meld.interfaces.ISystem

class meld.interfaces.ISystem

Bases: 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
density
builder_info
extra_bonds
extra_restricted_angles
extra_torsions

abstract add_extra_angle(i, j, k, angle, force_constant)

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)

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)

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

abstract property barostat: MonteCarloBarostat

Get the barostat

abstract get_pdb_writer()

Get the PDBWriter

Return type

PDBWriter

abstract get_state_template()

Get a template state for this system

Return type

IState

abstract property integrator: LangevinIntegrator

Get the integrator

abstract property n_atoms: int

number of atoms

abstract property num_alignments: int

Number of rdc alignments

abstract property omm_system: System

Get the openmm system

abstract property residue_names: List[str]

residue names for each atom

abstract property residue_numbers: List[int]

residue numbers for each atom

abstract property solvation: str

Get the solvation model

abstract property template_box_vectors: Optional[ndarray]

Get the template box vectors

abstract property template_coordinates: ndarray

Get the template coordinates

abstract property template_velocities: ndarray

Get the template velocities

abstract property topology: Topology

Get the openmm topology