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