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

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

Return type

List[str]

property barostat

Get the barostat

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

Return type

int

property num_alignments: int

Number of rdc alignments

Return type

int

property omm_system

Get the openmm system

param_sampler: ParameterManager

The sampler for parameters

property residue_names: List[str]

residue names for each atom

Return type

List[str]

property residue_numbers: List[int]

residue numbers for each atom

Return type

List[int]

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

Return type

Optional[ndarray]

property template_coordinates: ndarray

Get the template coordinates

Return type

ndarray

property template_velocities: ndarray

Get the template velocities

Return type

ndarray

property topology

Get the openmm topology