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 the PDBWriter
Get a template state for this system
Attributes
names for each atom
Get the barostat
Get the integrator
number of atoms
Number of rdc alignments
Get the openmm system
residue names for each atom
residue numbers for each atom
Get the solvation model
Get the template box vectors
Get the template coordinates
Get the template velocities
Get the openmm topology
restraints
index
temperature_scaler
param_sampler
mapper
builder_info
extra_bonds
extra_restricted_angles
extra_torsions
- abstract add_extra_torsion(i, j, k, l, phase, energy, multiplicity)[source]
Add an extra torsion to the system
- 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 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