Open Force Field Toolkit
0.2.0
Open Force Field Initiative
Open Force Field Toolkit
Installation
Installing via
conda
Required dependencies
Release History
0.2.0
0.1.0
The SMIRks Native Open Force Field (SMIRNOFF) specification v0.2
Authors and acknowledgments
Representations and encodings
Reference implementation
Support for molecular simulation packages
Basic structure
Units
SMIRNOFF independently applies parameters to each class of potential energy terms
Partial charge and electrostatics models
Parameter sections
Advanced features
The
openforcefield
reference implementation
Version history
Examples using SMIRNOFF with the toolkit
Index of provided examples
Developing for the toolkit
Style guide
Contributing
How can I become a developer?
Frequently asked questions (FAQ)
Input files for applying SMIRNOFF parameters
Can I use an AMBER (or GROMACS) topology/coordinate file as a starting point for applying a SMIRNOFF force field?
What about starting from a PDB file?
What do you recommend as a starting point?
Molecular topology representations
Primary objects
Secondary objects
Forcefield typing tools
Chemical environments
Forcefield typing engines
Utilities
Toolkit wrappers
Serialization support
Structure tools
Miscellaneous utilities
Page
Index
_
|
A
|
B
|
C
|
E
|
F
|
G
|
I
|
K
|
M
|
N
|
O
|
P
|
R
|
S
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T
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V
_
__init__() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.VirtualSite method)
(openforcefield.typing.chemistry.ChemicalEnvironment method)
(openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.AngleHandler.AngleType method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler.BondType method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler.ImproperTorsionType method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterType method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler.ProperTorsionType method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler.vdWType method)
(openforcefield.utils.serialization.Serializable method)
(openforcefield.utils.toolkits.AmberToolsToolkitWrapper method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
(openforcefield.utils.toolkits.ToolkitRegistry method)
(openforcefield.utils.toolkits.ToolkitWrapper method)
A
add_atom() (openforcefield.topology.Molecule method)
add_bond() (openforcefield.topology.Atom method)
(openforcefield.topology.Molecule method)
add_bond_charge_virtual_site() (openforcefield.topology.Molecule method)
add_conformer() (openforcefield.topology.Molecule method)
add_constraint() (openforcefield.topology.Topology method)
add_divalent_lone_pair_virtual_site() (openforcefield.topology.Molecule method)
add_molecule() (openforcefield.topology.Topology method)
add_monovalent_lone_pair_virtual_site() (openforcefield.topology.Molecule method)
add_parameter() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
add_particle() (openforcefield.topology.Topology method)
add_toolkit() (openforcefield.utils.toolkits.ToolkitRegistry method)
add_trivalent_lone_pair_virtual_site() (openforcefield.topology.Molecule method)
add_virtual_site() (openforcefield.topology.Atom method)
addANDtype() (openforcefield.typing.chemistry.ChemicalEnvironment.Atom method)
(openforcefield.typing.chemistry.ChemicalEnvironment.Bond method)
addAtom() (openforcefield.typing.chemistry.ChemicalEnvironment method)
addORtype() (openforcefield.typing.chemistry.ChemicalEnvironment.Atom method)
(openforcefield.typing.chemistry.ChemicalEnvironment.Bond method)
all_subclasses() (in module openforcefield.utils.utils)
AmberToolsToolkitWrapper (class in openforcefield.utils.toolkits)
AngleHandler (class in openforcefield.typing.engines.smirnoff.parameters)
AngleHandler.AngleType (class in openforcefield.typing.engines.smirnoff.parameters)
angles (openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
(openforcefield.topology.Topology attribute)
AngleType (class in openforcefield.typing.engines.smirnoff.parameters.AngleHandler)
append() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
aromaticity_model (openforcefield.topology.Topology attribute)
assert_bonded() (openforcefield.topology.Topology method)
assign_charge_from_molecules() (openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
assign_parameters() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
asSMARTS() (openforcefield.typing.chemistry.ChemicalEnvironment.Atom method)
(openforcefield.typing.chemistry.ChemicalEnvironment.Bond method)
asSMIRKS() (openforcefield.typing.chemistry.ChemicalEnvironment method)
(openforcefield.typing.chemistry.ChemicalEnvironment.Atom method)
(openforcefield.typing.chemistry.ChemicalEnvironment.Bond method)
Atom (class in openforcefield.topology)
atom() (openforcefield.topology.Topology method)
atomic_number (openforcefield.topology.Atom attribute)
atoms (openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
(openforcefield.topology.VirtualSite attribute)
B
Bond (class in openforcefield.topology)
bond() (openforcefield.topology.Topology method)
bonded_atoms (openforcefield.topology.Atom attribute)
BondHandler (class in openforcefield.typing.engines.smirnoff.parameters)
BondHandler.BondType (class in openforcefield.typing.engines.smirnoff.parameters)
bonds (openforcefield.topology.Atom attribute)
(openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
BondType (class in openforcefield.typing.engines.smirnoff.parameters.BondHandler)
box_vectors (openforcefield.topology.Topology attribute)
C
call() (openforcefield.utils.toolkits.ToolkitRegistry method)
charge_increments (openforcefield.topology.VirtualSite attribute)
charge_model (openforcefield.topology.Topology attribute)
check_energy_is_finite() (in module openforcefield.utils.structure)
check_handler_compatibility() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
check_parameter_compatibility() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
chemical_environment_matches() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Topology method)
ChemicalEnvironment (class in openforcefield.typing.chemistry)
ChemicalEnvironment.Atom (class in openforcefield.typing.chemistry)
ChemicalEnvironment.Bond (class in openforcefield.typing.chemistry)
clear() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
combinePositions() (in module openforcefield.utils.structure)
combining_rules (openforcefield.typing.engines.smirnoff.parameters.vdWHandler attribute)
compute_partial_charges() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.AmberToolsToolkitWrapper method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
compute_partial_charges_am1bcc() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.AmberToolsToolkitWrapper method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
compute_wiberg_bond_orders() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
conformers (openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
constrained_atom_pairs (openforcefield.topology.Topology attribute)
copy() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
count() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
cutoff (openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler attribute)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler attribute)
E
ElectrostaticsHandler (class in openforcefield.typing.engines.smirnoff.parameters)
element (openforcefield.topology.Atom attribute)
epsilon (openforcefield.topology.VirtualSite attribute)
extend() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
extractPositionsFromOEMol() (in module openforcefield.utils.structure)
F
find_matches() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
find_smarts_matches() (openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
formal_charge (openforcefield.topology.Atom attribute)
fractional_bond_order_model (openforcefield.topology.Topology attribute)
from_bson() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology class method)
(openforcefield.topology.VirtualSite class method)
(openforcefield.utils.serialization.Serializable class method)
from_dict() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology class method)
(openforcefield.topology.VirtualSite static method)
from_file() (openforcefield.topology.FrozenMolecule static method)
(openforcefield.topology.Molecule static method)
(openforcefield.utils.toolkits.AmberToolsToolkitWrapper method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
(openforcefield.utils.toolkits.ToolkitWrapper method)
from_file_obj() (openforcefield.utils.toolkits.AmberToolsToolkitWrapper method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
(openforcefield.utils.toolkits.ToolkitWrapper method)
from_iupac() (openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
from_json() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology class method)
(openforcefield.topology.VirtualSite class method)
(openforcefield.utils.serialization.Serializable class method)
from_mdtraj() (openforcefield.topology.Topology static method)
from_messagepack() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology class method)
(openforcefield.topology.VirtualSite class method)
(openforcefield.utils.serialization.Serializable class method)
from_molecules() (openforcefield.topology.Topology class method)
from_object() (openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
from_openeye() (openforcefield.topology.FrozenMolecule static method)
(openforcefield.topology.Molecule static method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper static method)
from_openmm() (openforcefield.topology.Topology class method)
from_parmed() (openforcefield.topology.Topology static method)
from_pickle() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology class method)
(openforcefield.topology.VirtualSite class method)
(openforcefield.utils.serialization.Serializable class method)
from_rdkit() (openforcefield.topology.FrozenMolecule static method)
(openforcefield.topology.Molecule static method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
from_smiles() (openforcefield.topology.FrozenMolecule static method)
(openforcefield.topology.Molecule static method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
from_toml() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology class method)
(openforcefield.topology.VirtualSite class method)
(openforcefield.utils.serialization.Serializable class method)
from_topology() (openforcefield.topology.FrozenMolecule static method)
(openforcefield.topology.Molecule static method)
from_xml() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology class method)
(openforcefield.topology.VirtualSite class method)
(openforcefield.utils.serialization.Serializable class method)
from_yaml() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology class method)
(openforcefield.topology.VirtualSite class method)
(openforcefield.utils.serialization.Serializable class method)
FrozenMolecule (class in openforcefield.topology)
G
generate_conformers() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
generateProteinStructure() (in module openforcefield.utils.structure)
generateSMIRNOFFStructure() (in module openforcefield.utils.structure)
generateTopologyFromOEMol() (in module openforcefield.utils.structure)
get_bond_between() (openforcefield.topology.Topology method)
get_data_filename() (in module openforcefield.utils.utils)
get_energy() (in module openforcefield.utils.structure)
get_fractional_bond_order() (openforcefield.topology.Topology method)
get_fractional_bond_orders() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
get_molecule_parameterIDs() (in module openforcefield.utils.structure)
get_parameter() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
get_testdata_filename() (in module openforcefield.utils.structure)
getAlphaAtoms() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getAlphaBonds() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getANDtypes() (openforcefield.typing.chemistry.ChemicalEnvironment.Atom method)
(openforcefield.typing.chemistry.ChemicalEnvironment.Bond method)
getAtoms() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getBetaAtoms() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getBetaBonds() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getBond() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getBondOrder() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getBonds() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getComponentList() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getIndexedAtoms() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getIndexedBonds() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getMolParamIDToAtomIndex() (in module openforcefield.utils.structure)
getNeighbors() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getOrder() (openforcefield.typing.chemistry.ChemicalEnvironment.Bond method)
getORtypes() (openforcefield.typing.chemistry.ChemicalEnvironment.Atom method)
(openforcefield.typing.chemistry.ChemicalEnvironment.Bond method)
getType() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getUnindexedAtoms() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getUnindexedBonds() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getValence() (openforcefield.typing.chemistry.ChemicalEnvironment method)
I
impropers (openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
(openforcefield.topology.Topology attribute)
ImproperTorsionHandler (class in openforcefield.typing.engines.smirnoff.parameters)
ImproperTorsionHandler.ImproperTorsionType (class in openforcefield.typing.engines.smirnoff.parameters)
ImproperTorsionType (class in openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler)
index() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
inherit_docstrings() (in module openforcefield.utils.utils)
insert() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
is_aromatic (openforcefield.topology.Atom attribute)
is_available() (openforcefield.utils.toolkits.AmberToolsToolkitWrapper class method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper class method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper class method)
(openforcefield.utils.toolkits.ToolkitWrapper class method)
is_bonded() (openforcefield.topology.Topology method)
is_bonded_to() (openforcefield.topology.Atom method)
is_constrained() (openforcefield.topology.Topology method)
is_isomorphic() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
isAlpha() (openforcefield.typing.chemistry.ChemicalEnvironment method)
isBeta() (openforcefield.typing.chemistry.ChemicalEnvironment method)
isIndexed() (openforcefield.typing.chemistry.ChemicalEnvironment method)
isUnindexed() (openforcefield.typing.chemistry.ChemicalEnvironment method)
isValid() (openforcefield.typing.chemistry.ChemicalEnvironment method)
K
known_kwargs (openforcefield.typing.engines.smirnoff.parameters.AngleHandler attribute)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler attribute)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler attribute)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler attribute)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler attribute)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler attribute)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler attribute)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler attribute)
M
mass (openforcefield.topology.Atom attribute)
merge_system() (in module openforcefield.utils.structure)
mergeStructure() (in module openforcefield.utils.structure)
method (openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler attribute)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler attribute)
Molecule (class in openforcefield.topology)
molecule (openforcefield.topology.Atom attribute)
(openforcefield.topology.Particle attribute)
(openforcefield.topology.VirtualSite attribute)
molecule_atom_index (openforcefield.topology.Atom attribute)
molecule_bond_index (openforcefield.topology.Bond attribute)
molecule_particle_index (openforcefield.topology.Atom attribute)
(openforcefield.topology.Particle attribute)
(openforcefield.topology.VirtualSite attribute)
molecule_virtual_site_index (openforcefield.topology.VirtualSite attribute)
N
n_angles (openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
(openforcefield.topology.Topology attribute)
n_atoms (openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
n_bonds (openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
n_conformers (openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
n_impropers (openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
(openforcefield.topology.Topology attribute)
n_particles (openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
n_propers (openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
(openforcefield.topology.Topology attribute)
n_reference_molecules (openforcefield.topology.Topology attribute)
n_topology_atoms (openforcefield.topology.Topology attribute)
n_topology_bonds (openforcefield.topology.Topology attribute)
n_topology_molecules (openforcefield.topology.Topology attribute)
n_topology_particles (openforcefield.topology.Topology attribute)
n_topology_virtual_sites (openforcefield.topology.Topology attribute)
n_virtual_sites (openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
name (openforcefield.topology.Atom attribute)
(openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
(openforcefield.topology.Particle attribute)
(openforcefield.topology.VirtualSite attribute)
normalize_molecules() (in module openforcefield.utils.structure)
O
OpenEyeToolkitWrapper (class in openforcefield.utils.toolkits)
P
ParameterHandler (class in openforcefield.typing.engines.smirnoff.parameters)
ParameterList (class in openforcefield.typing.engines.smirnoff.parameters)
parameters (openforcefield.typing.engines.smirnoff.parameters.AngleHandler attribute)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler attribute)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler attribute)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler attribute)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler attribute)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler attribute)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler attribute)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler attribute)
ParameterType (class in openforcefield.typing.engines.smirnoff.parameters)
partial_charge (openforcefield.topology.Atom attribute)
partial_charges (openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
Particle (class in openforcefield.topology)
particles (openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
pop() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
positions_from_oemol() (in module openforcefield.utils.structure)
postprocess_system() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
potential (openforcefield.typing.engines.smirnoff.parameters.vdWHandler attribute)
propers (openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
(openforcefield.topology.Topology attribute)
properties (openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
ProperTorsionHandler (class in openforcefield.typing.engines.smirnoff.parameters)
ProperTorsionHandler.ProperTorsionType (class in openforcefield.typing.engines.smirnoff.parameters)
ProperTorsionType (class in openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler)
R
RDKitToolkitWrapper (class in openforcefield.utils.toolkits)
read_molecules() (in module openforcefield.utils.structure)
read_typelist() (in module openforcefield.utils.structure)
reference_molecules (openforcefield.topology.Topology attribute)
register_toolkit() (openforcefield.utils.toolkits.ToolkitRegistry method)
registered_toolkits (openforcefield.utils.toolkits.ToolkitRegistry attribute)
remove() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
removeAtom() (openforcefield.typing.chemistry.ChemicalEnvironment method)
resolve() (openforcefield.utils.toolkits.ToolkitRegistry method)
reverse() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
rmin_half (openforcefield.topology.VirtualSite attribute)
S
save_system_to_amber() (in module openforcefield.utils.structure)
save_system_to_gromacs() (in module openforcefield.utils.structure)
selectAtom() (openforcefield.typing.chemistry.ChemicalEnvironment method)
selectBond() (openforcefield.typing.chemistry.ChemicalEnvironment method)
Serializable (class in openforcefield.utils.serialization)
setANDtypes() (openforcefield.typing.chemistry.ChemicalEnvironment.Atom method)
(openforcefield.typing.chemistry.ChemicalEnvironment.Bond method)
setORtypes() (openforcefield.typing.chemistry.ChemicalEnvironment.Atom method)
(openforcefield.typing.chemistry.ChemicalEnvironment.Bond method)
setPositionsInOEMol() (in module openforcefield.utils.structure)
sigma (openforcefield.topology.VirtualSite attribute)
sort() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
stereochemistry (openforcefield.topology.Atom attribute)
switch_width (openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler attribute)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler attribute)
T
temporary_cd() (in module openforcefield.utils.utils)
temporary_directory() (in module openforcefield.utils.utils)
to_bson() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.VirtualSite method)
(openforcefield.utils.serialization.Serializable method)
to_dict() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.VirtualSite method)
(openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.AngleHandler.AngleType method)
,
[1]
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler.BondType method)
,
[1]
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler.ImproperTorsionType method)
,
[1]
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterType method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler.ProperTorsionType method)
,
[1]
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler.vdWType method)
,
[1]
to_file() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
to_file_obj() (openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
to_iupac() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
to_json() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.VirtualSite method)
(openforcefield.utils.serialization.Serializable method)
to_list() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
to_messagepack() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.VirtualSite method)
(openforcefield.utils.serialization.Serializable method)
to_networkx() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
to_openeye() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper static method)
to_parmed() (openforcefield.topology.Topology method)
to_pickle() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.VirtualSite method)
(openforcefield.utils.serialization.Serializable method)
to_rdkit() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper class method)
to_smiles() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper static method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper class method)
to_toml() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.VirtualSite method)
(openforcefield.utils.serialization.Serializable method)
to_topology() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
to_xml() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.VirtualSite method)
(openforcefield.utils.serialization.Serializable method)
to_yaml() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.VirtualSite method)
(openforcefield.utils.serialization.Serializable method)
toolkit_file_read_formats (openforcefield.utils.toolkits.AmberToolsToolkitWrapper attribute)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper attribute)
(openforcefield.utils.toolkits.RDKitToolkitWrapper attribute)
(openforcefield.utils.toolkits.ToolkitWrapper attribute)
toolkit_file_write_formats (openforcefield.utils.toolkits.AmberToolsToolkitWrapper attribute)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper attribute)
(openforcefield.utils.toolkits.RDKitToolkitWrapper attribute)
(openforcefield.utils.toolkits.ToolkitWrapper attribute)
toolkit_installation_instructions (openforcefield.utils.toolkits.AmberToolsToolkitWrapper attribute)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper attribute)
(openforcefield.utils.toolkits.RDKitToolkitWrapper attribute)
(openforcefield.utils.toolkits.ToolkitWrapper attribute)
toolkit_is_available() (openforcefield.utils.toolkits.AmberToolsToolkitWrapper static method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper static method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper static method)
(openforcefield.utils.toolkits.ToolkitWrapper static method)
toolkit_name (openforcefield.utils.toolkits.AmberToolsToolkitWrapper attribute)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper attribute)
(openforcefield.utils.toolkits.RDKitToolkitWrapper attribute)
(openforcefield.utils.toolkits.ToolkitWrapper attribute)
ToolkitAM1BCCHandler (class in openforcefield.typing.engines.smirnoff.parameters)
ToolkitRegistry (class in openforcefield.utils.toolkits)
ToolkitWrapper (class in openforcefield.utils.toolkits)
Topology (class in openforcefield.topology)
topology_atoms (openforcefield.topology.Topology attribute)
topology_bonds (openforcefield.topology.Topology attribute)
topology_molecules (openforcefield.topology.Topology attribute)
topology_particles (openforcefield.topology.Topology attribute)
topology_virtual_sites (openforcefield.topology.Topology attribute)
torsions (openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
total_charge (openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
type (openforcefield.topology.VirtualSite attribute)
V
validate() (openforcefield.typing.chemistry.ChemicalEnvironment static method)
vdWHandler (class in openforcefield.typing.engines.smirnoff.parameters)
vdWHandler.vdWType (class in openforcefield.typing.engines.smirnoff.parameters)
vdWType (class in openforcefield.typing.engines.smirnoff.parameters.vdWHandler)
virtual_site() (openforcefield.topology.Topology method)
virtual_sites (openforcefield.topology.Atom attribute)
(openforcefield.topology.FrozenMolecule attribute)
(openforcefield.topology.Molecule attribute)
VirtualSite (class in openforcefield.topology)