load_topology(topology, system=None, xyz=None, box=None, condense_atom_types=True)¶
parmed.structure.Structureinstance from an OpenMM Topology, optionally filling in parameters from a System
The Topology instance with the list of atoms and bonds for this system
simtk.openmm.Systemor str, optional
If provided, parameters from this System will be applied to the Structure. If a string is given, it will be interpreted as the file name of an XML-serialized System, and it will be deserialized into a System before used to supply parameters
- xyzstr or array of float
Name of a file containing coordinate information or an array of coordinates. If file has unit cell information, it also uses that information unless
box(below) is also specified
- boxarray of 6 floats
Unit cell dimensions
- condense_atom_typesbool, default=True
If True, create unique atom types based on de-duplicating properties. If False, create one atom type for each atom in the system, even if its properties match an existing atom type.
The structure from the provided topology
- OpenMMWarning if parameters are found that cannot be interpreted or
- processed by ParmEd
- TypeError if there are any mismatches between the provided topology and
- system (e.g., they have different numbers of atoms)
- IOError if system is a string and it is not an existing file
Due to its flexibility with CustomForces, it is entirely possible that the functional form of the potential will be unknown to ParmEd. This function will try to use the energy expression to identify supported potential types that are implemented as CustomForce objects. In particular, quadratic improper torsions, when recognized, will be extracted.
Other CustomForces, including the CustomNonbondedForce used to implement NBFIX (off-diagonal L-J modifications) and the 12-6-4 potential, will not be processed and will result in an unknown functional form.
If an OpenMM Atom.id attribute is populated by a non-integer, it will be used to name the corresponding ParmEd AtomType object.