meld.system.meld_system.System

class meld.system.meld_system.System(solvation, openmm_system, openmm_topology, integrator, barostat, template_coordinates, template_velocities, template_box_vectors, builder_info)[source]

Bases: ISystem

A class representing a MELD system.

__init__(solvation, openmm_system, openmm_topology, integrator, barostat, template_coordinates, template_velocities, template_box_vectors, builder_info)[source]

Initialize a MELD system

Parameters

solvation (str) – the solvation model to use
openmm_system (System) – the OpenMM system
openmm_topology (Topology) – the OpenMM topology
integrator (LangevinIntegrator) – the OpenMM integrator
barostat (Optional[MonteCarloBarostat]) – the OpenMM barostat
template_coordinates (ndarray) – the coordinates of the template
template_velocities (ndarray) – the velocities of the template
template_box_vectors (Optional[ndarray]) – the box vectors of the template
builder_info (dict) – a dictionary of extra information from the builder/patchers

Methods

`__init__`(solvation, openmm_system, ...)	Initialize a MELD system
`add_extra_angle`(i, j, k, angle, force_constant)	Add an extra angle to the system
`add_extra_bond`(i, j, length, force_constant)	Add an extra bond to the system
`add_extra_torsion`(i, j, k, l, phase, energy, ...)	Add an extra torsion to the system
`get_pdb_writer`()	Get the PDBWriter
`get_state_template`()	Get a template SystemState.

Attributes

`atom_names`	names for each atom
`barostat`	Get the barostat
`integrator`	Get the integrator
`n_atoms`	number of atoms
`num_alignments`	Number of rdc alignments
`omm_system`	Get the openmm system
`residue_names`	residue names for each atom
`residue_numbers`	residue numbers for each atom
`solvation`	Get the solvation model
`template_box_vectors`	Get the template box vectors
`template_coordinates`	Get the template coordinates
`template_velocities`	Get the template velocities
`topology`	Get the openmm topology
`restraints`	The object to handle managing restraints for the system
`density`	The object to handle managing densities for the system
`index`	The object to lookup atom and residue indices
`temperature_scaler`	The temperature scaler for the system
`param_sampler`	The sampler for parameters
`mapper`	The peak map manager

add_extra_angle(i, j, k, angle, force_constant)[source]

Add an extra angle to the system

Parameters

i (AtomIndex) – first atom in angle
j (AtomIndex) – second atom in angle
k (AtomIndex) – third atom in angle
angle (float) – equilibrium angle in degrees
force_constant (float) – strength of angle in kJ/mol/deg^2

Return type

None

add_extra_bond(i, j, length, force_constant)[source]

Add an extra bond to the system

Parameters

i (AtomIndex) – first atom in bond
j (AtomIndex) – second atom in bond
length (float) – length of bond, in nm
force_constant (float) – strength of bond in kJ/mol/nm^2

Return type

None

add_extra_torsion(i, j, k, l, phase, energy, multiplicity)[source]

Add an extra torsion to the system

Parameters

i (AtomIndex) – first atom in torsion
j (AtomIndex) – second atom in torsion
k (AtomIndex) – third atom in torsion
l (AtomIndex) – fourth atom in angle
phase (float) – phase angle in degrees
energy (float) – energy in kJ/mol
multiplicity (int) – periodicity of torsion

Return type

None

property atom_names: List[str]: names for each atom

property barostat: Get the barostat

density: DensityManager: The object to handle managing densities for the system

get_pdb_writer()[source]

Get the PDBWriter

Return type: PDBWriter

get_state_template()[source]

Get a template SystemState.

Return type: SystemState

index: Indexer: The object to lookup atom and residue indices

property integrator: Get the integrator

mapper: PeakMapManager: The peak map manager

property n_atoms: int: number of atoms

property num_alignments: int: Number of rdc alignments

property omm_system: Get the openmm system

param_sampler: ParameterManager: The sampler for parameters

property residue_names: List[str]: residue names for each atom

property residue_numbers: List[int]: residue numbers for each atom

restraints: RestraintManager: The object to handle managing restraints for the system

property solvation: Get the solvation model

temperature_scaler: Optional[TemperatureScaler]: The temperature scaler for the system

property template_box_vectors: Optional[ndarray]: Get the template box vectors

property template_coordinates: ndarray: Get the template coordinates

property template_velocities: ndarray: Get the template velocities

property topology: Get the openmm topology