meld.interfaces.ISystem

class meld.interfaces.ISystem[source]

Bases: abc.ABC

An interface for MELD systems

__init__()

Methods

__init__()

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 state for this system

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

index

temperature_scaler

param_sampler

mapper

builder_info

extra_bonds

extra_restricted_angles

extra_torsions

abstract 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

abstract 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

abstract 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

abstract property atom_names: List[str]

names for each atom

Return type

List[str]

abstract property barostat: openmm.openmm.MonteCarloBarostat

Get the barostat

Return type

MonteCarloBarostat

abstract get_pdb_writer()[source]

Get the PDBWriter

Return type

PDBWriter

abstract get_state_template()[source]

Get a template state for this system

Return type

IState

abstract property integrator: openmm.openmm.LangevinIntegrator

Get the integrator

Return type

LangevinIntegrator

abstract property n_atoms: int

number of atoms

Return type

int

abstract property num_alignments: int

Number of rdc alignments

Return type

int

abstract property omm_system: openmm.openmm.System

Get the openmm system

Return type

System

abstract property residue_names: List[str]

residue names for each atom

Return type

List[str]

abstract property residue_numbers: List[int]

residue numbers for each atom

Return type

List[int]

abstract property solvation: str

Get the solvation model

Return type

str

abstract property template_box_vectors: Optional[numpy.ndarray]

Get the template box vectors

Return type

Optional[ndarray]

abstract property template_coordinates: numpy.ndarray

Get the template coordinates

Return type

ndarray

abstract property template_velocities: numpy.ndarray

Get the template velocities

Return type

ndarray

abstract property topology: openmm.app.topology.Topology

Get the openmm topology

Return type

Topology