Index

A

active_plugins() (qmmm_pme.calculators.calculator.ModifiableCalculator method) (qmmm_pme.integrators.integrator.ModifiableIntegrator method) ae_atoms (qmmm_pme.records.topology.Topology attribute) align_dict() (in module qmmm_pme.common.utils)

atom_names (qmmm_pme.records.topology.Topology attribute) AtomEmbedding (class in qmmm_pme.plugins.atom_embedding.atom_embedding) atoms (qmmm_pme.hamiltonians.hamiltonian.Hamiltonian attribute) (qmmm_pme.records.topology.Topology attribute)

B

basis (qmmm_pme.interfaces.psi4_interface.Psi4Options attribute) basis_set (qmmm_pme.hamiltonians.qm_hamiltonian.QMHamiltonian attribute) (qmmm_pme.interfaces.interface.QMSettings attribute) box (qmmm_pme.records.state.State attribute) build_calculator() (qmmm_pme.hamiltonians.hamiltonian.Hamiltonian method) (qmmm_pme.hamiltonians.mm_hamiltonian.MMHamiltonian method) (qmmm_pme.hamiltonians.qm_hamiltonian.QMHamiltonian method) (qmmm_pme.hamiltonians.qmmm_hamiltonian.QMMMHamiltonian method)

build_integrator() (qmmm_pme.dynamics.dynamics.Dynamics method) (qmmm_pme.dynamics.dynamics.Langevin method) (qmmm_pme.dynamics.dynamics.VelocityVerlet method) (qmmm_pme.dynamics.dynamics.Verlet method)

C

calculate() (qmmm_pme.calculators.calculator.ModifiableCalculator method) (qmmm_pme.calculators.calculator.StandaloneCalculator method) (qmmm_pme.calculators.qmmm_calculator.QMMMCalculator method) calculate_energy_forces() (qmmm_pme.wrappers.simulation.Simulation method) calculate_forces() (qmmm_pme.wrappers.simulation.Simulation method) CalculatorPlugin (class in qmmm_pme.plugins.plugin) calculators (qmmm_pme.calculators.qmmm_calculator.QMMMCalculator attribute) CalculatorType (class in qmmm_pme.calculators.calculator) charge (qmmm_pme.hamiltonians.qm_hamiltonian.QMHamiltonian attribute) (qmmm_pme.interfaces.interface.QMSettings attribute) charges (qmmm_pme.records.state.State attribute) components (qmmm_pme.calculators.calculator.Results attribute) compute_components() (qmmm_pme.interfaces.interface.SoftwareInterface method) (qmmm_pme.interfaces.openmm_interface.OpenMMInterface method) (qmmm_pme.interfaces.psi4_interface.Psi4Interface method) compute_embedding() (qmmm_pme.calculators.qmmm_calculator.QMMMCalculator method) compute_energy() (qmmm_pme.interfaces.interface.SoftwareInterface method) (qmmm_pme.interfaces.openmm_interface.OpenMMInterface method) (qmmm_pme.interfaces.psi4_interface.Psi4Interface method)

compute_forces() (qmmm_pme.interfaces.interface.SoftwareInterface method) (qmmm_pme.interfaces.openmm_interface.OpenMMInterface method) (qmmm_pme.interfaces.psi4_interface.Psi4Interface method) compute_kinetic_energy() (qmmm_pme.integrators.integrator.Integrator method) (qmmm_pme.integrators.integrator.ModifiableIntegrator method) compute_lattice_constants() (in module qmmm_pme.common.utils) compute_least_mirror() (in module qmmm_pme.common.utils) compute_pme_potential() (qmmm_pme.interfaces.openmm_interface.OpenMMInterface method) compute_quadrature() (qmmm_pme.interfaces.psi4_interface.Psi4Interface method) compute_velocities() (qmmm_pme.integrators.integrator.Integrator method) (qmmm_pme.integrators.integrator.ModifiableIntegrator method) context (qmmm_pme.interfaces.openmm_interface.OpenMMInterface attribute) (qmmm_pme.interfaces.pme_openmm_interface.PMEOpenMMInterface attribute) (qmmm_pme.interfaces.psi4_interface.Psi4Interface attribute) csv_write_interval (qmmm_pme.wrappers.logger.Logger attribute)

D

dcd_write_interval (qmmm_pme.wrappers.logger.Logger attribute) decimal_places (qmmm_pme.wrappers.logger.Logger attribute) dft_radial_points (qmmm_pme.interfaces.psi4_interface.Psi4Options attribute)

dft_spherical_points (qmmm_pme.interfaces.psi4_interface.Psi4Options attribute) Dynamics (class in qmmm_pme.dynamics.dynamics) dynamics (qmmm_pme.wrappers.simulation.Simulation attribute)

E

elements (qmmm_pme.records.topology.Topology attribute) EMBEDDING (qmmm_pme.interfaces.interface.SystemTypes attribute) embedding_cutoff (qmmm_pme.calculators.qmmm_calculator.QMMMCalculator attribute) (qmmm_pme.hamiltonians.qmmm_hamiltonian.QMMMHamiltonian attribute)

end_log() (qmmm_pme.common.file_manager.FileManager method) energy (qmmm_pme.calculators.calculator.Results attribute) (qmmm_pme.wrappers.simulation.Simulation attribute) exchange_correlation (qmmm_pme.interfaces.psi4_interface.Psi4Reference attribute)

F

FileManager (class in qmmm_pme.common.file_manager) Files (class in qmmm_pme.records.files) FilesVariable (class in qmmm_pme.records.files) forcefield (qmmm_pme.interfaces.openmm_interface.OpenMMInterface attribute) (qmmm_pme.interfaces.pme_openmm_interface.PMEOpenMMInterface attribute) forcefield_list (qmmm_pme.records.files.Files attribute) forces (qmmm_pme.calculators.calculator.Results attribute) (qmmm_pme.records.state.State attribute)

frame (qmmm_pme.wrappers.simulation.Simulation attribute) friction (qmmm_pme.dynamics.dynamics.Langevin attribute) (qmmm_pme.integrators.langevin_integrator.LangevinIntegrator attribute) (qmmm_pme.interfaces.interface.MMSettings attribute) functional (qmmm_pme.hamiltonians.qm_hamiltonian.QMHamiltonian attribute) (qmmm_pme.interfaces.interface.QMSettings attribute) (qmmm_pme.interfaces.psi4_interface.Psi4Interface attribute)

G

generate_molecule() (qmmm_pme.interfaces.psi4_interface.Psi4Context method) get_software_factories() (in module qmmm_pme.interfaces.interface_manager) get_state_notifiers() (qmmm_pme.interfaces.interface.SoftwareInterface method) (qmmm_pme.interfaces.openmm_interface.OpenMMInterface method) (qmmm_pme.interfaces.psi4_interface.Psi4Interface method)

get_topology_notifiers() (qmmm_pme.interfaces.interface.SoftwareInterface method) (qmmm_pme.interfaces.openmm_interface.OpenMMInterface method) (qmmm_pme.interfaces.psi4_interface.Psi4Interface method)

H

Hamiltonian (class in qmmm_pme.hamiltonians.hamiltonian)

hamiltonian (qmmm_pme.wrappers.simulation.Simulation attribute)

I

input_json (qmmm_pme.records.files.Files attribute) integrate() (qmmm_pme.integrators.integrator.ModifiableIntegrator method) (qmmm_pme.integrators.langevin_integrator.LangevinIntegrator method) (qmmm_pme.integrators.velocity_verlet_integrator.VelocityVerletIntegrator method) (qmmm_pme.integrators.verlet_integrator.VerletIntegrator method)

Integrator (class in qmmm_pme.integrators.integrator) IntegratorPlugin (class in qmmm_pme.plugins.plugin) interface (qmmm_pme.calculators.calculator.StandaloneCalculator attribute)

K

kinetic (qmmm_pme.interfaces.psi4_interface.Psi4Reference attribute)

L

Langevin (class in qmmm_pme.dynamics.dynamics) LangevinIntegrator (class in qmmm_pme.integrators.langevin_integrator) load() (qmmm_pme.common.file_manager.FileManager method)

log_write_interval (qmmm_pme.wrappers.logger.Logger attribute) Logger (class in qmmm_pme.wrappers.logger) logger (qmmm_pme.wrappers.simulation.Simulation attribute)

M

masses (qmmm_pme.records.state.State attribute) ME (qmmm_pme.calculators.calculator.CalculatorType attribute) memory (qmmm_pme.wrappers.simulation.Simulation attribute) MM (qmmm_pme.calculators.calculator.CalculatorType attribute) (qmmm_pme.interfaces.interface.SoftwareTypes attribute) mm_atoms (qmmm_pme.records.topology.Topology attribute) mm_hamiltonian (qmmm_pme.hamiltonians.qmmm_hamiltonian.QMMMHamiltonian attribute) MMHamiltonian (class in qmmm_pme.hamiltonians.mm_hamiltonian) MMHamiltonianInterface (class in qmmm_pme.hamiltonians.hamiltonian) MMSettings (class in qmmm_pme.interfaces.interface) modeller (qmmm_pme.interfaces.openmm_interface.OpenMMInterface attribute) (qmmm_pme.interfaces.pme_openmm_interface.PMEOpenMMInterface attribute) ModifiableCalculator (class in qmmm_pme.calculators.calculator) ModifiableIntegrator (class in qmmm_pme.integrators.integrator) modify() (qmmm_pme.plugins.atom_embedding.atom_embedding.AtomEmbedding method) (qmmm_pme.plugins.plugin.CalculatorPlugin method) (qmmm_pme.plugins.plugin.IntegratorPlugin method) (qmmm_pme.plugins.plugin.QMMMCalculatorPlugin method) (qmmm_pme.plugins.pme.pme.PME method) (qmmm_pme.plugins.rigid.rigid.RigidBody method) (qmmm_pme.plugins.rigid.rigid.Stationary method) (qmmm_pme.plugins.settle.settle.SETTLE method) module qmmm_pme qmmm_pme.calculators qmmm_pme.calculators.calculator qmmm_pme.calculators.qmmm_calculator qmmm_pme.common qmmm_pme.common.file_manager qmmm_pme.common.units qmmm_pme.common.utils qmmm_pme.dynamics qmmm_pme.dynamics.dynamics qmmm_pme.hamiltonians qmmm_pme.hamiltonians.hamiltonian qmmm_pme.hamiltonians.mm_hamiltonian qmmm_pme.hamiltonians.qm_hamiltonian qmmm_pme.hamiltonians.qmmm_hamiltonian qmmm_pme.integrators qmmm_pme.integrators.integrator qmmm_pme.integrators.langevin_integrator qmmm_pme.integrators.velocity_verlet_integrator qmmm_pme.integrators.verlet_integrator qmmm_pme.interfaces qmmm_pme.interfaces.interface qmmm_pme.interfaces.interface_manager qmmm_pme.interfaces.openmm_interface qmmm_pme.interfaces.pme_openmm_interface qmmm_pme.interfaces.psi4_interface qmmm_pme.plugins qmmm_pme.plugins.atom_embedding qmmm_pme.plugins.atom_embedding.atom_embedding qmmm_pme.plugins.plugin qmmm_pme.plugins.pme qmmm_pme.plugins.pme.pme qmmm_pme.plugins.pme.pme_utils qmmm_pme.plugins.rigid qmmm_pme.plugins.rigid.rigid qmmm_pme.plugins.rigid.rigid_utils qmmm_pme.plugins.settle qmmm_pme.plugins.settle.settle qmmm_pme.plugins.settle.settle_utils qmmm_pme.records qmmm_pme.records.files qmmm_pme.records.record qmmm_pme.records.state qmmm_pme.records.topology qmmm_pme.wrappers qmmm_pme.wrappers.logger qmmm_pme.wrappers.simulation qmmm_pme.wrappers.system

momenta (qmmm_pme.records.state.State attribute)

N

NameVariable (class in qmmm_pme.records.topology) nonbonded_cutoff (qmmm_pme.hamiltonians.mm_hamiltonian.MMHamiltonian attribute) (qmmm_pme.interfaces.interface.MMSettings attribute) nonbonded_method (qmmm_pme.hamiltonians.mm_hamiltonian.MMHamiltonian attribute) (qmmm_pme.interfaces.interface.MMSettings attribute)

nuclear_repulsion (qmmm_pme.interfaces.psi4_interface.Psi4Reference attribute) NullLogger (class in qmmm_pme.wrappers.logger) num_threads (qmmm_pme.wrappers.simulation.Simulation attribute)

O

one_electron (qmmm_pme.interfaces.psi4_interface.Psi4Reference attribute) openmm_embedding_factory() (in module qmmm_pme.interfaces.openmm_interface) openmm_subsystem_factory() (in module qmmm_pme.interfaces.openmm_interface) openmm_system_factory() (in module qmmm_pme.interfaces.openmm_interface)

OpenMMInterface (class in qmmm_pme.interfaces.openmm_interface) options (qmmm_pme.calculators.calculator.StandaloneCalculator attribute) (qmmm_pme.calculators.qmmm_calculator.QMMMCalculator attribute) (qmmm_pme.interfaces.psi4_interface.Psi4Interface attribute) output_directory (qmmm_pme.wrappers.logger.Logger attribute)

P

parse_atoms() (qmmm_pme.hamiltonians.hamiltonian.Hamiltonian method) pdb (qmmm_pme.interfaces.openmm_interface.OpenMMInterface attribute) (qmmm_pme.interfaces.pme_openmm_interface.PMEOpenMMInterface attribute) pdb_list (qmmm_pme.records.files.Files attribute) Plugin (class in qmmm_pme.plugins.plugin) plugins (qmmm_pme.wrappers.simulation.Simulation attribute) PME (class in qmmm_pme.plugins.pme.pme) pme_alpha (qmmm_pme.hamiltonians.mm_hamiltonian.MMHamiltonian attribute) (qmmm_pme.interfaces.interface.MMSettings attribute) pme_components() (in module qmmm_pme.plugins.pme.pme_utils) pme_gridnumber (qmmm_pme.hamiltonians.mm_hamiltonian.MMHamiltonian attribute) (qmmm_pme.interfaces.interface.MMSettings attribute)

pme_openmm_embedding_factory() (in module qmmm_pme.interfaces.pme_openmm_interface) pme_openmm_subsystem_factory() (in module qmmm_pme.interfaces.pme_openmm_interface) pme_openmm_system_factory() (in module qmmm_pme.interfaces.pme_openmm_interface) PMEOpenMMInterface (class in qmmm_pme.interfaces.pme_openmm_interface) positions (qmmm_pme.records.state.State attribute) potential (qmmm_pme.interfaces.psi4_interface.Psi4Reference attribute) project_to_grid() (in module qmmm_pme.plugins.pme.pme_utils) psi4_system_factory() (in module qmmm_pme.interfaces.psi4_interface) Psi4Context (class in qmmm_pme.interfaces.psi4_interface) Psi4Interface (class in qmmm_pme.interfaces.psi4_interface) Psi4Options (class in qmmm_pme.interfaces.psi4_interface) Psi4Reference (class in qmmm_pme.interfaces.psi4_interface)

Q

QM (qmmm_pme.calculators.calculator.CalculatorType attribute) (qmmm_pme.interfaces.interface.SoftwareTypes attribute) qm_atoms (qmmm_pme.records.topology.Topology attribute) qm_hamiltonian (qmmm_pme.hamiltonians.qmmm_hamiltonian.QMMMHamiltonian attribute) QMHamiltonian (class in qmmm_pme.hamiltonians.qm_hamiltonian) QMHamiltonianInterface (class in qmmm_pme.hamiltonians.hamiltonian) qmmm_pme module qmmm_pme.calculators module qmmm_pme.calculators.calculator module qmmm_pme.calculators.qmmm_calculator module qmmm_pme.common module qmmm_pme.common.file_manager module qmmm_pme.common.units module qmmm_pme.common.utils module qmmm_pme.dynamics module qmmm_pme.dynamics.dynamics module qmmm_pme.hamiltonians module qmmm_pme.hamiltonians.hamiltonian module qmmm_pme.hamiltonians.mm_hamiltonian module qmmm_pme.hamiltonians.qm_hamiltonian module qmmm_pme.hamiltonians.qmmm_hamiltonian module qmmm_pme.integrators module qmmm_pme.integrators.integrator module qmmm_pme.integrators.langevin_integrator module qmmm_pme.integrators.velocity_verlet_integrator module qmmm_pme.integrators.verlet_integrator module qmmm_pme.interfaces module qmmm_pme.interfaces.interface module qmmm_pme.interfaces.interface_manager module qmmm_pme.interfaces.openmm_interface module qmmm_pme.interfaces.pme_openmm_interface module

qmmm_pme.interfaces.psi4_interface module qmmm_pme.plugins module qmmm_pme.plugins.atom_embedding module qmmm_pme.plugins.atom_embedding.atom_embedding module qmmm_pme.plugins.plugin module qmmm_pme.plugins.pme module qmmm_pme.plugins.pme.pme module qmmm_pme.plugins.pme.pme_utils module qmmm_pme.plugins.rigid module qmmm_pme.plugins.rigid.rigid module qmmm_pme.plugins.rigid.rigid_utils module qmmm_pme.plugins.settle module qmmm_pme.plugins.settle.settle module qmmm_pme.plugins.settle.settle_utils module qmmm_pme.records module qmmm_pme.records.files module qmmm_pme.records.record module qmmm_pme.records.state module qmmm_pme.records.topology module qmmm_pme.wrappers module qmmm_pme.wrappers.logger module qmmm_pme.wrappers.simulation module qmmm_pme.wrappers.system module QMMMCalculator (class in qmmm_pme.calculators.qmmm_calculator) QMMMCalculatorPlugin (class in qmmm_pme.plugins.plugin) QMMMHamiltonian (class in qmmm_pme.hamiltonians.qmmm_hamiltonian) QMMMHamiltonianInterface (class in qmmm_pme.hamiltonians.hamiltonian) QMSettings (class in qmmm_pme.interfaces.interface) quadrature_radial (qmmm_pme.hamiltonians.qm_hamiltonian.QMHamiltonian attribute) (qmmm_pme.interfaces.interface.QMSettings attribute) quadrature_spherical (qmmm_pme.hamiltonians.qm_hamiltonian.QMHamiltonian attribute) (qmmm_pme.interfaces.interface.QMSettings attribute)

R

read_guess (qmmm_pme.hamiltonians.qm_hamiltonian.QMHamiltonian attribute) (qmmm_pme.interfaces.interface.QMSettings attribute) Record (class in qmmm_pme.records.record) record() (qmmm_pme.wrappers.logger.Logger method) (qmmm_pme.wrappers.logger.NullLogger method) reference (qmmm_pme.interfaces.psi4_interface.Psi4Interface attribute) reference_energy (qmmm_pme.hamiltonians.qm_hamiltonian.QMHamiltonian attribute) (qmmm_pme.interfaces.interface.QMSettings attribute)

register_notifier() (qmmm_pme.records.record.Variable method) register_plugin() (qmmm_pme.calculators.calculator.ModifiableCalculator method) (qmmm_pme.integrators.integrator.ModifiableIntegrator method) residue_names (qmmm_pme.records.topology.Topology attribute) ResidueVariable (class in qmmm_pme.records.topology) Results (class in qmmm_pme.calculators.calculator) RigidBody (class in qmmm_pme.plugins.rigid.rigid) run_dynamics() (qmmm_pme.wrappers.simulation.Simulation method)

S

scf__guess (qmmm_pme.interfaces.psi4_interface.Psi4Options attribute) scf__reference (qmmm_pme.interfaces.psi4_interface.Psi4Options attribute) scf_type (qmmm_pme.hamiltonians.qm_hamiltonian.QMHamiltonian attribute) (qmmm_pme.interfaces.interface.QMSettings attribute) (qmmm_pme.interfaces.psi4_interface.Psi4Options attribute) SETTLE (class in qmmm_pme.plugins.settle.settle) settle_positions() (in module qmmm_pme.plugins.settle.settle_utils) settle_velocities() (in module qmmm_pme.plugins.settle.settle_utils) Simulation (class in qmmm_pme.wrappers.simulation) SoftwareInterface (class in qmmm_pme.interfaces.interface) SoftwareSettings (class in qmmm_pme.interfaces.interface) SoftwareTypes (class in qmmm_pme.interfaces.interface) spin (qmmm_pme.hamiltonians.qm_hamiltonian.QMHamiltonian attribute) (qmmm_pme.interfaces.interface.QMSettings attribute) StandaloneCalculator (class in qmmm_pme.calculators.calculator) start_csv() (qmmm_pme.common.file_manager.FileManager method) start_dcd() (qmmm_pme.common.file_manager.FileManager method) start_log() (qmmm_pme.common.file_manager.FileManager method) State (class in qmmm_pme.records.state)

StateVariable (class in qmmm_pme.records.state) Stationary (class in qmmm_pme.plugins.rigid.rigid) SUBSYSTEM (qmmm_pme.interfaces.interface.SystemTypes attribute) System (class in qmmm_pme.wrappers.system) system (qmmm_pme.calculators.calculator.ModifiableCalculator attribute) (qmmm_pme.calculators.calculator.StandaloneCalculator attribute) (qmmm_pme.calculators.qmmm_calculator.QMMMCalculator attribute) (qmmm_pme.integrators.integrator.Integrator attribute) (qmmm_pme.integrators.integrator.ModifiableIntegrator attribute) (qmmm_pme.integrators.velocity_verlet_integrator.VelocityVerletIntegrator attribute) (qmmm_pme.integrators.verlet_integrator.VerletIntegrator attribute) (qmmm_pme.interfaces.interface.MMSettings attribute) (qmmm_pme.interfaces.interface.QMSettings attribute) SYSTEM (qmmm_pme.interfaces.interface.SystemTypes attribute) system (qmmm_pme.interfaces.openmm_interface.OpenMMInterface attribute) (qmmm_pme.interfaces.pme_openmm_interface.PMEOpenMMInterface attribute) (qmmm_pme.wrappers.logger.Logger attribute) (qmmm_pme.wrappers.simulation.Simulation attribute) system_type (qmmm_pme.hamiltonians.hamiltonian.Hamiltonian attribute) SystemTypes (class in qmmm_pme.interfaces.interface)

T

temperature (qmmm_pme.dynamics.dynamics.Langevin attribute) (qmmm_pme.dynamics.dynamics.VelocityVerlet attribute) (qmmm_pme.dynamics.dynamics.Verlet attribute) (qmmm_pme.integrators.integrator.Integrator attribute) (qmmm_pme.integrators.integrator.ModifiableIntegrator attribute) (qmmm_pme.integrators.velocity_verlet_integrator.VelocityVerletIntegrator attribute) (qmmm_pme.integrators.verlet_integrator.VerletIntegrator attribute) (qmmm_pme.interfaces.interface.MMSettings attribute) timestep (qmmm_pme.dynamics.dynamics.Dynamics attribute) (qmmm_pme.integrators.integrator.Integrator attribute) (qmmm_pme.integrators.integrator.ModifiableIntegrator attribute) (qmmm_pme.integrators.velocity_verlet_integrator.VelocityVerletIntegrator attribute) (qmmm_pme.integrators.verlet_integrator.VerletIntegrator attribute) (qmmm_pme.interfaces.interface.MMSettings attribute)

Topology (class in qmmm_pme.records.topology) topology_list (qmmm_pme.records.files.Files attribute) total (qmmm_pme.interfaces.psi4_interface.Psi4Reference attribute) two_electron (qmmm_pme.interfaces.psi4_interface.Psi4Reference attribute)

U

update() (qmmm_pme.records.files.FilesVariable method) (qmmm_pme.records.state.StateVariable method) (qmmm_pme.records.topology.NameVariable method) (qmmm_pme.records.topology.ResidueVariable method) update_box() (qmmm_pme.interfaces.openmm_interface.OpenMMInterface method) update_charges() (qmmm_pme.interfaces.openmm_interface.OpenMMInterface method)

update_embedding() (qmmm_pme.interfaces.psi4_interface.Psi4Context method) (qmmm_pme.interfaces.psi4_interface.Psi4Interface method) update_memory() (qmmm_pme.interfaces.psi4_interface.Psi4Interface method) update_num_threads() (qmmm_pme.interfaces.psi4_interface.Psi4Interface method) update_positions() (qmmm_pme.interfaces.openmm_interface.OpenMMInterface method) (qmmm_pme.interfaces.psi4_interface.Psi4Context method) (qmmm_pme.interfaces.psi4_interface.Psi4Interface method)

V

Variable (class in qmmm_pme.records.record) velocities (qmmm_pme.records.state.State attribute) VelocityVerlet (class in qmmm_pme.dynamics.dynamics)

VelocityVerletIntegrator (class in qmmm_pme.integrators.velocity_verlet_integrator) Verlet (class in qmmm_pme.dynamics.dynamics) VerletIntegrator (class in qmmm_pme.integrators.verlet_integrator)

W

wrap_positions() (qmmm_pme.wrappers.simulation.Simulation method) write_to_csv (qmmm_pme.wrappers.logger.Logger attribute) write_to_csv() (qmmm_pme.common.file_manager.FileManager method) write_to_dcd (qmmm_pme.wrappers.logger.Logger attribute)

write_to_dcd() (qmmm_pme.common.file_manager.FileManager method) write_to_log (qmmm_pme.wrappers.logger.Logger attribute) write_to_log() (qmmm_pme.common.file_manager.FileManager method) write_to_pdb (qmmm_pme.wrappers.logger.Logger attribute) write_to_pdb() (qmmm_pme.common.file_manager.FileManager method)