def __call__(self, pars, namespace, values, option_string=None):
"""This function is executed when Torsion maker is called."""
# TODO Should this be here?
# load in the ligand molecule
mol = Ligand(values)
# Prompt the user for the scan order
scanner = TorsionScan(mol)
scanner.find_scan_order()
# Write out the scan file
with open('QUBE_torsions.txt', 'w+') as qube:
qube.write(
'# dihedral definition by atom indices starting from 1\n# i j k l\n'
)
for scan in mol.scan_order:
scan_di = mol.dihedrals[scan][0]
qube.write(
f' {scan_di[0]:2} {scan_di[1]:2} {scan_di[2]:2} {scan_di[3]:2}\n'
)
printf('QUBE_torsions.txt made.')
sys.exit()
def __call__(self, pars, namespace, values, option_string=None):
# load in the ligand
mol = Ligand(values)
# Prompt the user for the scan order
scanner = TorsionScan(mol)
scanner.find_scan_order()
# Write out the scan file
with open(f'{mol.name}.dihedrals', 'w+') as qube:
qube.write('# dihedral definition by atom indices starting from 0\n# i j k l\n')
for scan in mol.scan_order:
scan_di = mol.dihedrals[scan][0]
qube.write(f' {scan_di[0]:2} {scan_di[1]:2} {scan_di[2]:2} {scan_di[3]:2}\n')
printf(f'{mol.name}.dihedrals made.')
sys.exit()
def torsion_scan(molecule):
"""Perform torsion scan."""
scan = TorsionScan(molecule)
# Try to find a scan file; if none provided and more than one torsion detected: prompt user
try:
copy('../../QUBE_torsions.txt', 'QUBE_torsions.txt')
scan.find_scan_order(file='QUBE_torsions.txt')
except FileNotFoundError:
scan.find_scan_order()
scan.start_scan()
append_to_log('Torsion_scans complete')
return molecule
def torsion_scan(molecule):
"""Perform torsion scan."""
append_to_log('Starting torsion_scans')
tor_scan = TorsionScan(molecule)
# Check that we have a scan order for the molecule this should of been captured from the dihedral file
tor_scan.find_scan_order()
tor_scan.scan()
append_to_log('Finishing torsion_scans')
return molecule
def torsion_scan(molecule):
"""Perform torsion scan."""
# TODO find constraints file if present
append_to_log('Starting torsion_scans')
molecule.find_rotatable_dihedrals()
molecule.symmetrise_from_topo()
scan = TorsionScan(molecule)
# Try to find a scan file; if none provided and more than one torsion detected: prompt user
try:
copy('../../QUBE_torsions.txt', 'QUBE_torsions.txt')
scan.find_scan_order(file='QUBE_torsions.txt')
except FileNotFoundError:
scan.find_scan_order()
scan.scan()
append_to_log('Finishing torsion_scans')
return molecule
def torsion_optimise(molecule):
"""Perform torsion optimisation."""
append_to_log('Starting torsion_optimisations')
# First we should make sure we have collected the results of the scans
if molecule.qm_scans is None:
os.chdir(os.path.join(molecule.home, '09_torsion_scan'))
scan = TorsionScan(molecule)
if molecule.scan_order is None:
scan.find_scan_order()
scan.collect_scan()
os.chdir(os.path.join(molecule.home, '10_torsion_optimise'))
TorsionOptimiser(molecule).run()
append_to_log('Finishing torsion_optimisations')
return molecule
def torsion_optimise(molecule):
"""Perform torsion optimisation."""
append_to_log('Starting torsion_optimisations')
# First we should make sure we have collected the results of the scans
if not molecule.qm_scans:
os.chdir(os.path.join(molecule.home, '9_torsion_scan'))
scan = TorsionScan(molecule)
scan.find_scan_order()
scan.collect_scan()
os.chdir(os.path.join(molecule.home, '10_torsion_optimise'))
opt = TorsionOptimiser(molecule,
refinement=molecule.refinement_method,
vn_bounds=molecule.tor_limit)
opt.run()
append_to_log('Finishing torsion_optimisations')
return molecule