Index

_

__contains__() (bpforms.core.BpForm method) __delitem__() (bpforms.core.BpForm method) __eq__() (bpforms.core.Identifier method) __getitem__() (bpforms.core.BpForm method) __hash__() (bpforms.core.Identifier method) __iter__() (bpforms.core.BpForm method) __len__() (bpforms.core.BpForm method) __reversed__() (bpforms.core.BpForm method) __setitem__() (bpforms.core.AtomList method) (bpforms.core.BpForm method) (bpforms.core.MonomerDict method) (bpforms.core.MonomerSequence method)

__str__() (bpforms.core.Bond method) (bpforms.core.BpForm method) (bpforms.core.Monomer method) (bpforms.core.OntoBond method) _max_monomers (bpforms.core.AlphabetBuilder attribute) _parser (bpforms.core.BpForm attribute)

A

Abbreviation (bpforms.alphabet.dna.DnaAlphabetBuilder.ExpandedAlphabet attribute) add() (bpforms.core.BondSet method) (bpforms.core.BpFormFeatureSet method) (bpforms.core.IdentifierSet method) (bpforms.core.NickSet method) (bpforms.core.SynonymSet method) AlpabetResource (class in bpforms.rest) alphabet (bpforms.core.BpForm attribute) Alphabet (class in bpforms.core) alphabet() (bpforms.core.BpForm property) AlphabetBuilder (class in bpforms.core) AlphabetsResource (class in bpforms.rest) App (class in bpforms.__main__)

App.Meta (class in bpforms.__main__) append() (bpforms.core.AtomList method) (bpforms.core.MonomerSequence method) arguments (bpforms.__main__.BaseController.Meta attribute) (bpforms.__main__.BuildAlphabetsController.Meta attribute) (bpforms.__main__.ExportOntosController.Meta attribute) (bpforms.__main__.GetMajorMicroSpeciesController.Meta attribute) (bpforms.__main__.GetPropertiesController.Meta attribute) (bpforms.__main__.ValidateController.Meta attribute) (bpforms.__main__.VizAlphabetController.Meta attribute) aromatic (bpforms.core.BondOrder attribute) Atom (class in bpforms.core) AtomList (class in bpforms.core)

B

backbone (bpforms.core.BpForm attribute) Backbone (class in bpforms.core) backbone() (bpforms.core.BpForm property) backbone_bond_atoms (bpforms.core.Monomer attribute) backbone_bond_atoms() (bpforms.core.Monomer property) backbone_displaced_atoms (bpforms.core.Monomer attribute) backbone_displaced_atoms() (bpforms.core.Monomer property) base_controller (bpforms.__main__.App.Meta attribute) base_monomers (bpforms.core.Monomer attribute) base_monomers() (bpforms.core.Monomer property) BaseController (class in bpforms.__main__) BaseController.Meta (class in bpforms.__main__) baseid (bpforms.alphabet.dna.DnaAlphabetBuilder.ModBase attribute) bond (bpforms.core.BpForm attribute) Bond (class in bpforms.core) bond() (bpforms.core.BpForm property) BondBase (class in bpforms.core) BondOrder (class in bpforms.core) BondSet (class in bpforms.core) BondStereo (class in bpforms.core) BpForm (class in bpforms.core) Bpform (class in bpforms.rest) BpFormFeature (class in bpforms.core) BpFormFeatureSet (class in bpforms.core) bpforms (module) bpforms.__main__ (module) bpforms._version (module) bpforms.alphabet (module)

bpforms.alphabet.core (module) bpforms.alphabet.dna (module) bpforms.alphabet.protein (module) bpforms.alphabet.rna (module) bpforms.config (module) bpforms.config.core (module) bpforms.core (module) bpforms.rest (module) bpforms.util (module) bpforms.xlink (module) bpforms.xlink.core (module) bpforms.xlink.xlink_xlsx2yml (module) BpFormsWarning build() (bpforms.alphabet.dna.DnaAlphabetBuilder method) (bpforms.alphabet.protein.ProteinAlphabetBuilder method) (bpforms.alphabet.rna.RnaAlphabetBuilder method) (bpforms.core.AlphabetBuilder method) build_alphabets() (in module bpforms.util) build_dnamod() (bpforms.alphabet.dna.DnaAlphabetBuilder method) build_from_mod() (bpforms.alphabet.protein.ProteinAlphabetBuilder method) build_from_pdb() (bpforms.alphabet.protein.ProteinAlphabetBuilder method) build_from_resid() (bpforms.alphabet.protein.ProteinAlphabetBuilder method) build_modomics() (bpforms.alphabet.rna.RnaAlphabetBuilder method) build_pdb() (bpforms.alphabet.rna.RnaAlphabetBuilder method) build_pdb_ccd() (bpforms.alphabet.dna.DnaAlphabetBuilder method) build_repairtoire() (bpforms.alphabet.dna.DnaAlphabetBuilder method) build_rna_mod_db() (bpforms.alphabet.rna.RnaAlphabetBuilder method) BuildAlphabetsController (class in bpforms.__main__) BuildAlphabetsController.Meta (class in bpforms.__main__)

C

can_monomer_bond_left() (bpforms.core.BpForm method) can_monomer_bond_right() (bpforms.core.BpForm method) CanonicalDnaForm (class in bpforms.alphabet.dna) CanonicalProteinForm (class in bpforms.alphabet.protein) CanonicalRnaForm (class in bpforms.alphabet.rna) charge (bpforms.core.Atom attribute) charge() (bpforms.core.Atom property) chebiname (bpforms.alphabet.dna.DnaAlphabetBuilder.Names attribute) circular (bpforms.core.BpForm attribute) circular() (bpforms.core.BpForm property)

cmodid (bpforms.alphabet.dna.DnaAlphabetBuilder.CovMod attribute) (bpforms.alphabet.dna.DnaAlphabetBuilder.ModBase attribute) comments (bpforms.core.Bond attribute) (bpforms.core.Monomer attribute) comments() (bpforms.core.Bond property) (bpforms.core.Monomer property) Complement (bpforms.alphabet.dna.DnaAlphabetBuilder.ExpandedAlphabet attribute) crosslinks (bpforms.core.BpForm attribute) crosslinks() (bpforms.core.BpForm property) CrosslinksOnto (class in bpforms.xlink.core)

D

DEFAULT_FASTA_CODE (bpforms.alphabet.dna.CanonicalDnaForm attribute) (bpforms.alphabet.dna.DnaForm attribute) (bpforms.alphabet.protein.CanonicalProteinForm attribute) (bpforms.alphabet.protein.ProteinForm attribute) (bpforms.alphabet.rna.CanonicalRnaForm attribute) (bpforms.alphabet.rna.RnaForm attribute) (bpforms.core.BpForm attribute) definition (bpforms.alphabet.dna.DnaAlphabetBuilder.CovMod attribute) delta_charge (bpforms.core.Monomer attribute) delta_charge() (bpforms.core.Monomer property) delta_mass (bpforms.core.Monomer attribute) delta_mass() (bpforms.core.Monomer property) description (bpforms.__main__.BaseController.Meta attribute) (bpforms.__main__.BuildAlphabetsController.Meta attribute) (bpforms.__main__.ExportOntosController.Meta attribute) (bpforms.__main__.GetMajorMicroSpeciesController.Meta attribute) (bpforms.__main__.GetPropertiesController.Meta attribute) (bpforms.__main__.ValidateController.Meta attribute) (bpforms.__main__.VizAlphabetController.Meta attribute) (bpforms.core.Alphabet attribute)

diff() (bpforms.core.BpForm method) DnaAlphabetBuilder (class in bpforms.alphabet.dna) DnaAlphabetBuilder.CovMod (class in bpforms.alphabet.dna) DnaAlphabetBuilder.ExpandedAlphabet (class in bpforms.alphabet.dna) DnaAlphabetBuilder.ModBase (class in bpforms.alphabet.dna) DnaAlphabetBuilder.ModBaseParents (class in bpforms.alphabet.dna) DnaAlphabetBuilder.Names (class in bpforms.alphabet.dna) DnaForm (class in bpforms.alphabet.dna) double (bpforms.core.BondOrder attribute) down (bpforms.core.BondStereo attribute) download_pdb_ccd() (in module bpforms.alphabet.core)

E

element (bpforms.core.Atom attribute) element() (bpforms.core.Atom property) end_position (bpforms.core.BpFormFeature attribute) (bpforms.core.Monomer attribute) end_position() (bpforms.core.BpFormFeature property) (bpforms.core.Monomer property) endpoint (bpforms.rest.AlpabetResource attribute) (bpforms.rest.AlphabetsResource attribute) (bpforms.rest.Bpform attribute) (bpforms.rest.MonomerResource attribute)

export() (bpforms.core.Backbone method) (bpforms.core.BpForm method) (bpforms.core.Monomer method) export_ontos_to_obo() (in module bpforms.util) ExportOntosController (class in bpforms.__main__) ExportOntosController.Meta (class in bpforms.__main__) extend() (bpforms.core.AtomList method) (bpforms.core.MonomerSequence method)

F

features (bpforms.core.BpForm attribute) features() (bpforms.core.BpForm property) file (bpforms.core.BpForm attribute) form (bpforms.core.BpFormFeature attribute) (bpforms.core.BpFormFeatureSet attribute) form() (bpforms.core.BpFormFeature property) (bpforms.core.BpFormFeatureSet property)

formulaid (bpforms.alphabet.dna.DnaAlphabetBuilder.ModBase attribute) from_dict() (bpforms.core.Alphabet method) (bpforms.core.Atom method) (bpforms.core.Monomer method) from_list() (bpforms.core.AtomList method) from_str() (bpforms.core.BpForm method) from_yaml() (bpforms.core.Alphabet method)

G

gen_genomic_viz() (in module bpforms.util) gen_html_viz_alphabet() (in module bpforms.util) get() (bpforms.rest.AlpabetResource method) (bpforms.rest.AlphabetsResource method) (bpforms.rest.MonomerResource method) get_alphabet() (in module bpforms.rest) (in module bpforms.util) get_alphabets() (in module bpforms.util) get_can_smiles() (in module bpforms.alphabet.core) get_canonical_code() (bpforms.core.Monomer method) get_canonical_seq() (bpforms.core.BpForm method) get_charge() (bpforms.core.Backbone method) (bpforms.core.BondBase method) (bpforms.core.BpForm method) (bpforms.core.Monomer method) get_config() (in module bpforms.config.core) get_dnamod() (in module bpforms.alphabet.dna) get_form() (in module bpforms.util) get_formula() (bpforms.core.Backbone method) (bpforms.core.BondBase method) (bpforms.core.BpForm method) (bpforms.core.Monomer method) get_genomic_image() (bpforms.core.BpForm method) get_hydrogen_atom() (in module bpforms.core) get_image() (bpforms.core.BpForm method) (bpforms.core.Monomer method) get_image_url() (bpforms.core.Monomer method) get_l_bond_atoms() (bpforms.core.Bond method) (bpforms.core.BondBase method) (bpforms.core.OntoBond method) get_l_displaced_atoms() (bpforms.core.Bond method) (bpforms.core.BondBase method) (bpforms.core.OntoBond method) get_major_micro_species() (bpforms.core.Alphabet method) (bpforms.core.BpForm method) (bpforms.core.Monomer method)

get_mol_wt() (bpforms.core.Backbone method) (bpforms.core.BondBase method) (bpforms.core.BpForm method) (bpforms.core.Monomer method) get_monomer() (in module bpforms.rest) get_monomer_code() (bpforms.core.Alphabet method) get_monomer_counts() (bpforms.core.BpForm method) (bpforms.core.MonomerSequence method) get_monomer_properties() (in module bpforms.rest) get_nucleoside_details_from_modomics() (bpforms.alphabet.rna.RnaAlphabetBuilder method) get_order() (bpforms.core.Bond method) (bpforms.core.BondBase method) (bpforms.core.OntoBond method) get_pdb_ccd_open_babel_mol() (in module bpforms.alphabet.core) get_r_bond_atoms() (bpforms.core.Bond method) (bpforms.core.BondBase method) (bpforms.core.OntoBond method) get_r_displaced_atoms() (bpforms.core.Bond method) (bpforms.core.BondBase method) (bpforms.core.OntoBond method) get_resid_monomer_details() (bpforms.alphabet.protein.ProteinAlphabetBuilder method) get_resid_monomer_structure() (bpforms.alphabet.protein.ProteinAlphabetBuilder method) get_root_monomers() (bpforms.core.Monomer method) get_stereo() (bpforms.core.Bond method) (bpforms.core.BondBase method) (bpforms.core.OntoBond method) get_structure() (bpforms.core.BpForm method) get_termini() (bpforms.alphabet.protein.ProteinAlphabetBuilder method) GetMajorMicroSpeciesController (class in bpforms.__main__) GetMajorMicroSpeciesController.Meta (class in bpforms.__main__) GetPropertiesController (class in bpforms.__main__) GetPropertiesController.Meta (class in bpforms.__main__)

H

handlers (bpforms.__main__.App.Meta attribute) hash (bpforms.core.BondStereo attribute) help (bpforms.__main__.BaseController.Meta attribute) (bpforms.__main__.BuildAlphabetsController.Meta attribute) (bpforms.__main__.ExportOntosController.Meta attribute) (bpforms.__main__.GetMajorMicroSpeciesController.Meta attribute) (bpforms.__main__.GetPropertiesController.Meta attribute) (bpforms.__main__.ValidateController.Meta attribute) (bpforms.__main__.VizAlphabetController.Meta attribute)

I

id (bpforms.core.Alphabet attribute) (bpforms.core.Bond attribute) (bpforms.core.Identifier attribute) (bpforms.core.Monomer attribute) id() (bpforms.core.Bond property) (bpforms.core.Identifier property) (bpforms.core.Monomer property) Identifier (class in bpforms.core) identifiers (bpforms.core.Monomer attribute) identifiers() (bpforms.core.Monomer property) IdentifierSet (class in bpforms.core) IMAGE_URL_PATTERN (bpforms.core.Monomer attribute) inchi (bpforms.alphabet.dna.DnaAlphabetBuilder.Names attribute) inchikey (bpforms.alphabet.dna.DnaAlphabetBuilder.Names attribute) insert() (bpforms.core.AtomList method) (bpforms.core.MonomerSequence method) INVALID_IDS (bpforms.alphabet.dna.DnaAlphabetBuilder attribute) is_backbone_atom() (bpforms.alphabet.rna.RnaAlphabetBuilder method) is_c_terminus() (bpforms.alphabet.protein.ProteinAlphabetBuilder method) is_equal() (bpforms.core.Alphabet method) (bpforms.core.Atom method) (bpforms.core.AtomList method) (bpforms.core.Backbone method) (bpforms.core.Bond method) (bpforms.core.BondSet method) (bpforms.core.BpForm method) (bpforms.core.Monomer method) (bpforms.core.MonomerSequence method) (bpforms.core.Nick method) (bpforms.core.NickSet method) (bpforms.core.OntoBond method)

is_l_atom() (bpforms.alphabet.rna.RnaAlphabetBuilder method) is_n_terminus() (bpforms.alphabet.protein.ProteinAlphabetBuilder method) is_nucleobase_valid() (bpforms.alphabet.dna.DnaAlphabetBuilder method) is_nucleotide_terminus() (bpforms.alphabet.rna.RnaAlphabetBuilder method) is_r_bond_atom() (bpforms.alphabet.rna.RnaAlphabetBuilder method) is_terminus() (bpforms.alphabet.protein.ProteinAlphabetBuilder method) (bpforms.alphabet.rna.RnaAlphabetBuilder method) is_valid_nucleoside() (bpforms.alphabet.rna.RnaAlphabetBuilder method) iupacname (bpforms.alphabet.dna.DnaAlphabetBuilder.Names attribute)

L

l_bond_atoms (bpforms.core.Bond attribute) (bpforms.core.Monomer attribute) l_bond_atoms() (bpforms.core.Bond property) (bpforms.core.Monomer property) l_displaced_atoms (bpforms.core.Bond attribute) (bpforms.core.Monomer attribute) l_displaced_atoms() (bpforms.core.Bond property) (bpforms.core.Monomer property) l_monomer (bpforms.core.Bond attribute) (bpforms.core.OntoBond attribute) l_monomer() (bpforms.core.Bond property) (bpforms.core.OntoBond property)

label (bpforms.__main__.App.Meta attribute) (bpforms.__main__.BaseController.Meta attribute) (bpforms.__main__.BuildAlphabetsController.Meta attribute) (bpforms.__main__.ExportOntosController.Meta attribute) (bpforms.__main__.GetMajorMicroSpeciesController.Meta attribute) (bpforms.__main__.GetPropertiesController.Meta attribute) (bpforms.__main__.ValidateController.Meta attribute) (bpforms.__main__.VizAlphabetController.Meta attribute) load_onto() (in module bpforms.xlink.core) load_session() (bpforms.alphabet.dna.DnaAlphabetBuilder method)

M

main() (in module bpforms.__main__) (in module bpforms.xlink.xlink_xlsx2yml) MAX_RETRIES (bpforms.alphabet.protein.ProteinAlphabetBuilder attribute) (bpforms.alphabet.rna.RnaAlphabetBuilder attribute) mediatypes() (bpforms.rest.AlpabetResource method) (bpforms.rest.AlphabetsResource method) (bpforms.rest.Bpform method) (bpforms.rest.MonomerResource method) methods (bpforms.rest.AlpabetResource attribute) (bpforms.rest.AlphabetsResource attribute) (bpforms.rest.Bpform attribute) (bpforms.rest.MonomerResource attribute) MODOMICS_ENTRY_ENDPOINT (bpforms.alphabet.rna.RnaAlphabetBuilder attribute) MODOMICS_INDEX_ASCII_ENDPOINT (bpforms.alphabet.rna.RnaAlphabetBuilder attribute) MODOMICS_INDEX_ENDPOINT (bpforms.alphabet.rna.RnaAlphabetBuilder attribute)

molecule (bpforms.core.Atom attribute) molecule() (bpforms.core.Atom property) monomer (bpforms.core.Atom attribute) Monomer (class in bpforms.core) monomer() (bpforms.core.Atom property) monomer_bond_atoms (bpforms.core.Backbone attribute) monomer_bond_atoms() (bpforms.core.Backbone property) monomer_displaced_atoms (bpforms.core.Backbone attribute) monomer_displaced_atoms() (bpforms.core.Backbone property) MonomerDict (class in bpforms.core) MonomerResource (class in bpforms.rest) monomers (bpforms.core.Alphabet attribute) monomers() (bpforms.core.Alphabet property) monomers_position (bpforms.core.Monomer attribute) monomers_position() (bpforms.core.Monomer property) MonomerSequence (class in bpforms.core)

N

Name (bpforms.alphabet.dna.DnaAlphabetBuilder.ExpandedAlphabet attribute) name (bpforms.core.Alphabet attribute) (bpforms.core.Bond attribute) (bpforms.core.Monomer attribute) name() (bpforms.core.Bond property) (bpforms.core.Monomer property) nameid (bpforms.alphabet.dna.DnaAlphabetBuilder.ExpandedAlphabet attribute) (bpforms.alphabet.dna.DnaAlphabetBuilder.ModBase attribute) (bpforms.alphabet.dna.DnaAlphabetBuilder.ModBaseParents attribute) (bpforms.alphabet.dna.DnaAlphabetBuilder.Names attribute)

netcharge (bpforms.alphabet.dna.DnaAlphabetBuilder.CovMod attribute) Nick (class in bpforms.core) nicks (bpforms.core.BpForm attribute) nicks() (bpforms.core.BpForm property) NickSet (class in bpforms.core) ns (bpforms.core.Identifier attribute) ns() (bpforms.core.Identifier property)

O

OntoBond (class in bpforms.core) order (bpforms.core.Bond attribute)

order() (bpforms.core.Bond property) othernames (bpforms.alphabet.dna.DnaAlphabetBuilder.Names attribute)

P

parentid (bpforms.alphabet.dna.DnaAlphabetBuilder.ModBaseParents attribute) parse_atom() (in module bpforms.xlink.core) parse_pdb_ccd() (in module bpforms.alphabet.core) parse_pdb_ccd_entry() (in module bpforms.alphabet.core) parse_yaml() (in module bpforms.core) position (bpforms.alphabet.dna.DnaAlphabetBuilder.ModBase attribute) (bpforms.core.Atom attribute) (bpforms.core.Nick attribute)

position() (bpforms.core.Atom property) (bpforms.core.Nick property) post() (bpforms.rest.Bpform method) PrefixMiddleware (class in bpforms.rest) ProteinAlphabetBuilder (class in bpforms.alphabet.protein) ProteinForm (class in bpforms.alphabet.protein)

R

r_bond_atoms (bpforms.core.Bond attribute) (bpforms.core.Monomer attribute) r_bond_atoms() (bpforms.core.Bond property) (bpforms.core.Monomer property) r_displaced_atoms (bpforms.core.Bond attribute) (bpforms.core.Monomer attribute) r_displaced_atoms() (bpforms.core.Bond property) (bpforms.core.Monomer property) r_monomer (bpforms.core.Bond attribute) (bpforms.core.OntoBond attribute) r_monomer() (bpforms.core.Bond property) (bpforms.core.OntoBond property)

read_from_fasta() (in module bpforms.util) remove() (bpforms.core.BpFormFeatureSet method) RNA_MOD_DB_ENTRY_ENDPOINT (bpforms.alphabet.rna.RnaAlphabetBuilder attribute) RNA_MOD_DB_INDEX_ENDPOINT (bpforms.alphabet.rna.RnaAlphabetBuilder attribute) RnaAlphabetBuilder (class in bpforms.alphabet.rna) RnaForm (class in bpforms.alphabet.rna) run() (bpforms.alphabet.dna.DnaAlphabetBuilder method) (bpforms.alphabet.protein.ProteinAlphabetBuilder method) (bpforms.alphabet.rna.RnaAlphabetBuilder method) (bpforms.core.AlphabetBuilder method)

S

save() (bpforms.core.AlphabetBuilder method) seq (bpforms.core.BpForm attribute) seq() (bpforms.core.BpForm property) set_termini() (bpforms.alphabet.protein.ProteinAlphabetBuilder method) single (bpforms.core.BondOrder attribute) smiles (bpforms.alphabet.dna.DnaAlphabetBuilder.Names attribute) stacked_on (bpforms.__main__.BuildAlphabetsController.Meta attribute) (bpforms.__main__.ExportOntosController.Meta attribute) (bpforms.__main__.GetMajorMicroSpeciesController.Meta attribute) (bpforms.__main__.GetPropertiesController.Meta attribute) (bpforms.__main__.ValidateController.Meta attribute) (bpforms.__main__.VizAlphabetController.Meta attribute) stacked_type (bpforms.__main__.BuildAlphabetsController.Meta attribute) (bpforms.__main__.ExportOntosController.Meta attribute) (bpforms.__main__.GetMajorMicroSpeciesController.Meta attribute) (bpforms.__main__.GetPropertiesController.Meta attribute) (bpforms.__main__.ValidateController.Meta attribute) (bpforms.__main__.VizAlphabetController.Meta attribute) start_position (bpforms.core.BpFormFeature attribute) (bpforms.core.Monomer attribute)

start_position() (bpforms.core.BpFormFeature property) (bpforms.core.Monomer property) stereo (bpforms.core.Bond attribute) stereo() (bpforms.core.Bond property) structure (bpforms.core.Backbone attribute) (bpforms.core.Monomer attribute) structure() (bpforms.core.Backbone property) (bpforms.core.Monomer property) symbol (bpforms.alphabet.dna.DnaAlphabetBuilder.CovMod attribute) Symbol (bpforms.alphabet.dna.DnaAlphabetBuilder.ExpandedAlphabet attribute) symmetric_difference_update() (bpforms.core.BondSet method) (bpforms.core.BpFormFeatureSet method) (bpforms.core.IdentifierSet method) (bpforms.core.NickSet method) (bpforms.core.SynonymSet method) synonyms (bpforms.core.Bond attribute) (bpforms.core.Monomer attribute) synonyms() (bpforms.core.Bond property) (bpforms.core.Monomer property) SynonymSet (class in bpforms.core)

T

to_dict() (bpforms.core.Alphabet method) (bpforms.core.Atom method) (bpforms.core.Monomer method) to_list() (bpforms.core.AtomList method)

to_yaml() (bpforms.core.Alphabet method) triple (bpforms.core.BondOrder attribute) type (bpforms.core.OntoBond attribute) type() (bpforms.core.OntoBond property)

U

up (bpforms.core.BondStereo attribute) update() (bpforms.core.BondSet method) (bpforms.core.BpFormFeatureSet method) (bpforms.core.IdentifierSet method) (bpforms.core.NickSet method) (bpforms.core.SynonymSet method)

V

validate() (bpforms.core.BpForm method) validate_bpform_bonds() (in module bpforms.util) ValidateController (class in bpforms.__main__)

ValidateController.Meta (class in bpforms.__main__) verifiedstatus (bpforms.alphabet.dna.DnaAlphabetBuilder.ModBase attribute) VizAlphabetController (class in bpforms.__main__) VizAlphabetController.Meta (class in bpforms.__main__)

W

wedge (bpforms.core.BondStereo attribute)

write_to_fasta() (in module bpforms.util)