qmmm_pme.records package

Submodules

qmmm_pme.records.files module

A module defining the Files data container.

class qmmm_pme.records.files.Files(pdb_list=<qmmm_pme.records.files.FilesVariable object>, topology_list=<qmmm_pme.records.files.FilesVariable object>, forcefield_list=<qmmm_pme.records.files.FilesVariable object>, input_json=<qmmm_pme.records.files.FilesVariable object>)[source]

Bases: Record

A data container for records about input file paths.

Parameters:
forcefield_list: FilesVariable = <qmmm_pme.records.files.FilesVariable object>
Return type:

list[str]

input_json: FilesVariable = <qmmm_pme.records.files.FilesVariable object>
Return type:

list[str]

pdb_list: FilesVariable = <qmmm_pme.records.files.FilesVariable object>
Return type:

list[str]

topology_list: FilesVariable = <qmmm_pme.records.files.FilesVariable object>
Return type:

list[str]

class qmmm_pme.records.files.FilesVariable[source]

Bases: Variable

A wrapper class for variables belonging to the Files record.

update(value)[source]

Update the value of the FilesVariable.

Parameters:

value (list[str]) – The updated value to set the FilesVariable value to.

Return type:

None

qmmm_pme.records.record module

A module defining the Record and Variable classes.

class qmmm_pme.records.record.Record[source]

Bases: object

A base class for defining records.

Warning

This class currently has no implementation.

class qmmm_pme.records.record.Variable[source]

Bases: object

A base class for wrapping a variable belonging to a Record.

register_notifier(notifier)[source]

Add a notifier to the Variable, which will be called whenever the Variable is changed.

Parameters:

notifier (Callable[[...], None]) – The method which will be called when the Variable is changed.

Return type:

None

qmmm_pme.records.state module

A module defining the State data container.

class qmmm_pme.records.state.State(masses=<qmmm_pme.records.state.StateVariable object>, charges=<qmmm_pme.records.state.StateVariable object>, positions=<qmmm_pme.records.state.StateVariable object>, velocities=<qmmm_pme.records.state.StateVariable object>, momenta=<qmmm_pme.records.state.StateVariable object>, forces=<qmmm_pme.records.state.StateVariable object>, box=<qmmm_pme.records.state.StateVariable object>)[source]

Bases: Record

A data container for state information about the the System, comprising atomic masses, charges, positions, velocities, momenta, and forces; and the box vectors defining the periodic boundary condition.

Parameters:
box: StateVariable = <qmmm_pme.records.state.StateVariable object>
Return type:

NDArray[np.float64]

charges: StateVariable = <qmmm_pme.records.state.StateVariable object>
Return type:

NDArray[np.float64]

forces: StateVariable = <qmmm_pme.records.state.StateVariable object>
Return type:

NDArray[np.float64]

masses: StateVariable = <qmmm_pme.records.state.StateVariable object>
Return type:

NDArray[np.float64]

momenta: StateVariable = <qmmm_pme.records.state.StateVariable object>
Return type:

NDArray[np.float64]

positions: StateVariable = <qmmm_pme.records.state.StateVariable object>
Return type:

NDArray[np.float64]

velocities: StateVariable = <qmmm_pme.records.state.StateVariable object>
Return type:

NDArray[np.float64]

class qmmm_pme.records.state.StateVariable[source]

Bases: Variable

A wrapper class for variables belonging to the State record.

update(value)[source]

Update the value of the StateVariable.

Parameters:

value (ndarray[Any, dtype[float64]]) – The updated value to set the StateVariable value to.

Return type:

None

qmmm_pme.records.topology module

A module defining the Topology data container.

class qmmm_pme.records.topology.NameVariable[source]

Bases: Variable

A wrapper class for name variables belonging to the Topology record.

update(value)[source]

Update the value of the NameVariable.

Parameters:

value (list[str]) – The updated value to set the NameVariable value to.

Return type:

None

class qmmm_pme.records.topology.ResidueVariable[source]

Bases: Variable

A wrapper class for residue group variables belonging to the Topology record.

update(value)[source]

Update the value of the ResidueVariable.

Parameters:

value (list[list[int]]) – The updated value to set the ResidueVariable value to.

Return type:

None

class qmmm_pme.records.topology.Topology(atoms=<qmmm_pme.records.topology.ResidueVariable object>, qm_atoms=<qmmm_pme.records.topology.ResidueVariable object>, mm_atoms=<qmmm_pme.records.topology.ResidueVariable object>, ae_atoms=<qmmm_pme.records.topology.ResidueVariable object>, elements=<qmmm_pme.records.topology.NameVariable object>, residue_names=<qmmm_pme.records.topology.NameVariable object>, atom_names=<qmmm_pme.records.topology.NameVariable object>)[source]

Bases: Record

A data container for information about the topology of the System, comprising atom groups, residue names, element symbols, and atom names.

Parameters:
ae_atoms: ResidueVariable = <qmmm_pme.records.topology.ResidueVariable object>
Return type:

list[list[int]]

atom_names: NameVariable = <qmmm_pme.records.topology.NameVariable object>
Return type:

list[str]

atoms: ResidueVariable = <qmmm_pme.records.topology.ResidueVariable object>
Return type:

list[list[int]]

elements: NameVariable = <qmmm_pme.records.topology.NameVariable object>
Return type:

list[str]

mm_atoms: ResidueVariable = <qmmm_pme.records.topology.ResidueVariable object>
Return type:

list[list[int]]

qm_atoms: ResidueVariable = <qmmm_pme.records.topology.ResidueVariable object>
Return type:

list[list[int]]

residue_names: NameVariable = <qmmm_pme.records.topology.NameVariable object>
Return type:

list[str]

Module contents

A sub-package to define records kept by the System, which include data pertaining to input files and the state and topology of atoms and residues.