Index

_

_CLOSE_EMBEDDING (in module pydft_qmmm.hamiltonians.qmmm_hamiltonian) _DEFAULT_FORCE_MATRIX (in module pydft_qmmm.hamiltonians.qmmm_hamiltonian) _frame (pydft_qmmm.wrappers.optimization.Optimization attribute) (pydft_qmmm.wrappers.simulation.Simulation attribute)

_LONG_EMBEDDING (in module pydft_qmmm.hamiltonians.qmmm_hamiltonian) _notifiers (pydft_qmmm.system.variable.ObservedArray attribute) _plugins (pydft_qmmm.calculators.calculator.Calculator attribute) (pydft_qmmm.integrators.integrator.Integrator attribute) _SUPPORTED_EMBEDDING (in module pydft_qmmm.hamiltonians.qmmm_hamiltonian)

A

acquire() (pydft_qmmm.utils.logging.DCDHandler method) active_plugins() (pydft_qmmm.calculators.calculator.Calculator method) (pydft_qmmm.calculators.composite_calculator.CompositeCalculator method) (pydft_qmmm.calculators.potential_calculator.PotentialCalculator method) (pydft_qmmm.integrators.integrator.Integrator method) (pydft_qmmm.integrators.langevin_integrator.LangevinIntegrator method) (pydft_qmmm.integrators.verlet_integrator.VerletIntegrator method) add_electronic_potential() (pydft_qmmm.interfaces.interface.QMInterface method) (pydft_qmmm.interfaces.interface.QMPotential method) (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Interface method) (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Potential method) add_non_elst() (pydft_qmmm.interfaces.interface.MMInterface method) (pydft_qmmm.interfaces.interface.MMPotential method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMPotential method) add_real_elst() (pydft_qmmm.interfaces.interface.MMInterface method) (pydft_qmmm.interfaces.interface.MMPotential method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMPotential method)

addFilter() (pydft_qmmm.utils.logging.DCDHandler method) all() (pydft_qmmm.system.variable.ObservedArray method) any() (pydft_qmmm.system.variable.ObservedArray method) apply_exclusions() (pydft_qmmm.hamiltonians.qmmm_hamiltonian.QMMMHamiltonian method) argmax() (pydft_qmmm.system.variable.ObservedArray method) argmin() (pydft_qmmm.system.variable.ObservedArray method) argpartition() (pydft_qmmm.system.variable.ObservedArray method) argsort() (pydft_qmmm.system.variable.ObservedArray method) ArrayValue (class in pydft_qmmm.system.variable) AssetImportError (class in pydft_qmmm.utils.exceptions) astype() (pydft_qmmm.system.variable.ObservedArray method) Atom (class in pydft_qmmm.system.atom) AtomicPotential (class in pydft_qmmm.potentials.potential) AtomPartition (class in pydft_qmmm.plugins.atom_partition) atoms (pydft_qmmm.hamiltonians.hamiltonian.PotentialHamiltonian attribute)

B

base (pydft_qmmm.system.variable.ObservedArray attribute) BOHR_PER_ANGSTROM (in module pydft_qmmm.utils.constants) box (pydft_qmmm.utils.logging.PositionRecord attribute) build_calculator() (pydft_qmmm.hamiltonians.hamiltonian.CompositeHamiltonian method) (pydft_qmmm.hamiltonians.hamiltonian.PotentialHamiltonian method) (pydft_qmmm.hamiltonians.hamiltonian.StandaloneHamiltonian method) (pydft_qmmm.hamiltonians.mm_hamiltonian.MMHamiltonian method) (pydft_qmmm.hamiltonians.qm_hamiltonian.QMHamiltonian method)

byteswap() (pydft_qmmm.system.variable.ObservedArray method)

C

calculate() (pydft_qmmm.calculators.calculator.Calculator method) (pydft_qmmm.calculators.composite_calculator.CompositeCalculator method) (pydft_qmmm.calculators.potential_calculator.PotentialCalculator method) calculate_energy_forces() (pydft_qmmm.wrappers.optimization.Optimization method) (pydft_qmmm.wrappers.simulation.Simulation method) Calculator (class in pydft_qmmm.calculators.calculator) CalculatorCenter (class in pydft_qmmm.plugins.center) CalculatorPlugin (class in pydft_qmmm.calculators.calculator) CalculatorWrap (class in pydft_qmmm.plugins.wrap) center_positions() (in module pydft_qmmm.utils.misc) CentroidPartition (class in pydft_qmmm.plugins.centroid_partition) check_array() (in module pydft_qmmm.utils.misc) choose() (pydft_qmmm.system.variable.ObservedArray method) clip() (pydft_qmmm.system.variable.ObservedArray method) close() (pydft_qmmm.utils.logging.DCDHandler method) CompositeCalculator (class in pydft_qmmm.calculators.composite_calculator) CompositeCalculatorPlugin (class in pydft_qmmm.calculators.composite_calculator) CompositeHamiltonian (class in pydft_qmmm.hamiltonians.hamiltonian) compress() (pydft_qmmm.system.variable.ObservedArray method) compute_components() (pydft_qmmm.interfaces.interface.MMPotential method) (pydft_qmmm.interfaces.interface.QMPotential method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMPotential method) (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Potential method) (pydft_qmmm.potentials.pme_potential.PMEExcludedPotential method) (pydft_qmmm.potentials.pme_potential.PMENuclearPotential method) (pydft_qmmm.potentials.potential.AtomicPotential method) compute_energy() (pydft_qmmm.interfaces.interface.MMPotential method) (pydft_qmmm.interfaces.interface.QMPotential method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMPotential method) (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Potential method) (pydft_qmmm.potentials.pme_potential.PMEExcludedPotential method) (pydft_qmmm.potentials.pme_potential.PMENuclearPotential method) (pydft_qmmm.potentials.potential.AtomicPotential method)

compute_forces() (pydft_qmmm.interfaces.interface.MMPotential method) (pydft_qmmm.interfaces.interface.QMPotential method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMPotential method) (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Potential method) (pydft_qmmm.potentials.pme_potential.PMEExcludedPotential method) (pydft_qmmm.potentials.pme_potential.PMENuclearPotential method) (pydft_qmmm.potentials.potential.AtomicPotential method) compute_kinetic_energy() (pydft_qmmm.integrators.integrator.Integrator method) (pydft_qmmm.integrators.langevin_integrator.LangevinIntegrator method) (pydft_qmmm.integrators.verlet_integrator.VerletIntegrator method) compute_lattice_constants() (in module pydft_qmmm.utils.lattice) compute_lattice_vectors() (in module pydft_qmmm.utils.lattice) compute_least_mirror() (in module pydft_qmmm.utils.lattice) compute_potential() (pydft_qmmm.potentials.pme_potential.PMEElectronicPotential method) (pydft_qmmm.potentials.potential.ElectronicPotential method) compute_potential_and_derivs() (pydft_qmmm.potentials.pme_potential.PMEExcludedPotential method) (pydft_qmmm.potentials.pme_potential.PMENuclearPotential method) conj() (pydft_qmmm.system.variable.ObservedArray method) conjugate() (pydft_qmmm.system.variable.ObservedArray method) constrain_velocities() (pydft_qmmm.plugins.rigid.Stationary method) (pydft_qmmm.plugins.settle.SETTLE method) converter() (pydft_qmmm.utils.logging.PyDFTQMMMCSVFormatter method) (pydft_qmmm.utils.logging.PyDFTQMMMLogFormatter method) copy() (pydft_qmmm.system.variable.ObservedArray method) count() (pydft_qmmm.system.system.System method) CouplingHamiltonian (class in pydft_qmmm.hamiltonians.hamiltonian) createLock() (pydft_qmmm.utils.logging.DCDHandler method) cumprod() (pydft_qmmm.system.variable.ObservedArray method) cumsum() (pydft_qmmm.system.variable.ObservedArray method) cutoff (pydft_qmmm.calculators.composite_calculator.PartitionPlugin attribute)

D

DCDHandler (class in pydft_qmmm.utils.logging) decompose() (in module pydft_qmmm.system.selection_utils) DependencyImportError (class in pydft_qmmm.utils.exceptions) diagonal() (pydft_qmmm.system.variable.ObservedArray method) disable_logging() (in module pydft_qmmm.interfaces.psi4.psi4_utils)

DISCOVERED_INTERFACES (in module pydft_qmmm.interfaces.interface_manager) DISCOVERED_PLUGINS (in module pydft_qmmm.plugins.plugin_manager) dot() (pydft_qmmm.system.variable.ObservedArray method) dump() (pydft_qmmm.system.variable.ObservedArray method) dumps() (pydft_qmmm.system.variable.ObservedArray method)

E

ElectronicPotential (class in pydft_qmmm.potentials.potential) ELEMENT_TO_MASS (in module pydft_qmmm.utils.constants) emit() (pydft_qmmm.utils.logging.DCDHandler method)

energy (pydft_qmmm.utils.logging.EnergyRecord attribute) EnergyRecord (class in pydft_qmmm.utils.logging) evaluate() (in module pydft_qmmm.system.selection_utils) evaluate_math() (in module pydft_qmmm.system.selection_utils)

F

FAST_KEYWORDS (in module pydft_qmmm.system.selection_utils) FAST_SELECTORS (in module pydft_qmmm.system.selection_utils) FAST_VARIABLES (in module pydft_qmmm.system.selection_utils) fill() (pydft_qmmm.system.variable.ObservedArray method) filter() (pydft_qmmm.utils.logging.DCDHandler method) (pydft_qmmm.utils.logging.PyDFTQMMMEnergyFilter method) (pydft_qmmm.utils.logging.PyDFTQMMMIntervalFilter method) (pydft_qmmm.utils.logging.PyDFTQMMMPositionFilter method) FirstAtomPartition (class in pydft_qmmm.plugins.firstatom_partition) flatten() (pydft_qmmm.system.variable.ObservedArray method) flush() (pydft_qmmm.utils.logging.DCDHandler method) force_matrix (pydft_qmmm.hamiltonians.hamiltonian.CouplingHamiltonian attribute) format() (pydft_qmmm.utils.logging.DCDHandler method) (pydft_qmmm.utils.logging.PyDFTQMMMCSVFormatter method) (pydft_qmmm.utils.logging.PyDFTQMMMLogFormatter method)

formatException() (pydft_qmmm.utils.logging.PyDFTQMMMCSVFormatter method) (pydft_qmmm.utils.logging.PyDFTQMMMLogFormatter method) formatMessage() (pydft_qmmm.utils.logging.PyDFTQMMMCSVFormatter method) (pydft_qmmm.utils.logging.PyDFTQMMMLogFormatter method) formatStack() (pydft_qmmm.utils.logging.PyDFTQMMMCSVFormatter method) (pydft_qmmm.utils.logging.PyDFTQMMMLogFormatter method) formatTime() (pydft_qmmm.utils.logging.PyDFTQMMMCSVFormatter method) (pydft_qmmm.utils.logging.PyDFTQMMMLogFormatter method) frame (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Interface attribute) (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Potential attribute) (pydft_qmmm.utils.logging.FrameRecord attribute) FrameRecord (class in pydft_qmmm.utils.logging) FUNCTIONS (in module pydft_qmmm.system.selection_utils)

G

generate_partition() (pydft_qmmm.calculators.composite_calculator.PartitionPlugin method) (pydft_qmmm.plugins.atom_partition.AtomPartition method) (pydft_qmmm.plugins.centroid_partition.CentroidPartition method) (pydft_qmmm.plugins.firstatom_partition.FirstAtomPartition method) generate_velocities() (in module pydft_qmmm.utils.misc) get_interfaces() (in module pydft_qmmm.interfaces.interface_manager) get_name() (pydft_qmmm.utils.logging.DCDHandler method) get_nuclear_charges() (pydft_qmmm.potentials.pme_potential.PMEExcludedPotential method) (pydft_qmmm.potentials.pme_potential.PMENuclearPotential method)

get_plugins() (in module pydft_qmmm.plugins.plugin_manager) get_pme_parameters() (pydft_qmmm.interfaces.interface.MMInterface method) (pydft_qmmm.interfaces.interface.MMPotential method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMPotential method) getfield() (pydft_qmmm.system.variable.ObservedArray method) getMessage() (pydft_qmmm.utils.logging.EnergyRecord method) (pydft_qmmm.utils.logging.FrameRecord method) (pydft_qmmm.utils.logging.PositionRecord method)

H

Hamiltonian (class in pydft_qmmm.hamiltonians.hamiltonian) handle() (pydft_qmmm.utils.logging.DCDHandler method)

handleError() (pydft_qmmm.utils.logging.DCDHandler method) HelPMEPyInterface (class in pydft_qmmm.potentials.pme_potential)

I

index() (pydft_qmmm.system.system.System method) integrate() (pydft_qmmm.integrators.integrator.Integrator method) (pydft_qmmm.integrators.langevin_integrator.LangevinIntegrator method) (pydft_qmmm.integrators.verlet_integrator.VerletIntegrator method) Integrator (class in pydft_qmmm.integrators.integrator) IntegratorCenter (class in pydft_qmmm.plugins.center)

IntegratorPlugin (class in pydft_qmmm.integrators.integrator) IntegratorWrap (class in pydft_qmmm.plugins.wrap) interface (pydft_qmmm.hamiltonians.hamiltonian.PotentialHamiltonian attribute) InterfaceImportError (class in pydft_qmmm.utils.exceptions) interpret() (in module pydft_qmmm.system.selection_utils) isvalue() (in module pydft_qmmm.system.selection_utils) item() (pydft_qmmm.system.variable.ObservedArray method)

K

KB (in module pydft_qmmm.utils.constants)

KEYWORDS (in module pydft_qmmm.system.selection_utils) KJMOL_PER_EH (in module pydft_qmmm.utils.constants)

L

LangevinIntegrator (class in pydft_qmmm.integrators.langevin_integrator) line_slice() (in module pydft_qmmm.system.selection_utils) load() (pydft_qmmm.system.system.System static method)

load_system() (in module pydft_qmmm.system.file_manager) LOADED_INTERFACES (in module pydft_qmmm.interfaces.interface_manager) LOADED_PLUGINS (in module pydft_qmmm.plugins.plugin_manager) Loggable (class in pydft_qmmm.utils.logging)

M

make_csv_handler() (in module pydft_qmmm.utils.logging) make_dcd_handler() (in module pydft_qmmm.utils.logging) make_file_handler() (in module pydft_qmmm.utils.logging) make_log_handler() (in module pydft_qmmm.utils.logging) MATH_KEYWORDS (in module pydft_qmmm.system.selection_utils) max() (pydft_qmmm.system.variable.ObservedArray method) mean() (pydft_qmmm.system.variable.ObservedArray method) min() (pydft_qmmm.system.variable.ObservedArray method) MMHamiltonian (class in pydft_qmmm.hamiltonians.mm_hamiltonian) MMInterface (class in pydft_qmmm.interfaces.interface) MMPotential (class in pydft_qmmm.interfaces.interface) modify() (pydft_qmmm.calculators.calculator.CalculatorPlugin method) (pydft_qmmm.calculators.composite_calculator.CompositeCalculatorPlugin method) (pydft_qmmm.calculators.composite_calculator.PartitionPlugin method) (pydft_qmmm.integrators.integrator.IntegratorPlugin method) (pydft_qmmm.plugins.atom_partition.AtomPartition method) (pydft_qmmm.plugins.center.CalculatorCenter method) (pydft_qmmm.plugins.center.IntegratorCenter method) (pydft_qmmm.plugins.centroid_partition.CentroidPartition method) (pydft_qmmm.plugins.firstatom_partition.FirstAtomPartition method) (pydft_qmmm.plugins.plumed.Plumed method) (pydft_qmmm.plugins.rigid.Stationary method) (pydft_qmmm.plugins.settle.SETTLE method) (pydft_qmmm.plugins.wrap.CalculatorWrap method) (pydft_qmmm.plugins.wrap.IntegratorWrap method) modify_calculator() (pydft_qmmm.hamiltonians.hamiltonian.CouplingHamiltonian method) (pydft_qmmm.hamiltonians.qmmm_hamiltonian.QMMMHamiltonian method) modify_composite() (pydft_qmmm.calculators.composite_calculator.CompositeCalculatorPlugin method) (pydft_qmmm.calculators.composite_calculator.PartitionPlugin method) (pydft_qmmm.plugins.atom_partition.AtomPartition method) (pydft_qmmm.plugins.centroid_partition.CentroidPartition method) (pydft_qmmm.plugins.firstatom_partition.FirstAtomPartition method) module pydft_qmmm.calculators pydft_qmmm.calculators.calculator pydft_qmmm.calculators.composite_calculator pydft_qmmm.calculators.potential_calculator pydft_qmmm.hamiltonians pydft_qmmm.hamiltonians.hamiltonian pydft_qmmm.hamiltonians.mm_hamiltonian pydft_qmmm.hamiltonians.qm_hamiltonian pydft_qmmm.hamiltonians.qmmm_hamiltonian pydft_qmmm.integrators pydft_qmmm.integrators.integrator pydft_qmmm.integrators.langevin_integrator pydft_qmmm.integrators.verlet_integrator pydft_qmmm.interfaces pydft_qmmm.interfaces.interface pydft_qmmm.interfaces.interface_manager pydft_qmmm.interfaces.openmm pydft_qmmm.interfaces.openmm.openmm_factory pydft_qmmm.interfaces.openmm.openmm_interface pydft_qmmm.interfaces.openmm.openmm_utils pydft_qmmm.interfaces.psi4 pydft_qmmm.interfaces.psi4.psi4_factory pydft_qmmm.interfaces.psi4.psi4_interface pydft_qmmm.interfaces.psi4.psi4_utils pydft_qmmm.plugins pydft_qmmm.plugins.atom_partition pydft_qmmm.plugins.center pydft_qmmm.plugins.centroid_partition pydft_qmmm.plugins.firstatom_partition pydft_qmmm.plugins.plugin_manager pydft_qmmm.plugins.plumed pydft_qmmm.plugins.rigid pydft_qmmm.plugins.settle pydft_qmmm.plugins.wrap pydft_qmmm.potentials pydft_qmmm.potentials.pme_potential pydft_qmmm.potentials.potential pydft_qmmm.system pydft_qmmm.system.atom pydft_qmmm.system.file_manager pydft_qmmm.system.selection_utils pydft_qmmm.system.system pydft_qmmm.system.variable pydft_qmmm.utils pydft_qmmm.utils.constants pydft_qmmm.utils.descriptor pydft_qmmm.utils.exceptions pydft_qmmm.utils.lattice pydft_qmmm.utils.logging pydft_qmmm.utils.misc pydft_qmmm.wrappers pydft_qmmm.wrappers.optimization pydft_qmmm.wrappers.simulation

N

NEEDS_CUTOFF (in module pydft_qmmm.interfaces.openmm.openmm_factory)

nonzero() (pydft_qmmm.system.variable.ObservedArray method) numerical_gradient() (in module pydft_qmmm.utils.misc)

O

observed_class() (in module pydft_qmmm.system.variable) ObservedArray (class in pydft_qmmm.system.variable) openmm_interface_factory() (in module pydft_qmmm.interfaces.openmm.openmm_factory) OpenMMInterface (class in pydft_qmmm.interfaces.openmm.openmm_interface)

OpenMMPotential (class in pydft_qmmm.interfaces.openmm.openmm_interface) OPERATORS (in module pydft_qmmm.system.selection_utils) Optimization (class in pydft_qmmm.wrappers.optimization) optimize() (pydft_qmmm.wrappers.optimization.Optimization method)

P

partition() (pydft_qmmm.system.variable.ObservedArray method) PartitionPlugin (class in pydft_qmmm.calculators.composite_calculator) PERIODIC (in module pydft_qmmm.interfaces.openmm.openmm_factory) pluggable_method() (in module pydft_qmmm.utils.descriptor) PluginImportError (class in pydft_qmmm.utils.exceptions) Plumed (class in pydft_qmmm.plugins.plumed) pme (pydft_qmmm.potentials.pme_potential.HelPMEPyInterface attribute) (pydft_qmmm.potentials.pme_potential.PMEElectronicPotential attribute) (pydft_qmmm.potentials.pme_potential.PMEExcludedPotential attribute) (pydft_qmmm.potentials.pme_potential.PMENuclearPotential attribute) PMEElectronicPotential (class in pydft_qmmm.potentials.pme_potential) PMEExcludedPotential (class in pydft_qmmm.potentials.pme_potential) PMENuclearPotential (class in pydft_qmmm.potentials.pme_potential) position (pydft_qmmm.utils.logging.PositionRecord attribute) PositionRecord (class in pydft_qmmm.utils.logging) PotentialCalculator (class in pydft_qmmm.calculators.potential_calculator) PotentialHamiltonian (class in pydft_qmmm.hamiltonians.hamiltonian) potentials (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Interface attribute) (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Potential attribute) prod() (pydft_qmmm.system.variable.ObservedArray method) psi4_interface_factory() (in module pydft_qmmm.interfaces.psi4.psi4_factory) Psi4Interface (class in pydft_qmmm.interfaces.psi4.psi4_interface) Psi4Potential (class in pydft_qmmm.interfaces.psi4.psi4_interface) put() (pydft_qmmm.system.variable.ObservedArray method) pydft_qmmm.calculators module pydft_qmmm.calculators.calculator module pydft_qmmm.calculators.composite_calculator module pydft_qmmm.calculators.potential_calculator module pydft_qmmm.hamiltonians module pydft_qmmm.hamiltonians.hamiltonian module pydft_qmmm.hamiltonians.mm_hamiltonian module pydft_qmmm.hamiltonians.qm_hamiltonian module pydft_qmmm.hamiltonians.qmmm_hamiltonian module pydft_qmmm.integrators module pydft_qmmm.integrators.integrator module pydft_qmmm.integrators.langevin_integrator module pydft_qmmm.integrators.verlet_integrator module pydft_qmmm.interfaces module pydft_qmmm.interfaces.interface module pydft_qmmm.interfaces.interface_manager module pydft_qmmm.interfaces.openmm module pydft_qmmm.interfaces.openmm.openmm_factory module pydft_qmmm.interfaces.openmm.openmm_interface module pydft_qmmm.interfaces.openmm.openmm_utils module pydft_qmmm.interfaces.psi4 module pydft_qmmm.interfaces.psi4.psi4_factory module

pydft_qmmm.interfaces.psi4.psi4_interface module pydft_qmmm.interfaces.psi4.psi4_utils module pydft_qmmm.plugins module pydft_qmmm.plugins.atom_partition module pydft_qmmm.plugins.center module pydft_qmmm.plugins.centroid_partition module pydft_qmmm.plugins.firstatom_partition module pydft_qmmm.plugins.plugin_manager module pydft_qmmm.plugins.plumed module pydft_qmmm.plugins.rigid module pydft_qmmm.plugins.settle module pydft_qmmm.plugins.wrap module pydft_qmmm.potentials module pydft_qmmm.potentials.pme_potential module pydft_qmmm.potentials.potential module pydft_qmmm.system module pydft_qmmm.system.atom module pydft_qmmm.system.file_manager module pydft_qmmm.system.selection_utils module pydft_qmmm.system.system module pydft_qmmm.system.variable module pydft_qmmm.utils module pydft_qmmm.utils.constants module pydft_qmmm.utils.descriptor module pydft_qmmm.utils.exceptions module pydft_qmmm.utils.lattice module pydft_qmmm.utils.logging module pydft_qmmm.utils.misc module pydft_qmmm.wrappers module pydft_qmmm.wrappers.optimization module pydft_qmmm.wrappers.simulation module PyDFTQMMMCSVFormatter (class in pydft_qmmm.utils.logging) PyDFTQMMMEnergyFilter (class in pydft_qmmm.utils.logging) PyDFTQMMMException (class in pydft_qmmm.utils.exceptions) PyDFTQMMMIntervalFilter (class in pydft_qmmm.utils.logging) PyDFTQMMMLogFormatter (class in pydft_qmmm.utils.logging) PyDFTQMMMPositionFilter (class in pydft_qmmm.utils.logging)

Q

QMHamiltonian (class in pydft_qmmm.hamiltonians.qm_hamiltonian) QMInterface (class in pydft_qmmm.interfaces.interface)

QMMMHamiltonian (class in pydft_qmmm.hamiltonians.qmmm_hamiltonian) QMPotential (class in pydft_qmmm.interfaces.interface) query (pydft_qmmm.calculators.composite_calculator.PartitionPlugin attribute)

R

ravel() (pydft_qmmm.system.variable.ObservedArray method) register_notifier() (pydft_qmmm.system.variable.ObservedArray method) register_plugin() (pydft_qmmm.calculators.calculator.Calculator method) (pydft_qmmm.calculators.composite_calculator.CompositeCalculator method) (pydft_qmmm.calculators.potential_calculator.PotentialCalculator method) (pydft_qmmm.integrators.integrator.Integrator method) (pydft_qmmm.integrators.langevin_integrator.LangevinIntegrator method) (pydft_qmmm.integrators.verlet_integrator.VerletIntegrator method)

release() (pydft_qmmm.utils.logging.DCDHandler method) removeFilter() (pydft_qmmm.utils.logging.DCDHandler method) repeat() (pydft_qmmm.system.variable.ObservedArray method) reshape() (pydft_qmmm.system.variable.ObservedArray method) residue_partition() (in module pydft_qmmm.utils.misc) resize() (pydft_qmmm.system.variable.ObservedArray method) Results (class in pydft_qmmm.calculators.calculator) round() (pydft_qmmm.system.variable.ObservedArray method) run_dynamics() (pydft_qmmm.wrappers.simulation.Simulation method)

S

searchsorted() (pydft_qmmm.system.variable.ObservedArray method) select() (pydft_qmmm.system.system.System method) SELECT_KEYWORDS (in module pydft_qmmm.system.selection_utils) SELECTORS (in module pydft_qmmm.system.selection_utils) set_name() (pydft_qmmm.utils.logging.DCDHandler method) set_options() (in module pydft_qmmm.interfaces.psi4.psi4_utils) setfield() (pydft_qmmm.system.variable.ObservedArray method) setflags() (pydft_qmmm.system.variable.ObservedArray method) setFormatter() (pydft_qmmm.utils.logging.DCDHandler method) setLevel() (pydft_qmmm.utils.logging.DCDHandler method) SETTLE (class in pydft_qmmm.plugins.settle) Simulation (class in pydft_qmmm.wrappers.simulation) SLOW_KEYWORDS (in module pydft_qmmm.system.selection_utils)

SLOW_SELECTORS (in module pydft_qmmm.system.selection_utils) SLOW_VARIABLES (in module pydft_qmmm.system.selection_utils) SoftwareInterface (class in pydft_qmmm.interfaces.interface) sort() (pydft_qmmm.system.variable.ObservedArray method) squeeze() (pydft_qmmm.system.variable.ObservedArray method) StandaloneHamiltonian (class in pydft_qmmm.hamiltonians.hamiltonian) Stationary (class in pydft_qmmm.plugins.rigid) std() (pydft_qmmm.system.variable.ObservedArray method) Subsystem (class in pydft_qmmm.utils.constants) sum() (pydft_qmmm.system.variable.ObservedArray method) SUPPORTED_FORCES (in module pydft_qmmm.interfaces.openmm.openmm_factory) swapaxes() (pydft_qmmm.system.variable.ObservedArray method) System (class in pydft_qmmm.system.system) system_cache() (in module pydft_qmmm.utils.descriptor)

T

take() (pydft_qmmm.system.variable.ObservedArray method) theory_level (pydft_qmmm.hamiltonians.hamiltonian.PotentialHamiltonian attribute) (pydft_qmmm.interfaces.interface.MMInterface attribute) (pydft_qmmm.interfaces.interface.QMInterface attribute) TheoryLevel (class in pydft_qmmm.utils.constants) TheoryLevelError (class in pydft_qmmm.utils.exceptions)

to_device() (pydft_qmmm.system.variable.ObservedArray method) tobytes() (pydft_qmmm.system.variable.ObservedArray method) tofile() (pydft_qmmm.system.variable.ObservedArray method) tolist() (pydft_qmmm.system.variable.ObservedArray method) trace() (pydft_qmmm.system.variable.ObservedArray method) transpose() (pydft_qmmm.system.variable.ObservedArray method)

U

update() (pydft_qmmm.system.variable.ArrayValue method) update_box() (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMPotential method) (pydft_qmmm.potentials.pme_potential.HelPMEPyInterface method) (pydft_qmmm.potentials.pme_potential.PMEElectronicPotential method) (pydft_qmmm.potentials.pme_potential.PMEExcludedPotential method) (pydft_qmmm.potentials.pme_potential.PMENuclearPotential method) update_charges() (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMPotential method)

update_options() (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Interface method) (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Potential method) update_positions() (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMPotential method) update_subsystems() (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMPotential method) usesTime() (pydft_qmmm.utils.logging.PyDFTQMMMCSVFormatter method) (pydft_qmmm.utils.logging.PyDFTQMMMLogFormatter method)

V

value() (pydft_qmmm.system.variable.ArrayValue method) var() (pydft_qmmm.system.variable.ObservedArray method)

VARIABLES (in module pydft_qmmm.system.selection_utils) VerletIntegrator (class in pydft_qmmm.integrators.verlet_integrator) view() (pydft_qmmm.system.variable.ObservedArray method)

W

wrap_positions() (in module pydft_qmmm.utils.misc)

write_to_pdb() (in module pydft_qmmm.system.file_manager)

Z

zero_charges() (pydft_qmmm.interfaces.interface.MMInterface method) (pydft_qmmm.interfaces.interface.MMPotential method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMPotential method) zero_forces() (pydft_qmmm.interfaces.interface.MMInterface method) (pydft_qmmm.interfaces.interface.MMPotential method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMPotential method)

zero_intermolecular() (pydft_qmmm.interfaces.interface.MMInterface method) (pydft_qmmm.interfaces.interface.MMPotential method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMPotential method) zero_intramolecular() (pydft_qmmm.interfaces.interface.MMInterface method) (pydft_qmmm.interfaces.interface.MMPotential method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMPotential method)