update variable to be more uniform
@@ -2177,21 +2177,21 @@ class ExperimentBuilder(object):
logger.debug('DSL string for the solvent: "{}"'.format(solvent_dsl))
# Determine complex and solvent phase solvents while also getting regions
- db_system = self._db.systems[system_id]
+ system_description = self._db.systems[system_id]
try: # binding free energy calculations
- solvent_ids = [db_system['solvent'],
- db_system['solvent']]
- ligand_regions = self._db.molecules.get(db_system.get('ligand'), {}).get('regions', {})
- receptor_regions = self._db.molecules.get(db_system.get('receptor'), {}).get('regions', {})
+ system_description = [system_description['solvent'],
+ system_description['solvent']]
+ ligand_regions = self._db.molecules.get(system_description.get('ligand'), {}).get('regions', {})
+ receptor_regions = self._db.molecules.get(system_description.get('receptor'), {}).get('regions', {})
# Name clashes have been resolved in the yaml validation
regions = {**ligand_regions, **receptor_regions}
except KeyError: # partition/solvation free energy calculations
try:
- solvent_ids = [db_system['solvent1'],
- db_system['solvent2']]
- regions = self._db.molecules.get(db_system.get('solute'), {}).get('regions', {})
+ solvent_ids = [system_description['solvent1'],
+ system_description['solvent2']]
+ regions = self._db.molecules.get(system_description.get('solute'), {}).get('regions', {})
except KeyError: # from xml/pdb system files
- assert 'phase1_path' in db_system
+ assert 'phase1_path' in system_description
solvent_ids = [None, None]
regions = {}
