Index

_

__init__() (constraints.BaseAtPositionFilter method) (constraints.BaseCountFilter method) (constraints.BaseEndFilter method) (constraints.BulkConstraint method) (constraints.Complex method) (constraints.ComplexConstraint method) (constraints.ComplexesConstraint method) (constraints.Constraint method) (constraints.ConstraintWithComplexes method) (constraints.ConstraintWithDomainPairs method) (constraints.ConstraintWithDomains method) (constraints.ConstraintWithStrandPairs method) (constraints.ConstraintWithStrands method) (constraints.Design method) (constraints.Domain method) (constraints.DomainConstraint method) (constraints.DomainPair method) (constraints.DomainPairConstraint method) (constraints.DomainPairsConstraint method) (constraints.DomainPool method) (constraints.DomainsConstraint method) (constraints.ForbiddenSubstringFilter method) (constraints.NearestNeighborEnergyFilter method) (constraints.NumpyFilter method) (constraints.Part method) (constraints.RestrictBasesFilter method) (constraints.Result method) (constraints.RunsOfBasesFilter method) (constraints.SingularConstraint method) (constraints.Strand method) (constraints.StrandConstraint method) (constraints.StrandDomainAddress method) (constraints.StrandPair method) (constraints.StrandPairConstraint method) (constraints.StrandPairsConstraint method) (constraints.StrandsConstraint method) (constraints.SubstringSampler method) (constraints.VendorFields method) (modifications.Modification method) (modifications.Modification3Prime method) (modifications.Modification5Prime method) (modifications.ModificationInternal method) (np.DNASeqList method)

A

add_domain() (constraints.Design method) add_strand() (constraints.Design method) address_of_domain() (constraints.Strand method) address_of_first_domain_occurence() (constraints.Strand method) address_of_last_domain_occurence() (constraints.Strand method) address_of_nth_domain_occurence() (constraints.Strand method) ADJACENT_TO_EXTERIOR_BASE_PAIR (constraints.BasePairType attribute) all_dna_bases (in module constraints) all_domains_in_tree() (constraints.Domain method) all_domains_intersecting() (constraints.Domain method) all_pairs() (in module constraints) all_pairs_iterator() (in module constraints)

all_possible_substrings() (constraints.SubstringSampler method) allowed_bases (modifications.ModificationInternal attribute) ancestors() (constraints.Domain method) append_domain() (constraints.Strand method) arr2seq() (in module np) arr2seqs() (in module np) assign_dna() (constraints.Strand method) assign_fields_to_scadnano_design() (constraints.Design method) assign_idt_fields_to_scadnano_design() (constraints.Design method) assign_modifications_to_scadnano_design() (constraints.Design method) assign_sequences_to_scadnano_design() (constraints.Design method) assign_strand_groups_to_labels() (constraints.Design method)

B

BaseAddress (in module constraints) BaseAtPositionFilter (class in constraints) BaseCountFilter (class in constraints) BaseEndFilter (class in constraints) BasePairAddress (in module constraints) BasePairType (class in constraints) bases (constraints.BaseAtPositionFilter attribute) (constraints.BaseCountFilter attribute) (constraints.BaseEndFilter attribute) (constraints.RestrictBasesFilter attribute) (constraints.RunsOfBasesFilter attribute)

binding() (in module vienna_nupack) binding_complement() (in module vienna_nupack) BLUNT_END (constraints.BasePairType attribute) BoundDomains (in module constraints) BULGE_LOOP_3P (constraints.BasePairType attribute) BULGE_LOOP_5P (constraints.BasePairType attribute) BulkConstraint (class in constraints)

C

calculate_loop_energies() (in module np) calculate_strand_association_penalty() (in module vienna_nupack) calculate_wc_energies() (in module np) call_evaluate() (constraints.SingularConstraint method) call_subprocess() (in module vienna_nupack) check_all_subdomain_graphs_acyclic() (constraints.Design method) check_all_subdomain_graphs_uniquely_assignable() (constraints.Design method) check_domain_against_itself (constraints.ConstraintWithDomainPairs attribute) check_strand_against_itself (constraints.ConstraintWithStrandPairs attribute) chunker() (in module constraints) circular (constraints.SubstringSampler attribute) clone() (constraints.Strand method) complementary_domain_name() (constraints.Domain static method) Complex (class in constraints) ComplexConstraint (class in constraints) complexes (constraints.ConstraintWithComplexes attribute) ComplexesConstraint (class in constraints)

compute_derived_fields() (constraints.Design method) (constraints.Strand method) concatenate() (np.DNASeqList method) concrete_sequence() (constraints.Domain method) Constraint (class in constraints) constraints module ConstraintWithComplexes (class in constraints) ConstraintWithDomainPairs (class in constraints) ConstraintWithDomains (class in constraints) ConstraintWithStrandPairs (class in constraints) ConstraintWithStrands (class in constraints) contains_in_subtree() (constraints.Domain method) convert_threshold() (in module constraints) copy_sequences_from() (constraints.Design method) cpu_count() (in module constraints) create_toeplitz() (in module np)

D

DANGLE_3P (constraints.BasePairType attribute) DANGLE_5P (constraints.BasePairType attribute) DANGLE_5P_3P (constraints.BasePairType attribute) default_adjacent_to_exterior_base_pair (in module constraints) default_blunt_end_probability (in module constraints) default_bulge_loop_3p_probability (in module constraints) default_bulge_loop_5p_probability (in module constraints) default_dangle_3p_probability (in module constraints) default_dangle_5p_3p_probability (in module constraints) default_dangle_5p_probability (in module constraints) default_five_arm_junction_probability (in module constraints) default_four_arm_junction_probability (in module constraints) default_interior_to_strand_probability (in module constraints) default_mismatch_probability (in module constraints) default_nick_3p_probability (in module constraints) default_nick_5p_probability (in module constraints) default_other_probability (in module constraints) default_overhang_on_adjacent_strand_3p_probability (in module constraints) default_overhang_on_adjacent_strand_5p_probability (in module constraints) default_overhang_on_both_strand_3p_probability (in module constraints) default_overhang_on_both_strand_5p_probability (in module constraints) default_overhang_on_this_strand_3p_probability (in module constraints) default_overhang_on_this_strand_5p_probability (in module constraints) default_score_transfer_function() (in module constraints) default_three_arm_junction_probability (in module constraints) default_unpaired_probability (in module constraints) dependent (constraints.Domain attribute) description (constraints.Constraint attribute) Design (class in constraints)

distance_from_end (constraints.BaseEndFilter attribute) DNASeqList (class in np) Domain (class in constraints) domain() (constraints.StrandDomainAddress method) domain1 (constraints.DomainPair attribute) domain2 (constraints.DomainPair attribute) domain_concatenated_no_4g_or_4c() (in module vienna_nupack) domain_concatenated_no_4gc() (in module vienna_nupack) domain_idx (constraints.StrandDomainAddress attribute) domain_names_concatenated() (constraints.Strand method) domain_names_tuple() (constraints.Strand method) domain_no_4gc() (in module vienna_nupack) domain_orthogonal() (in module vienna_nupack) domain_pairs (constraints.ConstraintWithDomainPairs attribute) domain_pairwise_concatenated_no_sec_struct() (in module vienna_nupack) domain_pools() (constraints.Design method) domain_pools_to_domain_map (constraints.Design attribute) DomainConstraint (class in constraints) DomainPair (class in constraints) DomainPairConstraint (class in constraints) DomainPairsConstraint (class in constraints) DomainPool (class in constraints) domains (constraints.ConstraintWithDomains attribute) (constraints.Design property) (constraints.Strand attribute) domains_by_name (constraints.Design attribute) domains_by_pool_name() (constraints.Design method) domains_neq_constraint() (in module constraints) DomainsConstraint (class in constraints)

E

energies() (np.DNASeqList method) energy_hist() (in module np) evaluate() (constraints.SingularConstraint method)

except_start_indices (constraints.SubstringSampler attribute) excess (constraints.Result attribute) extended_supersequence (constraints.SubstringSampler attribute)

F

filter_base_at_pos() (np.DNASeqList method) filter_base_count() (np.DNASeqList method) filter_base_nowhere() (np.DNASeqList method) filter_end_at() (np.DNASeqList method) filter_end_gc() (np.DNASeqList method) filter_energy() (np.DNASeqList method) FIVE_ARM_JUNCTION (constraints.BasePairType attribute) five_prime (constraints.BaseEndFilter attribute) (modifications.ModificationType attribute) fixed (constraints.Domain attribute) (constraints.Strand property)

forbidden_substring_strand_constraint() (in module constraints) ForbiddenSubstringFilter (class in constraints) FOUR_ARM_JUNCTION (constraints.BasePairType attribute) free_energy_single_strand() (in module vienna_nupack) from_design_file() (constraints.Design static method) from_json() (constraints.Design static method) from_json_serializable() (constraints.Design static method) (constraints.Domain static method) (constraints.Strand static method) from_scadnano_design() (constraints.Design static method) from_scadnano_file() (constraints.Design static method)

G

generate_all_sequences() (constraints.DomainPool method) generate_sequence() (constraints.DomainPool method) get_length() (constraints.Domain method)

get_name() (constraints.Domain method) get_seq_str() (np.DNASeqList method) get_seqs_str_list() (np.DNASeqList method) group (constraints.Strand attribute)

H

hamming_map() (np.DNASeqList method) hamming_probability (constraints.DomainPool attribute) has_length() (constraints.Domain method)

has_pool() (constraints.Domain method) has_sequence() (constraints.Domain method) high (constraints.BaseCountFilter attribute) high_energy (constraints.NearestNeighborEnergyFilter attribute)

I

id (modifications.Modification attribute) idx2seq() (in module np) independent_ancestor_or_descendent() (constraints.Domain method) independent_source() (constraints.Domain method)

indices (constraints.ForbiddenSubstringFilter attribute) insert_domain() (constraints.Strand method) INTERIOR_TO_STRAND (constraints.BasePairType attribute) internal (modifications.ModificationType attribute) intersects_domain() (constraints.Strand method)

K

keep_seqs_at_indices() (np.DNASeqList method)

L

label (constraints.Domain attribute) (constraints.Strand attribute) lcs_domain_pairs_constraint() (in module constraints) lcs_strand_pairs_constraint() (in module constraints) lcs_strand_pairs_constraints_by_number_matching_domains() (in module constraints) length (constraints.Domain attribute) (constraints.DomainPool attribute) (constraints.RunsOfBasesFilter attribute) length() (constraints.ForbiddenSubstringFilter method) (constraints.M13Variant method) (constraints.Strand method)

logger (in module constraints) longest_common_substring() (in module np) longest_common_substrings_all_pairs_strings() (in module np) longest_common_substrings_product() (in module np) longest_common_substrings_singlea1() (in module np) longest_complementary_subsequences() (in module constraints) longest_complementary_subsequences_python_loop() (in module constraints) longest_complementary_subsequences_two_loops() (in module constraints) low (constraints.BaseCountFilter attribute) low_energy (constraints.NearestNeighborEnergyFilter attribute)

M

m13() (in module constraints) m13_substrings_of_length() (in module constraints) M13Variant (class in constraints) make_array_with_all_dna_seqs() (in module np) make_array_with_all_dna_seqs_hamming_distance() (in module np) make_array_with_random_subset_of_dna_seqs() (in module np) make_array_with_random_subset_of_dna_seqs_hamming_distance() (in module np) min_wells_per_plate() (constraints.PlateType method) MISMATCH (constraints.BasePairType attribute) Modification (class in modifications) Modification3Prime (class in modifications) Modification5Prime (class in modifications)

modification_3p (constraints.Strand attribute) modification_5p (constraints.Strand attribute) ModificationInternal (class in modifications) modifications module modifications() (constraints.Design method) modifications_int (constraints.Strand attribute) ModificationType (class in modifications) module constraints modifications np vienna_nupack

N

name (constraints.Domain property) (constraints.DomainPool attribute) (constraints.NumpyFilter attribute) (constraints.Strand property) NearestNeighborEnergyFilter (class in constraints) neighbor_3p() (constraints.StrandDomainAddress method) neighbor_5p() (constraints.StrandDomainAddress method) NICK_3P (constraints.BasePairType attribute) NICK_5P (constraints.BasePairType attribute) np module num_wells_per_plate() (constraints.PlateType method)

numpy_filters (constraints.DomainPool attribute) NumpyFilter (class in constraints) numseqs (np.DNASeqList attribute) nupack_complex_base_pair_probabilities() (in module vienna_nupack) nupack_complex_base_pair_probability_constraint() (in module constraints) nupack_domain_free_energy_constraint() (in module constraints) nupack_domain_pair_constraint() (in module constraints) nupack_domain_pairs_nonorthogonal_constraint() (in module constraints) nupack_multiple_with_sodium_magnesium() (in module vienna_nupack) nupack_strand_free_energy_constraint() (in module constraints) nupack_strand_pair_constraint() (in module constraints) nupack_strand_pair_constraints_by_number_matching_domains() (in module constraints)

O

OTHER (constraints.BasePairType attribute) OVERHANG_ON_ADJACENT_STRAND_3P (constraints.BasePairType attribute) OVERHANG_ON_ADJACENT_STRAND_5P (constraints.BasePairType attribute)

OVERHANG_ON_BOTH_STRANDS_3P (constraints.BasePairType attribute) OVERHANG_ON_BOTH_STRANDS_5P (constraints.BasePairType attribute) OVERHANG_ON_THIS_STRAND_3P (constraints.BasePairType attribute) OVERHANG_ON_THIS_STRAND_5P (constraints.BasePairType attribute)

P

p7249 (constraints.M13Variant attribute) p7560 (constraints.M13Variant attribute) p8064 (constraints.M13Variant attribute) p8634 (constraints.M13Variant attribute) pairs (constraints.ConstraintWithDomainPairs attribute) (constraints.ConstraintWithStrandPairs attribute) parallel (constraints.SingularConstraint attribute) parent (constraints.Domain attribute) Part (class in constraints) part (constraints.Result attribute) part_name() (constraints.ComplexConstraint method) (constraints.ComplexesConstraint method) (constraints.Constraint static method) (constraints.DomainConstraint static method) (constraints.DomainPairConstraint static method) (constraints.DomainPairsConstraint static method) (constraints.DomainsConstraint static method) (constraints.StrandConstraint static method) (constraints.StrandPairConstraint static method) (constraints.StrandPairsConstraint static method) (constraints.StrandsConstraint static method)

pfunc() (in module vienna_nupack) plate (constraints.VendorFields attribute) PlateType (class in constraints) pool (constraints.Domain property) pop() (np.DNASeqList method) pop_array() (np.DNASeqList method) position (constraints.BaseAtPositionFilter attribute) possible_sequences (constraints.DomainPool attribute) prepend_domain() (constraints.Strand method) purification (constraints.VendorFields attribute)

R

random_choice() (np.DNASeqList method) random_dna_seq() (in module vienna_nupack) random_sequence() (np.DNASeqList method) rc() (in module vienna_nupack) remove_duplicates() (in module constraints) remove_violating_sequences() (constraints.BaseAtPositionFilter method) (constraints.BaseCountFilter method) (constraints.BaseEndFilter method) (constraints.ForbiddenSubstringFilter method) (constraints.NearestNeighborEnergyFilter method) (constraints.NumpyFilter method) (constraints.RestrictBasesFilter method) (constraints.RunsOfBasesFilter method) replace_with_close_sequences (constraints.DomainPool attribute) RestrictBasesFilter (class in constraints) Result (class in constraints) rna_duplex() (in module vienna_nupack) rna_duplex_domain_pairs_constraint() (in module constraints) rna_duplex_domain_pairs_nonorthogonal_constraint() (in module constraints)

rna_duplex_multiple() (in module vienna_nupack) rna_duplex_multiple_deprecated() (in module vienna_nupack) rna_duplex_multiple_parallel() (in module vienna_nupack) rna_duplex_strand_pair_constraint() (in module constraints) rna_duplex_strand_pair_constraints_by_number_matching_domains() (in module constraints) rna_duplex_strand_pairs_constraint() (in module constraints) rna_duplex_strand_pairs_constraints_by_number_matching_domains() (in module constraints) rna_multifold() (in module vienna_nupack) rna_multifold_domain_pairs_nonorthogonal_constraint() (in module constraints) rna_multifold_multiple() (in module vienna_nupack) rna_multifold_strand_pair_constraint() (in module constraints) rna_multifold_strand_pair_constraints_by_number_matching_domains() (in module constraints) rna_plex_domain_pairs_constraint() (in module constraints) rna_plex_domain_pairs_nonorthogonal_constraint() (in module constraints) rna_plex_multiple() (in module vienna_nupack) rna_plex_multiple_parallel() (in module vienna_nupack) rna_plex_strand_pairs_constraint() (in module constraints) rna_plex_strand_pairs_constraints_by_number_matching_domains() (in module constraints) rng (np.DNASeqList attribute) RunsOfBasesFilter (class in constraints)

S

sample_substring() (constraints.SubstringSampler method) satisfies_sequence_constraints() (constraints.DomainPool method) scale (constraints.VendorFields attribute) score (constraints.Result attribute) score_transfer_function (constraints.Constraint attribute) seq2arr() (in module np) seqarr (np.DNASeqList attribute) seqlen (np.DNASeqList attribute) seqs2arr() (in module np) sequence() (constraints.Domain method) (constraints.Strand method) sequence_filters (constraints.DomainPool attribute) SequenceFilter (in module constraints) set_fixed_sequence() (constraints.Domain method) (constraints.Strand method) set_sequence() (constraints.Domain method) shared_strands_with_scadnano_design() (constraints.Design method) short_description (constraints.Constraint attribute) SingularConstraint (class in constraints) starred1 (constraints.DomainPair attribute) starred2 (constraints.DomainPair attribute) starred_domain_indices (constraints.Strand attribute) starred_domains() (constraints.Strand method) starred_domains_set() (constraints.Strand method) starred_name (constraints.Domain property)

starred_sequence (constraints.Domain property) start_indices (constraints.SubstringSampler attribute) Strand (class in constraints) strand (constraints.StrandDomainAddress attribute) strand_pairs (constraints.ConstraintWithStrandPairs attribute) strand_pairs_by_lengths() (in module constraints) strand_pairs_by_number_matching_domains() (in module constraints) StrandConstraint (class in constraints) StrandDomainAddress (class in constraints) StrandPair (class in constraints) StrandPairConstraint (class in constraints) StrandPairsConstraint (class in constraints) strands (constraints.Complex attribute) (constraints.ConstraintWithStrands attribute) (constraints.Design attribute) strands_by_group_name (constraints.Design attribute) strands_by_name (constraints.Design attribute) StrandsConstraint (class in constraints) strongest_common_substrings_all_pairs_string() (in module np) subdomains (constraints.Domain property) sublist() (np.DNASeqList method) substring_length (constraints.SubstringSampler attribute) substrings (constraints.ForbiddenSubstringFilter attribute) SubstringSampler (class in constraints) summary (constraints.Result property) supersequence (constraints.SubstringSampler attribute)

T

temperature (constraints.NearestNeighborEnergyFilter attribute) THREE_ARM_JUNCTION (constraints.BasePairType attribute) three_prime (constraints.BaseEndFilter attribute) (modifications.ModificationType attribute) to_idt_bulk_input_format() (constraints.Design method)

to_json() (constraints.Design method) to_json_serializable() (constraints.Design method) (constraints.Domain method) (constraints.Strand method) to_list() (np.DNASeqList method)

U

unfixed_domains() (constraints.Strand method) unit (constraints.Result attribute)

UNPAIRED (constraints.BasePairType attribute) unstarred_domains() (constraints.Strand method) unstarred_domains_set() (constraints.Strand method)

V

value (constraints.Result attribute) vendor_code (modifications.Modification attribute) vendor_dna_sequence() (constraints.Strand method) vendor_fields (constraints.Strand attribute)

VendorFields (class in constraints) verify_designs_match() (in module constraints) vienna_nupack module

W

wc() (in module vienna_nupack) wc_arr() (in module np) wcenergy() (in module np) weight (constraints.Constraint attribute) (constraints.Domain attribute) well (constraints.VendorFields attribute)

wells384 (constraints.PlateType attribute) wells96 (constraints.PlateType attribute) write_design_file() (constraints.Design method) write_idt_bulk_input_file() (constraints.Design method) write_idt_plate_excel_file() (constraints.Design method) write_to_file() (np.DNASeqList method)