Index

_

_box (pydft_qmmm.system.system.System attribute) _charges (pydft_qmmm.system.system.System attribute) _CLOSE_EMBEDDING (in module pydft_qmmm.hamiltonians.qmmm_hamiltonian) _DEFAULT_FORCE_MATRIX (in module pydft_qmmm.hamiltonians.qmmm_hamiltonian) _elements (pydft_qmmm.system.system.System attribute) _forces (pydft_qmmm.system.system.System attribute) _frame (pydft_qmmm.wrappers.simulation.Simulation attribute) _key (pydft_qmmm.plugins.plugin.Plugin attribute) _LONG_EMBEDDING (in module pydft_qmmm.hamiltonians.qmmm_hamiltonian) _masses (pydft_qmmm.system.system.System attribute) _modifieds (pydft_qmmm.plugins.plugin.Plugin attribute)

_names (pydft_qmmm.system.system.System attribute) _notifiers (pydft_qmmm.system.variable.ObservedArray attribute) _plugins (pydft_qmmm.calculators.calculator.Calculator attribute) (pydft_qmmm.integrators.integrator.Integrator attribute) _positions (pydft_qmmm.system.system.System attribute) _query (pydft_qmmm.plugins.plugin.PartitionPlugin attribute) _residue_names (pydft_qmmm.system.system.System attribute) _residues (pydft_qmmm.system.system.System attribute) _subsystems (pydft_qmmm.system.system.System attribute) _SUPPORTED_EMBEDDING (in module pydft_qmmm.hamiltonians.qmmm_hamiltonian) _velocities (pydft_qmmm.system.system.System attribute)

A

active_plugins() (pydft_qmmm.calculators.calculator.Calculator method) (pydft_qmmm.integrators.integrator.Integrator method) add_non_elst() (pydft_qmmm.interfaces.interface.MMInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) add_real_elst() (pydft_qmmm.interfaces.interface.MMInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method)

align_dict() (in module pydft_qmmm.common.utils.misc_utils) and_slice() (in module pydft_qmmm.common.utils.selection_utils) ArrayValue (class in pydft_qmmm.system.variable) Atom (class in pydft_qmmm.common.atom) AtomPartition (class in pydft_qmmm.plugins.atom_partition.atom_partition) atoms (pydft_qmmm.hamiltonians.hamiltonian.CalculatorHamiltonian attribute), [1]

B

base (pydft_qmmm.system.variable.ObservedArray attribute) basis (pydft_qmmm.interfaces.psi4.psi4_utils.Psi4Options attribute) basis_set (pydft_qmmm.hamiltonians.qm_hamiltonian.QMHamiltonian attribute) (pydft_qmmm.interfaces.interface.QMSettings attribute) BOHR_PER_ANGSTROM (in module pydft_qmmm.common.constants)

box (pydft_qmmm.system.system.System property) build_calculator() (pydft_qmmm.hamiltonians.hamiltonian.CalculatorHamiltonian method) (pydft_qmmm.hamiltonians.hamiltonian.CompositeHamiltonian method) (pydft_qmmm.hamiltonians.mm_hamiltonian.MMHamiltonian method) (pydft_qmmm.hamiltonians.qm_hamiltonian.QMHamiltonian method)

C

calculate() (pydft_qmmm.calculators.calculator.Calculator method) (pydft_qmmm.calculators.composite_calculator.CompositeCalculator method) (pydft_qmmm.calculators.interface_calculator.InterfaceCalculator method) calculate_energy_forces() (pydft_qmmm.wrappers.simulation.Simulation method) Calculator (class in pydft_qmmm.calculators.calculator) CalculatorCenter (class in pydft_qmmm.plugins.center.center) CalculatorHamiltonian (class in pydft_qmmm.hamiltonians.hamiltonian) CalculatorPlugin (class in pydft_qmmm.plugins.plugin) calculators (pydft_qmmm.calculators.composite_calculator.CompositeCalculator attribute) CalculatorWrap (class in pydft_qmmm.plugins.wrap.wrap) center_positions() (in module pydft_qmmm.common.utils.misc_utils) CentroidPartition (class in pydft_qmmm.plugins.centroid_partition.centroid_partition) charge (pydft_qmmm.common.atom.Atom attribute) (pydft_qmmm.hamiltonians.qm_hamiltonian.QMHamiltonian attribute) (pydft_qmmm.interfaces.interface.QMSettings attribute) charges (pydft_qmmm.system.system.System property) close_range (pydft_qmmm.hamiltonians.qmmm_hamiltonian.QMMMHamiltonian attribute) Components (in module pydft_qmmm.common.utils.misc_utils) components (pydft_qmmm.common.utils.misc_utils.Results attribute) CompositeCalculator (class in pydft_qmmm.calculators.composite_calculator) CompositeCalculatorPlugin (class in pydft_qmmm.plugins.plugin) CompositeHamiltonian (class in pydft_qmmm.hamiltonians.hamiltonian)

compute_components() (pydft_qmmm.interfaces.interface.SoftwareInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Interface method) compute_energy() (pydft_qmmm.interfaces.interface.SoftwareInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Interface method) compute_forces() (pydft_qmmm.interfaces.interface.SoftwareInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Interface method) (pydft_qmmm.interfaces.qmmm_pme_psi4.psi4_interface.PMEPsi4Interface method) compute_kinetic_energy() (pydft_qmmm.integrators.integrator.Integrator method) compute_lattice_constants() (in module pydft_qmmm.common.utils.lattice_utils) compute_lattice_vectors() (in module pydft_qmmm.common.utils.lattice_utils) compute_least_mirror() (in module pydft_qmmm.common.utils.lattice_utils) compute_quadrature() (pydft_qmmm.interfaces.qmmm_pme_psi4.psi4_interface.PMEPsi4Interface method) compute_recip_potential() (pydft_qmmm.interfaces.qmmm_pme_openmm.openmm_interface.PMEOpenMMInterface method) constrain_velocities() (pydft_qmmm.plugins.rigid.rigid.Stationary method) (pydft_qmmm.plugins.settle.settle.SETTLE method) CouplingHamiltonian (class in pydft_qmmm.hamiltonians.hamiltonian) csv_write_interval (pydft_qmmm.wrappers.logger.Logger attribute) cutoff (pydft_qmmm.calculators.composite_calculator.CompositeCalculator attribute) (pydft_qmmm.hamiltonians.qmmm_hamiltonian.QMMMHamiltonian attribute)

D

dcd_write_interval (pydft_qmmm.wrappers.logger.Logger attribute) decimal_places (pydft_qmmm.wrappers.logger.Logger attribute) decompose() (in module pydft_qmmm.common.utils.selection_utils) dft_radial_points (pydft_qmmm.interfaces.psi4.psi4_utils.Psi4Options attribute)

dft_spherical_points (pydft_qmmm.interfaces.psi4.psi4_utils.Psi4Options attribute) disable_embedding() (pydft_qmmm.interfaces.interface.QMInterface method) (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Interface method) DISCOVERED_INTERFACES (in module pydft_qmmm.interfaces.interface_manager) DISCOVERED_PLUGINS (in module pydft_qmmm.plugins.plugin_manager)

E

element (pydft_qmmm.common.atom.Atom attribute) ELEMENT_TO_MASS (in module pydft_qmmm.common.constants) elements (pydft_qmmm.system.system.System property)

empty_array() (in module pydft_qmmm.common.utils.misc_utils) end_log() (in module pydft_qmmm.common.file_manager) energy (pydft_qmmm.common.utils.misc_utils.Results attribute) evaluate() (in module pydft_qmmm.common.utils.selection_utils)

F

FirstAtomPartition (class in pydft_qmmm.plugins.firstatom_partition.firstatom_partition) force (pydft_qmmm.common.atom.Atom attribute) force_matrix (pydft_qmmm.hamiltonians.hamiltonian.CouplingHamiltonian attribute), [1] forcefield (pydft_qmmm.hamiltonians.mm_hamiltonian.MMHamiltonian attribute) (pydft_qmmm.interfaces.interface.MMSettings attribute)

forces (pydft_qmmm.common.utils.misc_utils.Results attribute) (pydft_qmmm.system.system.System property) friction (pydft_qmmm.integrators.langevin_integrator.LangevinIntegrator attribute) functional (pydft_qmmm.hamiltonians.qm_hamiltonian.QMHamiltonian attribute) (pydft_qmmm.interfaces.interface.QMSettings attribute)

G

generate_external_potential() (pydft_qmmm.interfaces.psi4.psi4_utils.Psi4Context method) generate_molecule() (pydft_qmmm.interfaces.psi4.psi4_utils.Psi4Context method) generate_partition() (pydft_qmmm.plugins.atom_partition.atom_partition.AtomPartition method) (pydft_qmmm.plugins.centroid_partition.centroid_partition.CentroidPartition method) (pydft_qmmm.plugins.firstatom_partition.firstatom_partition.FirstAtomPartition method) (pydft_qmmm.plugins.plugin.PartitionPlugin method)

generate_velocities() (in module pydft_qmmm.common.utils.misc_utils) get_external_plugins() (in module pydft_qmmm.plugins.plugin_manager) get_software_factory() (in module pydft_qmmm.interfaces.interface_manager)

H

Hamiltonian (class in pydft_qmmm.hamiltonians.hamiltonian)

I

I (pydft_qmmm.common.constants.Subsystem attribute) II (pydft_qmmm.common.constants.Subsystem attribute) III (pydft_qmmm.common.constants.Subsystem attribute) 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.center) IntegratorPlugin (class in pydft_qmmm.plugins.plugin) IntegratorWrap (class in pydft_qmmm.plugins.wrap.wrap) interface (pydft_qmmm.calculators.interface_calculator.InterfaceCalculator attribute) InterfaceCalculator (class in pydft_qmmm.calculators.interface_calculator) interpret() (in module pydft_qmmm.common.utils.selection_utils)

K

KB (in module pydft_qmmm.common.constants)

KJMOL_PER_EH (in module pydft_qmmm.common.constants)

L

LangevinIntegrator (class in pydft_qmmm.integrators.langevin_integrator) lazy_load() (in module pydft_qmmm.common.utils.misc_utils) load() (pydft_qmmm.system.system.System static method)

load_system() (in module pydft_qmmm.common.file_manager) log_write_interval (pydft_qmmm.wrappers.logger.Logger attribute) Logger (class in pydft_qmmm.wrappers.logger) long_range (pydft_qmmm.hamiltonians.qmmm_hamiltonian.QMMMHamiltonian attribute)

M

mass (pydft_qmmm.common.atom.Atom attribute) masses (pydft_qmmm.system.system.System property) MM (pydft_qmmm.common.constants.TheoryLevel attribute) MMHamiltonian (class in pydft_qmmm.hamiltonians.mm_hamiltonian) MMInterface (class in pydft_qmmm.interfaces.interface) MMSettings (class in pydft_qmmm.interfaces.interface) modify() (pydft_qmmm.plugins.atom_partition.atom_partition.AtomPartition method) (pydft_qmmm.plugins.center.center.CalculatorCenter method) (pydft_qmmm.plugins.center.center.IntegratorCenter method) (pydft_qmmm.plugins.centroid_partition.centroid_partition.CentroidPartition method) (pydft_qmmm.plugins.firstatom_partition.firstatom_partition.FirstAtomPartition method) (pydft_qmmm.plugins.plugin.CalculatorPlugin method) (pydft_qmmm.plugins.plugin.CompositeCalculatorPlugin method) (pydft_qmmm.plugins.plugin.IntegratorPlugin method) (pydft_qmmm.plugins.plumed.plumed.Plumed method) (pydft_qmmm.plugins.pme.pme.PME method) (pydft_qmmm.plugins.rigid.rigid.RigidBody method) (pydft_qmmm.plugins.rigid.rigid.Stationary method) (pydft_qmmm.plugins.settle.settle.SETTLE method) (pydft_qmmm.plugins.wrap.wrap.CalculatorWrap method) (pydft_qmmm.plugins.wrap.wrap.IntegratorWrap method) modify_calculator() (pydft_qmmm.hamiltonians.hamiltonian.CouplingHamiltonian method) (pydft_qmmm.hamiltonians.qmmm_hamiltonian.QMMMHamiltonian method) modify_composite() (pydft_qmmm.hamiltonians.hamiltonian.CouplingHamiltonian method) (pydft_qmmm.hamiltonians.qmmm_hamiltonian.QMMMHamiltonian method) modify_mm_interface() (pydft_qmmm.hamiltonians.qmmm_hamiltonian.QMMMHamiltonian method) modify_qm_interface() (pydft_qmmm.hamiltonians.qmmm_hamiltonian.QMMMHamiltonian method) module pydft_qmmm pydft_qmmm.calculators pydft_qmmm.calculators.calculator pydft_qmmm.calculators.composite_calculator pydft_qmmm.calculators.interface_calculator pydft_qmmm.common pydft_qmmm.common.atom pydft_qmmm.common.constants pydft_qmmm.common.file_manager pydft_qmmm.common.resource_manager pydft_qmmm.common.utils pydft_qmmm.common.utils.lattice_utils pydft_qmmm.common.utils.misc_utils pydft_qmmm.common.utils.selection_utils 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_interface pydft_qmmm.interfaces.psi4.psi4_utils pydft_qmmm.interfaces.qmmm_pme_openmm pydft_qmmm.interfaces.qmmm_pme_openmm.openmm_factory pydft_qmmm.interfaces.qmmm_pme_openmm.openmm_interface pydft_qmmm.interfaces.qmmm_pme_openmm.openmm_utils pydft_qmmm.interfaces.qmmm_pme_psi4 pydft_qmmm.interfaces.qmmm_pme_psi4.psi4_interface pydft_qmmm.interfaces.qmmm_pme_psi4.psi4_utils pydft_qmmm.plugins pydft_qmmm.plugins.atom_partition pydft_qmmm.plugins.atom_partition.atom_partition pydft_qmmm.plugins.center pydft_qmmm.plugins.center.center pydft_qmmm.plugins.centroid_partition pydft_qmmm.plugins.centroid_partition.centroid_partition pydft_qmmm.plugins.firstatom_partition pydft_qmmm.plugins.firstatom_partition.firstatom_partition pydft_qmmm.plugins.plugin pydft_qmmm.plugins.plugin_manager pydft_qmmm.plugins.plumed pydft_qmmm.plugins.plumed.plumed pydft_qmmm.plugins.pme pydft_qmmm.plugins.pme.pme pydft_qmmm.plugins.pme.pme_utils pydft_qmmm.plugins.rigid pydft_qmmm.plugins.rigid.rigid pydft_qmmm.plugins.rigid.rigid_utils pydft_qmmm.plugins.settle pydft_qmmm.plugins.settle.settle pydft_qmmm.plugins.settle.settle_utils pydft_qmmm.plugins.wrap pydft_qmmm.plugins.wrap.wrap pydft_qmmm.system pydft_qmmm.system.system pydft_qmmm.system.system_atom pydft_qmmm.system.variable pydft_qmmm.wrappers pydft_qmmm.wrappers.logger pydft_qmmm.wrappers.simulation

MODULE_PATH (in module pydft_qmmm.interfaces.interface_manager)

N

name (pydft_qmmm.calculators.calculator.Calculator attribute), [1] (pydft_qmmm.common.atom.Atom attribute) names (pydft_qmmm.system.system.System property) NO (pydft_qmmm.common.constants.TheoryLevel attribute) nonbonded_cutoff (pydft_qmmm.hamiltonians.mm_hamiltonian.MMHamiltonian attribute) (pydft_qmmm.interfaces.interface.MMSettings attribute)

nonbonded_method (pydft_qmmm.hamiltonians.mm_hamiltonian.MMHamiltonian attribute) (pydft_qmmm.interfaces.interface.MMSettings attribute) not_slice() (in module pydft_qmmm.common.utils.selection_utils) NULL (pydft_qmmm.common.constants.Subsystem attribute) NullLogger (class in pydft_qmmm.wrappers.logger) numerical_gradient() (in module pydft_qmmm.common.utils.misc_utils)

O

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) or_slice() (in module pydft_qmmm.common.utils.selection_utils) output_directory (pydft_qmmm.wrappers.logger.Logger attribute)

P

parens_slice() (in module pydft_qmmm.common.utils.selection_utils) PartitionPlugin (class in pydft_qmmm.plugins.plugin) Plugin (class in pydft_qmmm.plugins.plugin) Plumed (class in pydft_qmmm.plugins.plumed.plumed) PME (class in pydft_qmmm.plugins.pme.pme) pme (pydft_qmmm.interfaces.qmmm_pme_psi4.psi4_utils.PMEPsi4Options attribute) pme_alpha (pydft_qmmm.hamiltonians.mm_hamiltonian.MMHamiltonian attribute) (pydft_qmmm.interfaces.interface.MMSettings attribute) pme_components() (in module pydft_qmmm.plugins.pme.pme_utils) pme_gridnumber (pydft_qmmm.hamiltonians.mm_hamiltonian.MMHamiltonian attribute) (pydft_qmmm.interfaces.interface.MMSettings attribute) pme_openmm_interface_factory() (in module pydft_qmmm.interfaces.qmmm_pme_openmm.openmm_factory) pme_psi4_interface_factory() (in module pydft_qmmm.interfaces.qmmm_pme_psi4.psi4_utils) PMEOpenMMInterface (class in pydft_qmmm.interfaces.qmmm_pme_openmm.openmm_interface) PMEPsi4Interface (class in pydft_qmmm.interfaces.qmmm_pme_psi4.psi4_interface) PMEPsi4Options (class in pydft_qmmm.interfaces.qmmm_pme_psi4.psi4_utils) position (pydft_qmmm.common.atom.Atom attribute) positions (pydft_qmmm.system.system.System property) project_to_grid() (in module pydft_qmmm.plugins.pme.pme_utils) psi4_interface_factory() (in module pydft_qmmm.interfaces.psi4.psi4_utils) Psi4Context (class in pydft_qmmm.interfaces.psi4.psi4_utils) Psi4Interface (class in pydft_qmmm.interfaces.psi4.psi4_interface) Psi4Options (class in pydft_qmmm.interfaces.psi4.psi4_utils) pydft_qmmm module pydft_qmmm.calculators module pydft_qmmm.calculators.calculator module pydft_qmmm.calculators.composite_calculator module pydft_qmmm.calculators.interface_calculator module pydft_qmmm.common module pydft_qmmm.common.atom module pydft_qmmm.common.constants module pydft_qmmm.common.file_manager module pydft_qmmm.common.resource_manager module pydft_qmmm.common.utils module pydft_qmmm.common.utils.lattice_utils module pydft_qmmm.common.utils.misc_utils module pydft_qmmm.common.utils.selection_utils 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_interface module pydft_qmmm.interfaces.psi4.psi4_utils module pydft_qmmm.interfaces.qmmm_pme_openmm module pydft_qmmm.interfaces.qmmm_pme_openmm.openmm_factory module pydft_qmmm.interfaces.qmmm_pme_openmm.openmm_interface module pydft_qmmm.interfaces.qmmm_pme_openmm.openmm_utils module pydft_qmmm.interfaces.qmmm_pme_psi4 module pydft_qmmm.interfaces.qmmm_pme_psi4.psi4_interface module pydft_qmmm.interfaces.qmmm_pme_psi4.psi4_utils module pydft_qmmm.plugins module pydft_qmmm.plugins.atom_partition module pydft_qmmm.plugins.atom_partition.atom_partition module pydft_qmmm.plugins.center module pydft_qmmm.plugins.center.center module pydft_qmmm.plugins.centroid_partition module pydft_qmmm.plugins.centroid_partition.centroid_partition module pydft_qmmm.plugins.firstatom_partition module pydft_qmmm.plugins.firstatom_partition.firstatom_partition module pydft_qmmm.plugins.plugin module pydft_qmmm.plugins.plugin_manager module pydft_qmmm.plugins.plumed module pydft_qmmm.plugins.plumed.plumed module pydft_qmmm.plugins.pme module pydft_qmmm.plugins.pme.pme module pydft_qmmm.plugins.pme.pme_utils module pydft_qmmm.plugins.rigid module pydft_qmmm.plugins.rigid.rigid module pydft_qmmm.plugins.rigid.rigid_utils module pydft_qmmm.plugins.settle module pydft_qmmm.plugins.settle.settle module pydft_qmmm.plugins.settle.settle_utils module pydft_qmmm.plugins.wrap module pydft_qmmm.plugins.wrap.wrap module pydft_qmmm.system module pydft_qmmm.system.system module pydft_qmmm.system.system_atom module pydft_qmmm.system.variable module pydft_qmmm.wrappers module pydft_qmmm.wrappers.logger module pydft_qmmm.wrappers.simulation module

Q

QM (pydft_qmmm.common.constants.TheoryLevel attribute) QMHamiltonian (class in pydft_qmmm.hamiltonians.qm_hamiltonian) QMInterface (class in pydft_qmmm.interfaces.interface) QMMMHamiltonian (class in pydft_qmmm.hamiltonians.qmmm_hamiltonian)

QMSettings (class in pydft_qmmm.interfaces.interface) quadrature_radial (pydft_qmmm.hamiltonians.qm_hamiltonian.QMHamiltonian attribute) (pydft_qmmm.interfaces.interface.QMSettings attribute) quadrature_spherical (pydft_qmmm.hamiltonians.qm_hamiltonian.QMHamiltonian attribute) (pydft_qmmm.interfaces.interface.QMSettings attribute)

R

read_guess (pydft_qmmm.hamiltonians.qm_hamiltonian.QMHamiltonian attribute) (pydft_qmmm.interfaces.interface.QMSettings attribute) record() (pydft_qmmm.wrappers.logger.Logger method) (pydft_qmmm.wrappers.logger.NullLogger 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.integrators.integrator.Integrator method) residue (pydft_qmmm.common.atom.Atom attribute)

residue_map (pydft_qmmm.system.system.System property) residue_name (pydft_qmmm.common.atom.Atom attribute) residue_names (pydft_qmmm.system.system.System property) residue_partition() (in module pydft_qmmm.common.utils.misc_utils) residues (pydft_qmmm.system.system.System property) ResourceManager (class in pydft_qmmm.common.resource_manager) Results (class in pydft_qmmm.common.utils.misc_utils) RigidBody (class in pydft_qmmm.plugins.rigid.rigid) run_dynamics() (pydft_qmmm.wrappers.simulation.Simulation method)

S

scf__guess (pydft_qmmm.interfaces.psi4.psi4_utils.Psi4Options attribute) scf__reference (pydft_qmmm.interfaces.psi4.psi4_utils.Psi4Options attribute) scf_type (pydft_qmmm.hamiltonians.qm_hamiltonian.QMHamiltonian attribute) (pydft_qmmm.interfaces.interface.QMSettings attribute) (pydft_qmmm.interfaces.psi4.psi4_utils.Psi4Options attribute) select() (pydft_qmmm.system.system.System method) SELECTORS (in module pydft_qmmm.common.utils.misc_utils) (in module pydft_qmmm.common.utils.selection_utils) set_default_interfaces() (in module pydft_qmmm.interfaces.interface_manager) set_interfaces() (in module pydft_qmmm.interfaces.interface_manager) set_memory() (pydft_qmmm.wrappers.simulation.Simulation method) set_threads() (pydft_qmmm.wrappers.simulation.Simulation method) SETTLE (class in pydft_qmmm.plugins.settle.settle) settle_positions() (in module pydft_qmmm.plugins.settle.settle_utils) settle_velocities() (in module pydft_qmmm.plugins.settle.settle_utils) Simulation (class in pydft_qmmm.wrappers.simulation) SoftwareInterface (class in pydft_qmmm.interfaces.interface)

SoftwareSettings (class in pydft_qmmm.interfaces.interface) spin (pydft_qmmm.hamiltonians.qm_hamiltonian.QMHamiltonian attribute) (pydft_qmmm.interfaces.interface.QMSettings attribute) start_csv() (in module pydft_qmmm.common.file_manager) start_dcd() (in module pydft_qmmm.common.file_manager) start_log() (in module pydft_qmmm.common.file_manager) Stationary (class in pydft_qmmm.plugins.rigid.rigid) Subsystem (class in pydft_qmmm.common.constants) subsystem (pydft_qmmm.common.atom.Atom attribute) subsystems (pydft_qmmm.system.system.System property) SUPPORTED_FORCES (in module pydft_qmmm.interfaces.openmm.openmm_factory) System (class in pydft_qmmm.system.system) system (pydft_qmmm.calculators.calculator.Calculator attribute), [1] (pydft_qmmm.calculators.composite_calculator.CompositeCalculator attribute) (pydft_qmmm.calculators.interface_calculator.InterfaceCalculator attribute) (pydft_qmmm.interfaces.interface.MMSettings attribute) (pydft_qmmm.interfaces.interface.QMSettings attribute) (pydft_qmmm.wrappers.logger.Logger attribute)

T

temperature (pydft_qmmm.integrators.langevin_integrator.LangevinIntegrator attribute) theory_level (pydft_qmmm.hamiltonians.hamiltonian.CalculatorHamiltonian attribute), [1] (pydft_qmmm.interfaces.interface.MMInterface attribute), [1] (pydft_qmmm.interfaces.interface.QMInterface attribute), [1] (pydft_qmmm.interfaces.interface.SoftwareInterface attribute), [1]

TheoryLevel (class in pydft_qmmm.common.constants) timestep (pydft_qmmm.integrators.integrator.Integrator attribute), [1] (pydft_qmmm.integrators.langevin_integrator.LangevinIntegrator attribute) (pydft_qmmm.integrators.verlet_integrator.VerletIntegrator attribute)

U

update() (pydft_qmmm.system.variable.ArrayValue method) update_box() (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) update_charges() (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Interface method) (pydft_qmmm.interfaces.psi4.psi4_utils.Psi4Context method) update_embedding() (pydft_qmmm.interfaces.psi4.psi4_utils.Psi4Context method) update_memory() (pydft_qmmm.common.resource_manager.ResourceManager method) (pydft_qmmm.interfaces.interface.SoftwareInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Interface method) update_nuc_extd_grad() (pydft_qmmm.interfaces.qmmm_pme_psi4.psi4_interface.PMEPsi4Interface method)

update_nuc_extd_pot() (pydft_qmmm.interfaces.qmmm_pme_psi4.psi4_interface.PMEPsi4Interface method) update_positions() (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Interface method) (pydft_qmmm.interfaces.psi4.psi4_utils.Psi4Context method) update_quad_extd_pot() (pydft_qmmm.interfaces.qmmm_pme_psi4.psi4_interface.PMEPsi4Interface method) update_subsystems() (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Interface method) update_threads() (pydft_qmmm.common.resource_manager.ResourceManager method) (pydft_qmmm.interfaces.interface.SoftwareInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) (pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Interface method)

V

value() (pydft_qmmm.system.variable.ArrayValue method) velocities (pydft_qmmm.system.system.System property)

velocity (pydft_qmmm.common.atom.Atom attribute) VerletIntegrator (class in pydft_qmmm.integrators.verlet_integrator)

W

wrap_positions() (in module pydft_qmmm.common.utils.misc_utils) write_to_csv (pydft_qmmm.wrappers.logger.Logger attribute) write_to_csv() (in module pydft_qmmm.common.file_manager) write_to_dcd (pydft_qmmm.wrappers.logger.Logger attribute)

write_to_dcd() (in module pydft_qmmm.common.file_manager) write_to_log (pydft_qmmm.wrappers.logger.Logger attribute) write_to_log() (in module pydft_qmmm.common.file_manager) write_to_pdb (pydft_qmmm.wrappers.logger.Logger attribute) write_to_pdb() (in module pydft_qmmm.common.file_manager)

Z

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

zero_intermolecular() (pydft_qmmm.interfaces.interface.MMInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) zero_intramolecular() (pydft_qmmm.interfaces.interface.MMInterface method) (pydft_qmmm.interfaces.openmm.openmm_interface.OpenMMInterface method) zero_vector() (in module pydft_qmmm.common.utils.misc_utils)