def load_restraints(filepath="restraints.json"):
"""Load restraints from a JSON file.
Parameters
----------
filepath: os.PathLike
The name of the JSON file to load.
Returns
-------
restraints: list
List of :class:`paprika.restraints.DAT_restraint`.
"""
log.debug("Loading restraint information from JSON.")
with open(os.path.join(filepath), "r") as f:
json_data = f.read()
restraint_json = json_data.split("\n")
restraints = []
for restraint in restraint_json:
if restraint == "":
continue
loaded = json.loads(restraint, object_hook=json_numpy_obj_hook)
tmp = DAT_restraint()
tmp.__dict__ = loaded
properties = [
"mask1",
"mask2",
"mask3",
"mask4",
"topology",
"instances",
"custom_restraint_values",
"auto_apr",
"continuous_apr",
"attach",
"pull",
"release",
"amber_index",
]
for class_property in properties:
if f"_{class_property}" in tmp.__dict__.keys():
tmp.__dict__[class_property] = tmp.__dict__[
f"_{class_property}"]
restraints.append(tmp)
return restraints
def _parse_restraints(cls, restraint_dictionaries):
"""Parses the dictionary representations of a list of `paprika` restraint
objects into a list of full restraint objects."""
from paprika.restraints import DAT_restraint
restraints = []
for restraint_dictionary in restraint_dictionaries:
restraint = DAT_restraint()
restraint.__dict__ = restraint_dictionary
properties = [
"mask1",
"mask2",
"mask3",
"mask4",
"topology",
"instances",
"custom_restraint_values",
"auto_apr",
"continuous_apr",
"attach",
"pull",
"release",
"amber_index",
]
for class_property in properties:
if f"_{class_property}" in restraint.__dict__.keys():
restraint.__dict__[class_property] = restraint.__dict__[
f"_{class_property}"
]
restraints.append(restraint)
return restraints
def load_restraints(filepath="restraints.json"):
log.debug("Loading restraint information from JSON.")
with open(os.path.join(filepath), "r") as f:
json_data = f.read()
restraint_json = json_data.split("\n")
restraints = []
for restraint in restraint_json:
if restraint == "":
continue
loaded = json.loads(restraint, object_hook=json_numpy_obj_hook)
tmp = DAT_restraint()
tmp.__dict__ = loaded
try:
log.debug("Setting topology from file name.")
tmp.topology = pmd.load_file(loaded["topology"], structure=True)
except IOError:
log.debug(
"Unable to set topology information after loading from JSON.")
log.debug("Topology is set to the file name of the topology file.")
tmp.topology = loaded["topology"]
restraints.append(tmp)
return restraints
