Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | U | V | W | Y | Z A add_electric_field() (in module mdhelper.openmm.system) add_image_charges() (in module mdhelper.openmm.system) add_slab_correction() (in module mdhelper.openmm.system) adjust_lightness() (in module mdhelper.plot.color) B biexp() (in module mdhelper.fit.exponential) C calculate_conductivity() (in module mdhelper.analysis.transport) (mdhelper.analysis.transport.Onsager method) calculate_coordination_numbers() (in module mdhelper.analysis.structure) (mdhelper.analysis.structure.RadialDistributionFunction method) calculate_electrophoretic_mobility() (in module mdhelper.analysis.transport) (mdhelper.analysis.transport.Onsager method) calculate_pmf() (mdhelper.analysis.structure.RadialDistributionFunction method) calculate_potential_profile() (in module mdhelper.analysis.profile) (mdhelper.analysis.profile.DensityProfile method) calculate_relative_permittivity() (in module mdhelper.analysis.electrostatics) (mdhelper.analysis.electrostatics.DipoleMoment method) calculate_relaxation_time() (in module mdhelper.analysis.polymer) (mdhelper.analysis.polymer.EndToEndVector method) calculate_structure_factor() (in module mdhelper.analysis.structure) (mdhelper.analysis.structure.RadialDistributionFunction method) calculate_transference_number() (in module mdhelper.analysis.transport) (mdhelper.analysis.transport.Onsager method) calculate_transport_coefficients() (in module mdhelper.analysis.transport) (mdhelper.analysis.transport.Onsager method) center_of_mass() (in module mdhelper.algorithm.molecule) clear() (mdhelper.analysis.base.Hash method) ConstantVolumeHeatCapacity (class in mdhelper.analysis.thermodynamics) copy() (mdhelper.analysis.base.Hash method) correlation_fft() (in module mdhelper.algorithm.correlation) (in module mdhelper.analysis.polymer) correlation_shift() (in module mdhelper.algorithm.correlation) (in module mdhelper.analysis.polymer) cosine_sum_1d() (in module mdhelper.algorithm.accelerated) cosine_sum_2d() (in module mdhelper.algorithm.accelerated) cosine_sum_inplace_2d() (in module mdhelper.algorithm.accelerated) cosine_sum_inplace_parallel_2d() (in module mdhelper.algorithm.accelerated) cosine_sum_parallel_2d() (in module mdhelper.algorithm.accelerated) coul_gauss() (in module mdhelper.openmm.pair) create_atoms() (in module mdhelper.algorithm.topology) (in module mdhelper.lammps.topology) (in module mdhelper.openmm.topology) D delta_fourier_transform_1d_1d() (in module mdhelper.algorithm.accelerated) delta_fourier_transform_sum_2d_2d() (in module mdhelper.algorithm.accelerated) delta_fourier_transform_sum_parallel_2d_2d() (in module mdhelper.algorithm.accelerated) DensityProfile (class in mdhelper.analysis.profile) depth_first_search() (in module mdhelper.algorithm.utility) describeNextReport() (mdhelper.openmm.reporter.NetCDFReporter method) DipoleMoment (class in mdhelper.analysis.electrostatics) dot_1d_1d() (in module mdhelper.algorithm.accelerated) dpd() (in module mdhelper.openmm.pair) DynamicAnalysisBase (class in mdhelper.analysis.base) E EndToEndVector (class in mdhelper.analysis.polymer) estimate_pressure_tensor() (in module mdhelper.openmm.system) exp() (in module mdhelper.fit.exponential) exp1() (in module mdhelper.fit.exponential) exp2() (in module mdhelper.fit.exponential) F fene() (in module mdhelper.openmm.bond) find_connected_nodes() (in module mdhelper.algorithm.utility) fourier() (in module mdhelper.fit.fourier) fourier1() (in module mdhelper.fit.fourier) fourier2() (in module mdhelper.fit.fourier) fourier3() (in module mdhelper.fit.fourier) fourier4() (in module mdhelper.fit.fourier) fourier5() (in module mdhelper.fit.fourier) fourier6() (in module mdhelper.fit.fourier) fourier7() (in module mdhelper.fit.fourier) fourier8() (in module mdhelper.fit.fourier) fromkeys() (mdhelper.analysis.base.Hash method) G gauss() (in module mdhelper.fit.gaussian) (in module mdhelper.openmm.pair) gauss1() (in module mdhelper.fit.gaussian) gauss2() (in module mdhelper.fit.gaussian) gauss3() (in module mdhelper.fit.gaussian) gauss4() (in module mdhelper.fit.gaussian) gauss5() (in module mdhelper.fit.gaussian) gauss6() (in module mdhelper.fit.gaussian) gauss7() (in module mdhelper.fit.gaussian) gauss8() (in module mdhelper.fit.gaussian) get() (mdhelper.analysis.base.Hash method) get_closest_factors() (in module mdhelper.algorithm.utility) get_dimensions() (mdhelper.openmm.file.NetCDFFile method) get_forces() (mdhelper.openmm.file.NetCDFFile method) get_lj_scaling_factors() (in module mdhelper.algorithm.unit) (in module mdhelper.openmm.unit) get_num_atoms() (mdhelper.openmm.file.NetCDFFile method) get_num_frames() (mdhelper.openmm.file.NetCDFFile method) get_positions() (mdhelper.openmm.file.NetCDFFile method) get_scaling_factors() (in module mdhelper.algorithm.unit) (in module mdhelper.openmm.unit) get_subset() (in module mdhelper.openmm.topology) get_times() (mdhelper.openmm.file.NetCDFFile method) get_velocities() (mdhelper.openmm.file.NetCDFFile method) Gyradius (class in mdhelper.analysis.polymer) H Hash (class in mdhelper.analysis.base) I inner_2d_2d() (in module mdhelper.algorithm.accelerated) inner_parallel_2d_2d() (in module mdhelper.algorithm.accelerated) IntermediateScatteringFunction (class in mdhelper.analysis.structure) items() (mdhelper.analysis.base.Hash method) K keys() (mdhelper.analysis.base.Hash method) L lj_coul() (in module mdhelper.openmm.pair) ljts() (in module mdhelper.openmm.pair) M mdhelper module mdhelper.algorithm module mdhelper.algorithm.accelerated module mdhelper.algorithm.correlation module mdhelper.algorithm.molecule module mdhelper.algorithm.topology module mdhelper.algorithm.unit module mdhelper.algorithm.utility module mdhelper.analysis module mdhelper.analysis.base module mdhelper.analysis.electrostatics module mdhelper.analysis.polymer module mdhelper.analysis.profile module mdhelper.analysis.structure module mdhelper.analysis.thermodynamics module mdhelper.analysis.transport module mdhelper.fit module mdhelper.fit.distribution module mdhelper.fit.exponential module mdhelper.fit.fourier module mdhelper.fit.gaussian module mdhelper.fit.polynomial module mdhelper.fit.power module mdhelper.lammps module mdhelper.lammps.topology module mdhelper.openmm module mdhelper.openmm.bond module mdhelper.openmm.file module mdhelper.openmm.pair module mdhelper.openmm.reporter module mdhelper.openmm.system module mdhelper.openmm.topology module mdhelper.openmm.unit module mdhelper.openmm.utility module mdhelper.plot module mdhelper.plot.axis module mdhelper.plot.color module mdhelper.plot.rcparam module module mdhelper mdhelper.algorithm mdhelper.algorithm.accelerated mdhelper.algorithm.correlation mdhelper.algorithm.molecule mdhelper.algorithm.topology mdhelper.algorithm.unit mdhelper.algorithm.utility mdhelper.analysis mdhelper.analysis.base mdhelper.analysis.electrostatics mdhelper.analysis.polymer mdhelper.analysis.profile mdhelper.analysis.structure mdhelper.analysis.thermodynamics mdhelper.analysis.transport mdhelper.fit mdhelper.fit.distribution mdhelper.fit.exponential mdhelper.fit.fourier mdhelper.fit.gaussian mdhelper.fit.polynomial mdhelper.fit.power mdhelper.lammps mdhelper.lammps.topology mdhelper.openmm mdhelper.openmm.bond mdhelper.openmm.file mdhelper.openmm.pair mdhelper.openmm.reporter mdhelper.openmm.system mdhelper.openmm.topology mdhelper.openmm.unit mdhelper.openmm.utility mdhelper.plot mdhelper.plot.axis mdhelper.plot.color mdhelper.plot.rcparam msd_fft() (in module mdhelper.algorithm.correlation) (in module mdhelper.analysis.transport) msd_shift() (in module mdhelper.algorithm.correlation) (in module mdhelper.analysis.transport) N NetCDFFile (class in mdhelper.openmm.file) NetCDFReporter (class in mdhelper.openmm.reporter) NumbaAnalysisBase (class in mdhelper.analysis.base) O Onsager (class in mdhelper.analysis.transport) optimize_pme() (in module mdhelper.openmm.utility) P ParallelAnalysisBase (class in mdhelper.analysis.base) poly() (in module mdhelper.fit.polynomial) poly1() (in module mdhelper.fit.polynomial) poly2() (in module mdhelper.fit.polynomial) poly3() (in module mdhelper.fit.polynomial) poly4() (in module mdhelper.fit.polynomial) poly5() (in module mdhelper.fit.polynomial) poly6() (in module mdhelper.fit.polynomial) poly7() (in module mdhelper.fit.polynomial) poly8() (in module mdhelper.fit.polynomial) poly9() (in module mdhelper.fit.polynomial) pop() (mdhelper.analysis.base.Hash method) popitem() (mdhelper.analysis.base.Hash method) power() (in module mdhelper.fit.power) power1() (in module mdhelper.fit.power) power2() (in module mdhelper.fit.power) psf_trigonometric_2d_2d() (mdhelper.analysis.structure.IntermediateScatteringFunction static method) (mdhelper.analysis.structure.StructureFactor static method) pythagorean_trigonometric_identity_1d() (in module mdhelper.algorithm.accelerated) pythagorean_trigonometric_identity_1d_1d() (in module mdhelper.algorithm.accelerated) R radial_fourier_transform() (in module mdhelper.analysis.structure) radial_histogram() (in module mdhelper.analysis.structure) RadialDistributionFunction (class in mdhelper.analysis.structure) radius_of_gyration() (in module mdhelper.algorithm.molecule) rebin() (in module mdhelper.algorithm.utility) register_particles() (in module mdhelper.openmm.system) replicate() (in module mdhelper.algorithm.utility) report() (mdhelper.openmm.reporter.NetCDFReporter method) run() (mdhelper.analysis.base.DynamicAnalysisBase method) (mdhelper.analysis.base.NumbaAnalysisBase method) (mdhelper.analysis.base.ParallelAnalysisBase method) (mdhelper.analysis.base.SerialAnalysisBase method) (mdhelper.analysis.electrostatics.DipoleMoment method) (mdhelper.analysis.polymer.EndToEndVector method) (mdhelper.analysis.polymer.Gyradius method) (mdhelper.analysis.polymer.SingleChainStructureFactor method) (mdhelper.analysis.profile.DensityProfile method) (mdhelper.analysis.structure.IntermediateScatteringFunction method) (mdhelper.analysis.structure.RadialDistributionFunction method) (mdhelper.analysis.structure.StructureFactor method) (mdhelper.analysis.thermodynamics.ConstantVolumeHeatCapacity method) (mdhelper.analysis.transport.Onsager method) S save() (mdhelper.analysis.base.DynamicAnalysisBase method) (mdhelper.analysis.base.NumbaAnalysisBase method) (mdhelper.analysis.base.ParallelAnalysisBase method) (mdhelper.analysis.base.SerialAnalysisBase method) (mdhelper.analysis.electrostatics.DipoleMoment method) (mdhelper.analysis.polymer.EndToEndVector method) (mdhelper.analysis.polymer.Gyradius method) (mdhelper.analysis.polymer.SingleChainStructureFactor method) (mdhelper.analysis.profile.DensityProfile method) (mdhelper.analysis.structure.IntermediateScatteringFunction method) (mdhelper.analysis.structure.RadialDistributionFunction method) (mdhelper.analysis.structure.StructureFactor method) (mdhelper.analysis.transport.Onsager method) SerialAnalysisBase (class in mdhelper.analysis.base) set_up_tabular_legend() (in module mdhelper.plot.axis) setdefault() (mdhelper.analysis.base.Hash method) sine_sum_1d() (in module mdhelper.algorithm.accelerated) sine_sum_2d() (in module mdhelper.algorithm.accelerated) sine_sum_inplace_2d() (in module mdhelper.algorithm.accelerated) sine_sum_inplace_parallel_2d() (in module mdhelper.algorithm.accelerated) sine_sum_parallel_2d() (in module mdhelper.algorithm.accelerated) SingleChainStructureFactor (class in mdhelper.analysis.polymer) solvation() (in module mdhelper.openmm.pair) ssf_trigonometric_2d() (mdhelper.analysis.structure.IntermediateScatteringFunction static method) (mdhelper.analysis.structure.StructureFactor static method) stretched_exp() (in module mdhelper.fit.exponential) strip_unit() (in module mdhelper.algorithm.unit) StructureFactor (class in mdhelper.analysis.structure) U unwrap() (in module mdhelper.algorithm.topology) unwrap_edge() (in module mdhelper.algorithm.topology) update() (in module mdhelper.plot.rcparam) (mdhelper.analysis.base.Hash method) V values() (mdhelper.analysis.base.Hash method) W wca() (in module mdhelper.openmm.pair) weibull() (in module mdhelper.fit.distribution) wrap() (in module mdhelper.algorithm.topology) write_data() (in module mdhelper.lammps.topology) write_file() (mdhelper.openmm.file.NetCDFFile method) write_header() (mdhelper.openmm.file.NetCDFFile method) write_model() (mdhelper.openmm.file.NetCDFFile method) Y yukawa() (in module mdhelper.openmm.pair) Z zeroth_order_hankel_transform() (in module mdhelper.analysis.structure)