT_LIG_NM_FILE + '.npy')
if os.path.exists(nm_lig_file):
nmodes_lig = read_nmodes(nm_lig_file)
for i, glowworm in enumerate(glowworms):
receptor_pose = receptor.atom_coordinates[glowworm.receptor_id].clone()
ligand_pose = ligand.atom_coordinates[glowworm.ligand_id].clone()
# Use normal modes if provided:
if nmodes_rec.any():
for nm in range(DEFAULT_NMODES_REC):
rec_extent = np.array([float(x) for x in glowworm.pose[7:7 + DEFAULT_NMODES_REC]])
receptor_pose.coordinates += nmodes_rec[nm] * rec_extent[nm]
if nmodes_lig.any():
for nm in range(DEFAULT_NMODES_LIG):
lig_extent = np.array([float(x) for x in glowworm.pose[-DEFAULT_NMODES_LIG:]])
ligand_pose.coordinates += nmodes_lig[nm] * lig_extent[nm]
# We rotate first, ligand it's at initial position
rotation = Quaternion(glowworm.pose[3], glowworm.pose[4], glowworm.pose[5], glowworm.pose[6])
ligand_pose.rotate(rotation)
ligand_pose.translate([glowworm.pose[0], glowworm.pose[1], glowworm.pose[2]])
write_pdb_to_file(receptor, os.path.join(destination_path, 'top_%s.pdb' % str(i+1)), receptor_pose)
write_pdb_to_file(ligand, os.path.join(destination_path, 'top_%s.pdb' % str(i+1)), ligand_pose)
log.info("Generated %d conformations" % args.top)
raise SystemExit
if len(lig_extents):
try:
for nm in range(num_anm_lig):
ligand_pose.coordinates += nmodes_lig[nm] * lig_extents[i][
nm]
except ValueError:
log.error("Problem found on calculating ANM for ligand:")
log.error("Number of atom coordinates is: %s" %
str(receptor_pose.coordinates.shape))
log.error("Number of ANM is: %s" % str(nmodes_rec.shape))
raise SystemExit
except IndexError:
log.error("Problem found on calculating ANM for ligand:")
log.error(
"If you have used anm_lig different than default, please use --setup"
)
raise SystemExit
# We rotate first, ligand it's at initial position
ligand_pose.rotate(rotations[i])
ligand_pose.translate(translations[i])
write_pdb_to_file(
receptor, os.path.join(destination_path, 'lightdock_%s.pdb' % i),
receptor_pose)
write_pdb_to_file(
ligand, os.path.join(destination_path, 'lightdock_%s.pdb' % i),
ligand_pose)
log.info("Generated %d conformations" % num_conformations)
except ValueError:
log.error("Problem found on calculating ANM for receptor:")
log.error("Number of atom coordinates is: %s" % str(receptor_pose.coordinates.shape))
log.error("Number of ANM is: %s" % str(nmodes_rec.shape))
raise SystemExit
except IndexError:
log.error("Problem found on calculating ANM for receptor:")
log.error("If you have used anm_rec different than default, please use --setup")
raise SystemExit
if len(lig_extents):
try:
for nm in range(num_anm_lig):
ligand_pose.coordinates += nmodes_lig[nm] * lig_extents[i][nm]
except ValueError:
log.error("Problem found on calculating ANM for ligand:")
log.error("Number of atom coordinates is: %s" % str(receptor_pose.coordinates.shape))
log.error("Number of ANM is: %s" % str(nmodes_rec.shape))
raise SystemExit
except IndexError:
log.error("Problem found on calculating ANM for ligand:")
log.error("If you have used anm_lig different than default, please use --setup")
raise SystemExit
# We rotate first, ligand it's at initial position
ligand_pose.rotate(rotations[i])
ligand_pose.translate(translations[i])
write_pdb_to_file(receptor, os.path.join(destination_path, 'lightdock_%s.pdb' % i), receptor_pose)
write_pdb_to_file(ligand, os.path.join(destination_path, 'lightdock_%s.pdb' % i), ligand_pose)
log.info("Generated %d conformations" % num_conformations)
glowworm.receptor_id].clone()
ligand_pose = ligand.atom_coordinates[glowworm.ligand_id].clone()
# Use normal modes if provided:
if nmodes_rec.any():
for nm in range(num_anm_rec):
rec_extent = np.array(
[float(x) for x in glowworm.pose[7:7 + num_anm_rec]])
receptor_pose.coordinates += nmodes_rec[nm] * rec_extent[nm]
if nmodes_lig.any():
for nm in range(num_anm_lig):
lig_extent = np.array(
[float(x) for x in glowworm.pose[-num_anm_lig:]])
ligand_pose.coordinates += nmodes_lig[nm] * lig_extent[nm]
# We rotate first, ligand it's at initial position
rotation = Quaternion(glowworm.pose[3], glowworm.pose[4],
glowworm.pose[5], glowworm.pose[6])
ligand_pose.rotate(rotation)
ligand_pose.translate(
[glowworm.pose[0], glowworm.pose[1], glowworm.pose[2]])
write_pdb_to_file(
receptor,
os.path.join(destination_path, 'top_%s.pdb' % str(i + 1)),
receptor_pose)
write_pdb_to_file(
ligand,
os.path.join(destination_path, 'top_%s.pdb' % str(i + 1)),
ligand_pose)
log.info("Generated %d conformations" % args.top)
nmodes_lig = None
for step in xrange(0, num_steps+1):
try:
# Parse each stored step file
file_name = 'gso_%d.out' % step
translation, rotation, nm_rec, nm_lig = parse_file(file_name, glowworm_id)
receptor_pose = receptor.atom_coordinates[0].clone()
ligand_pose = ligand.atom_coordinates[0].clone()
num_rec_nmodes = len(nm_rec)
if num_rec_nmodes:
for i in range(num_rec_nmodes):
receptor_pose.coordinates += nmodes_rec[i] * nm_rec[i]
num_lig_nmodes = len(nm_lig)
if num_lig_nmodes:
for i in range(num_lig_nmodes):
ligand_pose.coordinates += nmodes_lig[i] * nm_lig[i]
# We rotate first, ligand it's at initial position
ligand_pose.rotate(rotation)
ligand_pose.translate(translation)
output_file_name = 'trajectory_%s_step_%s.pdb' % (glowworm_id, step)
write_pdb_to_file(receptor, output_file_name, receptor_pose)
write_pdb_to_file(ligand, output_file_name, ligand_pose)
log.info("Generated trajectory for step %s" % (step))
except TypeError:
pass
