All modules for which code is available
- builtins
- jax_dna.energy
- jax_dna.energy.base
- jax_dna.energy.configuration
- jax_dna.energy.dna1
- jax_dna.energy.dna1.base_functions
- jax_dna.energy.dna1.base_smoothing_functions
- jax_dna.energy.dna1.bonded_excluded_volume
- jax_dna.energy.dna1.coaxial_stacking
- jax_dna.energy.dna1.cross_stacking
- jax_dna.energy.dna1.expected_hydrogen_bonding
- jax_dna.energy.dna1.expected_stacking
- jax_dna.energy.dna1.fene
- jax_dna.energy.dna1.hydrogen_bonding
- jax_dna.energy.dna1.interactions
- jax_dna.energy.dna1.nucleotide
- jax_dna.energy.dna1.stacking
- jax_dna.energy.dna1.unbonded_excluded_volume
- jax_dna.energy.dna2.base_functions
- jax_dna.energy.dna2.coaxial_stacking
- jax_dna.energy.dna2.debye
- jax_dna.energy.dna2.interactions
- jax_dna.energy.dna2.nucleotide
- jax_dna.energy.dna2.stacking
- jax_dna.energy.na1.bonded_excluded_volume
- jax_dna.energy.na1.coaxial_stacking
- jax_dna.energy.na1.cross_stacking
- jax_dna.energy.na1.debye
- jax_dna.energy.na1.fene
- jax_dna.energy.na1.hydrogen_bonding
- jax_dna.energy.na1.nucleotide
- jax_dna.energy.na1.stacking
- jax_dna.energy.na1.unbonded_excluded_volume
- jax_dna.energy.na1.utils
- jax_dna.energy.potentials
- jax_dna.energy.rna2.cross_stacking
- jax_dna.energy.rna2.interactions
- jax_dna.energy.rna2.nucleotide
- jax_dna.energy.rna2.stacking
- jax_dna.energy.utils
- jax_dna.gradient_estimators.difftre
- jax_dna.input.oxdna_input
- jax_dna.input.sequence_constraints
- jax_dna.input.toml
- jax_dna.input.topology
- jax_dna.input.trajectory
- jax_dna.input.tree
- jax_dna.losses.observable_wrappers
- jax_dna.observables.base
- jax_dna.observables.diameter
- jax_dna.observables.persistence_length
- jax_dna.observables.pitch
- jax_dna.observables.propeller
- jax_dna.observables.rise
- jax_dna.observables.rmse
- jax_dna.observables.stretch_torsion
- jax_dna.observables.wlc
- jax_dna.optimization.objective
- jax_dna.optimization.optimization
- jax_dna.optimization.simulator
- jax_dna.simulators.base
- jax_dna.simulators.io
- jax_dna.simulators.jax_md.jaxmd
- jax_dna.simulators.jax_md.utils
- jax_dna.simulators.oxdna.oxdna
- jax_dna.simulators.oxdna.utils
- jax_dna.ui.loggers.console
- jax_dna.ui.loggers.jupyter
- jax_dna.ui.loggers.logger
- jax_dna.utils.helpers
- jax_dna.utils.math
- jax_dna.utils.neighbors
- jax_dna.utils.types
- jax_dna.utils.units
- jaxlib.xla_extension