Index

A

add_from_candidates() (schemarecomb.ParentSequences method) align() (schemarecomb.ParentSequences method)

AminoAcid (class in schemarecomb.pdb_structure) Atom (class in schemarecomb.pdb_structure) average_mutations() (in module schemarecomb.libraries)

B

block_indices() (in module schemarecomb.breakpoints)

BreakPoint (class in schemarecomb.breakpoints) build_from_str() (in module schemarecomb.energy_functions)

C

calc_from_config() (schemarecomb.Library class method) calc_identity() (in module schemarecomb.parent_alignment)

calculate_breakpoints() (in module schemarecomb.breakpoints) choose_candidates() (in module schemarecomb.parent_alignment)

D

derenumber() (schemarecomb.PDBStructure method)

E

EnergyFunction (class in schemarecomb.energy_functions)

F

find_best_overhangs() (schemarecomb.Library method) from_fasta() (schemarecomb.ParentSequences class method) from_json() (schemarecomb.Library class method) (schemarecomb.ParentSequences class method) (schemarecomb.PDBStructure class method)

from_pdb_file() (schemarecomb.PDBStructure class method)

G

generate_libraries() (in module schemarecomb)

get_PDB() (schemarecomb.ParentSequences method)

L

Library (class in schemarecomb)

LibraryConfig (class in schemarecomb.libraries) local_muscle() (in module schemarecomb.parent_alignment)

M

module schemarecomb.breakpoints schemarecomb.energy_functions schemarecomb.libraries schemarecomb.optimizers schemarecomb.parent_alignment schemarecomb.pdb_structure schemarecomb.restriction_enzymes

MutationRateCache (class in schemarecomb.libraries)

N

new_alignment() (schemarecomb.ParentSequences method)

O

obtain_seqs() (schemarecomb.ParentSequences method)

Overhang (class in schemarecomb.breakpoints)

P

ParentSequences (class in schemarecomb)

PDBStructure (class in schemarecomb)

Q

query_blast() (in module schemarecomb.parent_alignment)

R

RASPP (class in schemarecomb.optimizers) read_ligation_data() (in module schemarecomb.restriction_enzymes)

renumber() (schemarecomb.PDBStructure method) RestrictionEnzyme (class in schemarecomb.restriction_enzymes)

S

SCHEMA (class in schemarecomb.energy_functions) schemarecomb.breakpoints module schemarecomb.energy_functions module schemarecomb.libraries module

schemarecomb.optimizers module schemarecomb.parent_alignment module schemarecomb.pdb_structure module schemarecomb.restriction_enzymes module

T

to_json() (schemarecomb.Library method) (schemarecomb.ParentSequences method) (schemarecomb.PDBStructure method)

W

web_muscle() (in module schemarecomb.parent_alignment)