Index

A

add_record() (dnacauldron.SequenceRepository method) add_records() (dnacauldron.SequenceRepository method) annotate_connector() (dnacauldron.Fragment.StickyEndFragment method) annotate_record() (in module dnacauldron.biotools.record_operations) assemble() (dnacauldron.AssemblyMix.StickyEndAssemblyMix static method) (dnacauldron.Fragment.HomologousFragment static method) (dnacauldron.Fragment.StickyEndFragment static method)

assemble_with() (dnacauldron.Fragment.HomologousFragment method) AssemblyMix (class in dnacauldron.AssemblyMix) AssemblyPlan (class in dnacauldron) AssemblyPlanSimulation (class in dnacauldron.AssemblyPlan) AssemblyReportWriter (class in dnacauldron) AssemblySimulation (class in dnacauldron.Assembly) autoselect_enzyme() (in module dnacauldron.biotools.autoselect_enzyme)

B

BackboneChoice (class in dnacauldron.utils)

BASICAssembly (class in dnacauldron) BioBrickStandardAssembly (class in dnacauldron)

C

check_homology() (dnacauldron.HomologyChecker method) circularized() (dnacauldron.Fragment.HomologousFragment method) (dnacauldron.Fragment.StickyEndFragment method) complement() (in module dnacauldron.biotools.record_operations) compute_all_construct_data_dicts() (dnacauldron.Assembly.AssemblySimulation method) (dnacauldron.AssemblyPlan.AssemblyPlanSimulation method) compute_construct_data_dict() (dnacauldron.Assembly.AssemblySimulation method)

compute_digest() (dnacauldron.AssemblyMix.RestrictionLigationMix method) compute_fragments() (dnacauldron.AssemblyMix.RestrictionLigationMix method) compute_stats() (dnacauldron.AssemblyPlan.AssemblyPlanSimulation method) compute_summary_dataframe() (dnacauldron.Assembly.AssemblySimulation method) compute_tm() (dnacauldron.HomologyChecker method) contains_record() (dnacauldron.SequenceRepository method) crop_record_with_saddling_features() (in module dnacauldron.biotools.record_operations)

D

dnacauldron.biotools.autoselect_enzyme (module) dnacauldron.biotools.record_operations (module)

dnacauldron.biotools.sequence_io (module) dnacauldron.utils (module)

F

find_end_homologies() (dnacauldron.HomologyChecker method) fragment_part() (dnacauldron.Assembly.AssemblySimulation static method)

from_biopython_record() (dnacauldron.Fragment.HomologousFragment static method) from_spreadsheet() (dnacauldron.AssemblyPlan static method)

G

get_all_part_names() (dnacauldron.SequenceRepository method) get_part_names_by_collection() (dnacauldron.SequenceRepository method)

get_record() (dnacauldron.SequenceRepository method) get_records() (dnacauldron.SequenceRepository method) GibsonAssembly (class in dnacauldron)

H

HomologousAssemblyMix (class in dnacauldron.AssemblyMix)

HomologousFragment (class in dnacauldron.Fragment) HomologyChecker (class in dnacauldron)

I

import_records() (dnacauldron.SequenceRepository method)

initialize() (dnacauldron.AssemblyMix.AssemblyMix method) insert_parts_on_backbones() (in module dnacauldron.utils)

L

LigaseCyclingReactionAssembly (class in dnacauldron) LigaseCyclingReactionMix (in module dnacauldron.AssemblyMix) list_all_parts_used() (dnacauldron.Assembly.AssemblySimulation method) list_digestion_overhangs() (in module dnacauldron.utils)

list_overhangs_from_record_annotations() (in module dnacauldron.utils) list_to_infos_spreadsheet() (dnacauldron.utils.BackboneChoice static method) load_record() (in module dnacauldron.biotools.sequence_io) load_records_from_file() (in module dnacauldron.biotools.sequence_io) load_records_from_files() (in module dnacauldron.biotools.sequence_io)

P

parameters_as_string() (dnacauldron.HomologyChecker method)

R

record_contains_backbone() (in module dnacauldron.utils)

RestrictionLigationMix (class in dnacauldron.AssemblyMix) reverse_complement() (in module dnacauldron.biotools.record_operations)

S

sequence_to_biopython_record() (in module dnacauldron.biotools.record_operations) SequenceRepository (class in dnacauldron) set_record_topology() (in module dnacauldron.biotools.record_operations) simulate() (dnacauldron.AssemblyPlan method) (dnacauldron.BASICAssembly method) (dnacauldron.BioBrickStandardAssembly method) (dnacauldron.GibsonAssembly method) (dnacauldron.LigaseCyclingReactionAssembly method) (dnacauldron.Type2sRestrictionAssembly method)

StickyEndAssemblyMix (class in dnacauldron.AssemblyMix) StickyEndFragment (class in dnacauldron.Fragment) string_to_records() (in module dnacauldron.biotools.sequence_io) substitute_overhangs() (in module dnacauldron.utils) suggest_part_names() (dnacauldron.SequenceRepository method) swap_donor_vector_part() (in module dnacauldron.utils)

T

text_representation_in_plots() (dnacauldron.Fragment.StickyEndFragment method) to_dataframe() (dnacauldron.AssemblyPlan method)

to_dict() (dnacauldron.utils.BackboneChoice method) to_standard_string() (dnacauldron.Fragment.StickyEndFragment method) Type2sRestrictionAssembly (class in dnacauldron)

W

will_clip_in_this_order() (dnacauldron.AssemblyMix.HomologousAssemblyMix method) (dnacauldron.AssemblyMix.StickyEndAssemblyMix static method) will_clip_in_this_order_with() (dnacauldron.Fragment.HomologousFragment method) (dnacauldron.Fragment.StickyEndFragment method)

write_final_records() (dnacauldron.utils.BackboneChoice static method) write_record() (in module dnacauldron.biotools.sequence_io) write_report() (dnacauldron.Assembly.AssemblySimulation method) (dnacauldron.AssemblyPlan.AssemblyPlanSimulation method) (dnacauldron.AssemblyReportWriter method)