Index

A

apply_point_mut() (crisprzip.nucleic_acid.GuideTargetHybrid method) (crisprzip.nucleic_acid.TargetDna method)

B

BareSearcher (class in crisprzip.kinetics) bind_guide_rna() (crisprzip.kinetics.BareSearcher method)

bp_map (crisprzip.nucleic_acid.GuideTargetHybrid attribute) (crisprzip.nucleic_acid.TargetDna attribute)

C

calculate_solution_energy() (crisprzip.kinetics.Searcher method) coarse_grain_landscape() (in module crisprzip.coarsegrain) CoarseGrainedComplex (class in crisprzip.coarsegrain) CoarseGrainedSequenceComplex (class in crisprzip.coarsegrain) convert_units() (crisprzip.nucleic_acid.NearestNeighborModel class method) crisprzip module crisprzip.coarsegrain module

crisprzip.kinetics module crisprzip.matrix_expon module crisprzip.nucleic_acid module crisprzip.plotting module

D

dna_dna_params (crisprzip.nucleic_acid.NearestNeighborModel attribute) dna_dna_params_file (crisprzip.nucleic_acid.NearestNeighborModel attribute)

dna_opening_energy() (crisprzip.nucleic_acid.NearestNeighborModel class method) dnstream_bp (crisprzip.nucleic_acid.TargetDna attribute)

E

energy_unit (crisprzip.nucleic_acid.NearestNeighborModel attribute), [1] exponentiate_fast() (in module crisprzip.matrix_expon)

exponentiate_fast_var_onrate() (in module crisprzip.matrix_expon) exponentiate_iterative() (in module crisprzip.matrix_expon) exponentiate_iterative_var_onrate() (in module crisprzip.matrix_expon)

F

find_average_mm_penalties() (in module crisprzip.nucleic_acid) find_mismatches() (crisprzip.nucleic_acid.GuideTargetHybrid method) find_mismatches_cached() (in module crisprzip.nucleic_acid) format_point_mutations() (in module crisprzip.nucleic_acid) from_cas9_offtarget() (crisprzip.nucleic_acid.GuideTargetHybrid class method)

from_cas9_protospacer() (crisprzip.nucleic_acid.GuideTargetHybrid class method) from_cas9_target() (crisprzip.nucleic_acid.TargetDna class method) from_mm_pos() (crisprzip.nucleic_acid.MismatchPattern class method) from_searcher() (crisprzip.kinetics.BareSearcher class method) from_string() (crisprzip.nucleic_acid.MismatchPattern class method) from_target_sequence() (crisprzip.nucleic_acid.MismatchPattern class method)

G

get_bound_fraction() (crisprzip.kinetics.SearcherTargetComplex method) get_cleaved_fraction() (crisprzip.kinetics.SearcherTargetComplex method) get_coarse_grained_rates() (crisprzip.coarsegrain.CoarseGrainedComplex method) get_forward_rate_array() (crisprzip.kinetics.Searcher method) get_hybridization_energy() (crisprzip.nucleic_acid.NearestNeighborModel class method) (in module crisprzip.nucleic_acid) get_mismatch_pattern() (crisprzip.nucleic_acid.GuideTargetHybrid method)

get_mm_pos() (crisprzip.nucleic_acid.MismatchPattern method) get_na_energies_cached() (in module crisprzip.nucleic_acid) get_rate_matrix() (crisprzip.kinetics.SearcherTargetComplex method) guide (crisprzip.nucleic_acid.GuideTargetHybrid attribute) guide_length (crisprzip.kinetics.Searcher attribute) GuidedSearcher (class in crisprzip.kinetics) GuideTargetHybrid (class in crisprzip.nucleic_acid)

I

internal_rates (crisprzip.kinetics.Searcher attribute)

is_on_target (crisprzip.nucleic_acid.MismatchPattern attribute)

L

label_style (crisprzip.plotting.SearcherPlotter attribute) length (crisprzip.nucleic_acid.MismatchPattern attribute)

line_style (crisprzip.plotting.SearcherPlotter attribute) load_data() (crisprzip.nucleic_acid.NearestNeighborModel class method) load_landscape() (in module crisprzip.kinetics)

M

make_hybr_energy_func() (in module crisprzip.nucleic_acid) make_random() (crisprzip.nucleic_acid.MismatchPattern class method) (crisprzip.nucleic_acid.TargetDna class method) mismatch_penalties (crisprzip.kinetics.Searcher attribute) MismatchPattern (class in crisprzip.nucleic_acid) mm_num (crisprzip.nucleic_acid.MismatchPattern attribute)

module crisprzip crisprzip.coarsegrain crisprzip.kinetics crisprzip.matrix_expon crisprzip.nucleic_acid crisprzip.plotting

N

NearestNeighborModel (class in crisprzip.nucleic_acid)

O

off_target_landscape (crisprzip.kinetics.SearcherTargetComplex attribute)

on_target_landscape (crisprzip.kinetics.Searcher attribute)

P

pam_detection (crisprzip.kinetics.Searcher attribute) pattern (crisprzip.nucleic_acid.MismatchPattern attribute) plot_internal_rates() (crisprzip.plotting.SearcherPlotter method) plot_mismatch_penalties() (crisprzip.plotting.SearcherPlotter method) plot_off_target_landscape() (crisprzip.plotting.SearcherPlotter method) plot_on_target_landscape() (crisprzip.plotting.SearcherPlotter method) prepare_landscape_canvas() (crisprzip.plotting.SearcherPlotter method)

prepare_landscape_line() (crisprzip.plotting.SearcherPlotter method) prepare_rates_canvas() (crisprzip.plotting.SearcherPlotter method) prepare_rates_line() (crisprzip.plotting.SearcherPlotter method) probe_sequence() (crisprzip.kinetics.BareSearcher method) (crisprzip.kinetics.GuidedSearcher method) probe_target() (crisprzip.kinetics.BareSearcher method) (crisprzip.kinetics.Searcher method)

R

rna_dna_params (crisprzip.nucleic_acid.NearestNeighborModel attribute)

rna_dna_params_file (crisprzip.nucleic_acid.NearestNeighborModel attribute) rna_duplex_energy() (crisprzip.nucleic_acid.NearestNeighborModel class method)

S

Searcher (class in crisprzip.kinetics) SearcherPlotter (class in crisprzip.plotting) SearcherSequenceComplex (class in crisprzip.kinetics) SearcherTargetComplex (class in crisprzip.kinetics) seq1 (crisprzip.nucleic_acid.TargetDna attribute) seq2 (crisprzip.nucleic_acid.TargetDna attribute)

set_energy_unit() (crisprzip.nucleic_acid.NearestNeighborModel class method) set_on_target() (crisprzip.kinetics.GuidedSearcher method) set_rloop_state() (crisprzip.nucleic_acid.GuideTargetHybrid method) set_temperature() (crisprzip.nucleic_acid.NearestNeighborModel class method) solve_master_equation() (crisprzip.kinetics.SearcherTargetComplex method) state (crisprzip.nucleic_acid.GuideTargetHybrid attribute)

T

target (crisprzip.nucleic_acid.GuideTargetHybrid attribute) target_mismatches (crisprzip.kinetics.SearcherTargetComplex attribute) TargetDna (class in crisprzip.nucleic_acid) temperature (crisprzip.nucleic_acid.NearestNeighborModel attribute)

tick_style (crisprzip.plotting.SearcherPlotter attribute) title_style (crisprzip.plotting.SearcherPlotter attribute) to_bare_searcher() (crisprzip.kinetics.GuidedSearcher method) to_searcher() (crisprzip.kinetics.BareSearcher method) (crisprzip.kinetics.GuidedSearcher method)

U

update_mismatches() (crisprzip.plotting.SearcherPlotter method) update_on_target_landscape() (crisprzip.plotting.SearcherPlotter method) update_rate_matrix() (in module crisprzip.matrix_expon)

update_rates() (crisprzip.plotting.SearcherPlotter method) update_solution_energies() (crisprzip.plotting.SearcherPlotter method) upstream_bp (crisprzip.nucleic_acid.TargetDna attribute)