Index

_

__str__() (bcforms.core.Atom method) (bcforms.core.BcForm method) (bcforms.core.Crosslink method) (bcforms.core.InlineCrosslink method) (bcforms.core.OntologyCrosslink method)

_xlink_atom_parser (bcforms.core.OntologyCrosslink attribute)

A

App (class in bcforms.__main__) App.Meta (class in bcforms.__main__) arguments (bcforms.__main__.BaseController.Meta attribute) (bcforms.__main__.GetChargeController.Meta attribute) (bcforms.__main__.GetFormulaController.Meta attribute) (bcforms.__main__.GetMolWtController.Meta attribute) (bcforms.__main__.ValidateController.Meta attribute)

Atom (class in bcforms.core) atom_charge() (bcforms.core.OntologyCrosslink.ParseTreeTransformer method) atom_element() (bcforms.core.OntologyCrosslink.ParseTreeTransformer method) atom_position() (bcforms.core.OntologyCrosslink.ParseTreeTransformer method)

B

base_controller (bcforms.__main__.App.Meta attribute) BaseController (class in bcforms.__main__) BaseController.Meta (class in bcforms.__main__) BcForm (class in bcforms.core) Bcform (class in bcforms.rest)

bcforms (module) bcforms.__main__ (module) bcforms._version (module) bcforms.core (module) bcforms.rest (module)

C

charge (bcforms.core.Atom attribute) (bcforms.core.Subunit attribute) charge() (bcforms.core.Atom property) (bcforms.core.Subunit property) clean() (bcforms.core.BcForm method) comments (bcforms.core.InlineCrosslink attribute)

comments() (bcforms.core.InlineCrosslink property) component_type (bcforms.core.Atom attribute) component_type() (bcforms.core.Atom property) Crosslink (class in bcforms.core) CrosslinkResource (class in bcforms.rest) crosslinks (bcforms.core.BcForm attribute) crosslinks() (bcforms.core.BcForm property)

D

description (bcforms.__main__.BaseController.Meta attribute) (bcforms.__main__.GetChargeController.Meta attribute) (bcforms.__main__.GetFormulaController.Meta attribute) (bcforms.__main__.GetMolWtController.Meta attribute) (bcforms.__main__.ValidateController.Meta attribute)

draw_xlink() (in module bcforms.core)

E

element (bcforms.core.Atom attribute) element() (bcforms.core.Atom property) endpoint (bcforms.rest.Bcform attribute) (bcforms.rest.CrosslinkResource attribute)

export() (bcforms.core.BcForm method) (bcforms.core.Subunit method)

F

file (bcforms.core.BcForm attribute) formula (bcforms.core.Subunit attribute)

formula() (bcforms.core.Subunit property) from_set() (bcforms.core.BcForm method) from_str() (bcforms.core.BcForm method)

G

get() (bcforms.rest.CrosslinkResource method) get_charge() (bcforms.core.BcForm method) (bcforms.core.Subunit method) get_crosslinks() (in module bcforms.rest) get_details() (bcforms.core.OntologyCrosslink method) get_formula() (bcforms.core.BcForm method) (bcforms.core.Subunit method) get_genomic_image() (bcforms.core.BcForm method) get_hydrogen_atom() (in module bcforms.core) get_l_bond_atoms() (bcforms.core.Crosslink method) (bcforms.core.InlineCrosslink method) (bcforms.core.OntologyCrosslink method) get_l_displaced_atoms() (bcforms.core.Crosslink method) (bcforms.core.InlineCrosslink method) (bcforms.core.OntologyCrosslink method) get_mol_wt() (bcforms.core.BcForm method) (bcforms.core.Subunit method) get_order() (bcforms.core.Crosslink method) (bcforms.core.InlineCrosslink method) (bcforms.core.OntologyCrosslink method)

get_r_bond_atoms() (bcforms.core.Crosslink method) (bcforms.core.InlineCrosslink method) (bcforms.core.OntologyCrosslink method) get_r_displaced_atoms() (bcforms.core.Crosslink method) (bcforms.core.InlineCrosslink method) (bcforms.core.OntologyCrosslink method) get_stereo() (bcforms.core.Crosslink method) (bcforms.core.InlineCrosslink method) (bcforms.core.OntologyCrosslink method) get_structure() (bcforms.core.BcForm method) (bcforms.core.Subunit method) get_subunit_attribute() (bcforms.core.BcForm method) GetChargeController (class in bcforms.__main__) GetChargeController.Meta (class in bcforms.__main__) GetFormulaController (class in bcforms.__main__) GetFormulaController.Meta (class in bcforms.__main__) GetMolWtController (class in bcforms.__main__) GetMolWtController.Meta (class in bcforms.__main__)

H

handlers (bcforms.__main__.App.Meta attribute) help (bcforms.__main__.BaseController.Meta attribute) (bcforms.__main__.GetChargeController.Meta attribute) (bcforms.__main__.GetFormulaController.Meta attribute) (bcforms.__main__.GetMolWtController.Meta attribute) (bcforms.__main__.ValidateController.Meta attribute)

I

id (bcforms.core.Subunit attribute) id() (bcforms.core.Subunit property) InlineCrosslink (class in bcforms.core)

is_equal() (bcforms.core.Atom method) (bcforms.core.BcForm method) (bcforms.core.Crosslink method) (bcforms.core.Subunit method)

L

l_bond_atoms (bcforms.core.InlineCrosslink attribute) l_bond_atoms() (bcforms.core.InlineCrosslink property) l_displaced_atoms (bcforms.core.InlineCrosslink attribute) l_displaced_atoms() (bcforms.core.InlineCrosslink property) l_monomer (bcforms.core.OntologyCrosslink attribute) l_monomer() (bcforms.core.OntologyCrosslink property) l_subunit (bcforms.core.OntologyCrosslink attribute) l_subunit() (bcforms.core.OntologyCrosslink property)

l_subunit_idx (bcforms.core.OntologyCrosslink attribute) l_subunit_idx() (bcforms.core.OntologyCrosslink property) label (bcforms.__main__.App.Meta attribute) (bcforms.__main__.BaseController.Meta attribute) (bcforms.__main__.GetChargeController.Meta attribute) (bcforms.__main__.GetFormulaController.Meta attribute) (bcforms.__main__.GetMolWtController.Meta attribute) (bcforms.__main__.ValidateController.Meta attribute)

M

main() (in module bcforms.__main__) mediatypes() (bcforms.rest.Bcform method) (bcforms.rest.CrosslinkResource method) methods (bcforms.rest.Bcform attribute) (bcforms.rest.CrosslinkResource attribute)

mol_wt (bcforms.core.Subunit attribute) mol_wt() (bcforms.core.Subunit property) monomer (bcforms.core.Atom attribute) monomer() (bcforms.core.Atom property)

O

OntologyCrosslink (class in bcforms.core) OntologyCrosslink.ParseTreeTransformer (class in bcforms.core)

order (bcforms.core.InlineCrosslink attribute) order() (bcforms.core.InlineCrosslink property)

P

parse_yaml() (in module bcforms.core) position (bcforms.core.Atom attribute)

position() (bcforms.core.Atom property) post() (bcforms.rest.Bcform method) PrefixMiddleware (class in bcforms.rest)

R

r_bond_atoms (bcforms.core.InlineCrosslink attribute) r_bond_atoms() (bcforms.core.InlineCrosslink property) r_displaced_atoms (bcforms.core.InlineCrosslink attribute) r_displaced_atoms() (bcforms.core.InlineCrosslink property) r_monomer (bcforms.core.OntologyCrosslink attribute)

r_monomer() (bcforms.core.OntologyCrosslink property) r_subunit (bcforms.core.OntologyCrosslink attribute) r_subunit() (bcforms.core.OntologyCrosslink property) r_subunit_idx (bcforms.core.OntologyCrosslink attribute) r_subunit_idx() (bcforms.core.OntologyCrosslink property)

S

set_subunit_attribute() (bcforms.core.BcForm method) stacked_on (bcforms.__main__.GetChargeController.Meta attribute) (bcforms.__main__.GetFormulaController.Meta attribute) (bcforms.__main__.GetMolWtController.Meta attribute) (bcforms.__main__.ValidateController.Meta attribute) stacked_type (bcforms.__main__.GetChargeController.Meta attribute) (bcforms.__main__.GetFormulaController.Meta attribute) (bcforms.__main__.GetMolWtController.Meta attribute) (bcforms.__main__.ValidateController.Meta attribute) start() (bcforms.core.OntologyCrosslink.ParseTreeTransformer method) stereo (bcforms.core.InlineCrosslink attribute)

stereo() (bcforms.core.InlineCrosslink property) stoichiometry (bcforms.core.Subunit attribute) stoichiometry() (bcforms.core.Subunit property) structure (bcforms.core.Subunit attribute) structure() (bcforms.core.Subunit property) subunit (bcforms.core.Atom attribute) Subunit (class in bcforms.core) subunit() (bcforms.core.Atom property) subunit_idx (bcforms.core.Atom attribute) subunit_idx() (bcforms.core.Atom property) subunits (bcforms.core.BcForm attribute) subunits() (bcforms.core.BcForm property)

T

type (bcforms.core.OntologyCrosslink attribute)

type() (bcforms.core.OntologyCrosslink property)

V

validate() (bcforms.core.BcForm method)

ValidateController (class in bcforms.__main__) ValidateController.Meta (class in bcforms.__main__)

X

xlink_details (bcforms.core.OntologyCrosslink attribute)