def parse(filename):
"""
Parses XML file and returns deserialized object. The return value
depends on the serialized object, summarized below
- System : returns simtk.openmm.System
- State : returns simtk.openmm.State
- Integrator : returns simtk.openmm.Integrator subclass
- ForceField : returns simtk.openmm.app.ForceField
Parameters
----------
filename : str or file-like
The file name or file object containing the XML-serialized object
Returns
-------
obj : System, State, Integrator, or ForceField
The deserialized object
Notes
-----
OpenMM requires the entire contents of this file read into memory. As a
result, this function may require a significant amount of memory.
"""
if isinstance(filename, string_types):
with closing(genopen(filename, 'r')) as f:
contents = f.read()
else:
contents = f.read()
# ForceField is not handled by XmlSerializer
if '<ForceField' in contents:
obj = StringIO()
obj.write(contents)
obj.seek(0)
return app.ForceField(obj)
obj = mm.XmlSerializer.deserialize(contents)
if isinstance(obj, (mm.System, mm.Integrator)):
return obj
elif isinstance(obj, mm.State):
return _OpenMMStateContents(obj)
return
def parse(filename):
"""
Parses XML file and returns deserialized object. The return value
depends on the serialized object, summarized below
- System : returns simtk.openmm.System
- State : returns simtk.openmm.State
- Integrator : returns simtk.openmm.Integrator subclass
- ForceField : returns simtk.openmm.app.ForceField
Parameters
----------
filename : str or file-like
The file name or file object containing the XML-serialized object
Returns
-------
obj : System, State, Integrator, or ForceField
The deserialized object
Notes
-----
OpenMM requires the entire contents of this file read into memory. As a
result, this function may require a significant amount of memory.
"""
import simtk.openmm as mm
from simtk.openmm import app
if isinstance(filename, string_types):
with closing(genopen(filename, 'r')) as f:
contents = f.read()
else:
contents = filename.read()
# ForceField is not handled by XmlSerializer
if '<ForceField' in contents:
obj = StringIO()
obj.write(contents)
obj.seek(0)
return app.ForceField(obj)
obj = mm.XmlSerializer.deserialize(contents)
if isinstance(obj, mm.State):
return _OpenMMStateContents(obj)
return obj
