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Merge branch 'master' into nathan/logging

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Nathan Baker
2020-11-29 16:14:43 -08:00
parent 9350799be1 f3bbd807ae
commit fda4fe577b
12 changed files with 70 additions and 323 deletions
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21
propka/conformation_container.py
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@@ -29,7 +29,13 @@ RESIDUE_MULTIPLIER = 1000
class ConformationContainer:
"""Container for molecular conformations"""
"""Container for molecular conformations
.. versionchanged:: 3.4.0
Removed :meth:`additional_setup_when_reading_input_files` as reading
PROPKA inputs is no longer supported.
"""
def __init__(self, name='', parameters=None, molecular_container=None):
"""Initialize conformation container.
@@ -63,19 +69,6 @@ class ConformationContainer:
if group:
self.setup_and_add_group(group)
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)
_LOGGER.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 set_common_charge_centres(self):
"""Assign charge centers to groups."""
for system in self.get_coupled_systems(