from .fourmer_breakage_rates import fourmer_breakage_rates
from .fourmer_mass_correction import mass_correction_rates
from .fourmer_production_rates import _compute_extended_end_motif_reaction_logc_rates, _compute_extending_beginning_motif_reaction_logc_rates
from .fourmer_production_rates import _compute_produced_motif_reaction_logc_rates, compute_total_extension_rates
from .fourmer_production_rates import _initialize_empty_fourmer_production_rates
from .fourmer_trajectory_from_rate_constants import fourmer_trajectory_from_rate_constants
from .fourmer_trajectory_from_rate_constants import _fourmer_breakage_equations
from .fourmer_trajectory_from_rate_constants import _fourmer_production_equations
from .fourmer_trajectory_from_rate_constants import _fourmer_rate_equations
from .fourmer_trajectory_from_rate_constants import _integrate_motif_rate_equations

from .collisions import collisions_from_motif_concentration_trajectory_array_and_collision_rate_constants_array
from .collisions import motifs_collisions_array_from_motifs_array
from .collisions import ligation_spot_formations_from_motifs_array

from .dissociation_constant import (dissociation_constant_from_strand_reactor_parameters,
                                    ligation_rate_constant_from_strand_reactor_parameters,
                                    template_averaged_dissociation_constant_from_strand_reactor_parameters,
                                    energy_continuous_block,
                                    _energy_continuous_blocks,)


from .effective_ligation_rates_from_parameters import (effective_ligation_rates_from_parameters,
                                                       separate_hybridization_and_ligation_parameters
                                                       )

from .mean_length import mean_length

from .motif_concentration_vector import motif_concentration_vector_from_motif_number_vector
from .motif_concentration_trajectory import motif_concentration_trajectory_from_motif_number_trajectory
from .motif_production_rates import motif_production_rates_array_from_motif_production_rate_constants_array_and_motif_concentrations_array
from .motif_production_rates import motif_production_rates_array_from_motif_production_counts
from .motif_production_rate_constants_extension_matrix import motif_production_rate_constants_extension_matrix
from .motif_production_rate_constants_from_strand_reactor_parameters import motif_production_rate_constants_from_strand_reactor_parameters

from .motif_production_transition_kernel import _hybridization_site_categories
from .motif_production_transition_kernel import _extend_motif_production_rate_constants_array_to_collisions_format
from .motif_production_transition_kernel import motif_production_transition_kernel_from_motif_production_rate_constants_array
from .motif_production_transition_kernel import motif_production_transition_kernel_matrix

from .motif_breakage_rate_constants_from_strand_reactor_parameters import motif_breakage_rate_constants_from_strand_reactor_parameters

from .onset import onset_of_growth, discretized_onset_of_growth, onset_of_growth_from_strand_trajectory_parameters

from ._rates_utils import _set_invalid_logc_diff_to_zero, _set_invalid_logc_to_log0

from ._smooth_rate_clipping import _clip_smoothly, _clip_concentration_vector_smoothly

from .total_mass import total_mass, total_mass_of_motif_concentration_trajectory_array, total_mass_trajectory
