def additional_setup_when_reading_input_file(self):
"""Generate interaction map and charge centers."""
# if a group is coupled and we are reading a .propka_input file, then
# some more configuration might be needed
map_ = make_interaction_map(
'Covalent coupling map for {0:s}'.format(str(self)),
self.get_covalently_coupled_groups(),
lambda g1, g2: g1 in g2.covalently_coupled_groups)
info(map_)
# check if we should set a common charge centre as well
if self.parameters.common_charge_centre:
self.set_common_charge_centres()
def print_out_swaps(self, conformation):
"""Print out something having to do with coupling interactions.
Args:
conformation: conformation to print
"""
map_ = make_interaction_map(
'Non-covalent coupling map for {0:s}'.format(str(conformation)),
conformation.get_non_covalently_coupled_groups(),
lambda g1, g2: g1 in g2.non_covalently_coupled_groups)
_LOGGER.info(map_)
for system in conformation.get_coupled_systems(
conformation.get_non_covalently_coupled_groups(),
Group.get_non_covalently_coupled_groups):
self.print_system(conformation, list(system))
def find_covalently_coupled_groups(self):
"""Find covalently coupled groups and set common charge centres."""
for group in self.get_titratable_groups():
# Find covalently bonded groups
bonded_groups = self.find_bonded_titratable_groups(
group.atom, 1, group.atom)
# coupled groups
for bond_group in bonded_groups:
if bond_group in group.covalently_coupled_groups:
continue
if bond_group.atom.sybyl_type == group.atom.sybyl_type:
group.couple_covalently(bond_group)
# check if we should set a common charge centre as well
if self.parameters.common_charge_centre:
self.set_common_charge_centres()
# print coupling map
map_ = make_interaction_map(
'Covalent coupling map for {0:s}'.format(str(self)),
self.get_covalently_coupled_groups(),
lambda g1, g2: g1 in g2.covalently_coupled_groups)
_LOGGER.info("Coupling map:\n%s", map_)