Index

A

abangle() (in module antibody_utils.geometry) (in module antibody_utils.geometry.orientation) accepts() (antibody_utils.regions.RegionSelector method) add_positions() (antibody_utils.regions.RegionSelector method) add_regions() (antibody_utils.regions.RegionSelector method) annotate_regions() (antibody_utils.numbering.anarcii.NumberedSequence method) (antibody_utils.numbering.NumberedSequence method) (in module antibody_utils.regions) antibody_utils module antibody_utils.geometry module antibody_utils.geometry.orientation module antibody_utils.geometry.superposition module antibody_utils.liabilities module antibody_utils.numbering module antibody_utils.numbering.anarcii module

antibody_utils.numbering.positions module antibody_utils.regions module antibody_utils.sequence module antibody_utils.structure module antibody_utils.structure.models module antibody_utils.structure.parser module antibody_utils.structure.selection module AntibodyChain (class in antibody_utils.structure) (class in antibody_utils.structure.models) AntibodyStructure (class in antibody_utils.structure) (class in antibody_utils.structure.models) apply() (antibody_utils.geometry.Superposition method) (antibody_utils.geometry.superposition.Superposition method) as_dict() (antibody_utils.geometry.orientation.OrientationAngles method) (antibody_utils.geometry.OrientationAngles method)

B

BACKBONE_ATOMS (in module antibody_utils.structure.selection)

C

cdr_lengths() (in module antibody_utils.sequence) cdr_sequences() (in module antibody_utils.sequence) chain (antibody_utils.liabilities.Liability attribute) (antibody_utils.numbering.anarcii.NumberedSequence property) (antibody_utils.numbering.NumberedSequence property) (antibody_utils.regions.Region property) (antibody_utils.structure.AntibodyChain property) (antibody_utils.structure.models.AntibodyChain property)

Chain (class in antibody_utils.numbering) (class in antibody_utils.numbering.positions) chain_type (antibody_utils.numbering.anarcii.NumberedSequence attribute) (antibody_utils.numbering.NumberedSequence attribute) chains (antibody_utils.structure.AntibodyStructure attribute) (antibody_utils.structure.models.AntibodyStructure attribute)

D

dc (antibody_utils.geometry.orientation.OrientationAngles attribute) (antibody_utils.geometry.OrientationAngles attribute)

Definition (class in antibody_utils.regions)

E

end (antibody_utils.liabilities.Liability attribute) (antibody_utils.numbering.anarcii.NumberedSequence attribute) (antibody_utils.numbering.NumberedSequence attribute)

exclude_positions() (antibody_utils.regions.RegionSelector method)

F

find_liabilities() (in module antibody_utils.liabilities) from_gemmi() (in module antibody_utils.structure) (in module antibody_utils.structure.parser)

from_tuple() (antibody_utils.numbering.Position class method) (antibody_utils.numbering.positions.Position class method) Fv (class in antibody_utils.structure) (class in antibody_utils.structure.models)

G

gemmi_chain (antibody_utils.structure.AntibodyChain property) (antibody_utils.structure.models.AntibodyChain property)

get_region() (in module antibody_utils.regions)

H

hc1 (antibody_utils.geometry.orientation.OrientationAngles attribute) (antibody_utils.geometry.OrientationAngles attribute) hc2 (antibody_utils.geometry.orientation.OrientationAngles attribute) (antibody_utils.geometry.OrientationAngles attribute) heavy (antibody_utils.structure.Fv property) (antibody_utils.structure.models.Fv property)

heavy_chains (antibody_utils.structure.AntibodyStructure property) (antibody_utils.structure.models.AntibodyStructure property) hl (antibody_utils.geometry.orientation.OrientationAngles attribute) (antibody_utils.geometry.OrientationAngles attribute)

I

identity() (in module antibody_utils.sequence) is_cdr (antibody_utils.regions.Region property)

iter_number() (in module antibody_utils.numbering) (in module antibody_utils.numbering.anarcii)

L

lc1 (antibody_utils.geometry.orientation.OrientationAngles attribute) (antibody_utils.geometry.OrientationAngles attribute) lc2 (antibody_utils.geometry.orientation.OrientationAngles attribute) (antibody_utils.geometry.OrientationAngles attribute)

Liability (class in antibody_utils.liabilities) light (antibody_utils.structure.Fv property) (antibody_utils.structure.models.Fv property) light_chains (antibody_utils.structure.AntibodyStructure property) (antibody_utils.structure.models.AntibodyStructure property)

M

model (antibody_utils.structure.AntibodyStructure property) (antibody_utils.structure.models.AntibodyStructure property) module antibody_utils antibody_utils.geometry antibody_utils.geometry.orientation antibody_utils.geometry.superposition antibody_utils.liabilities antibody_utils.numbering antibody_utils.numbering.anarcii antibody_utils.numbering.positions antibody_utils.regions antibody_utils.sequence antibody_utils.structure antibody_utils.structure.models antibody_utils.structure.parser antibody_utils.structure.selection

N

name (antibody_utils.liabilities.Liability attribute) (antibody_utils.numbering.anarcii.NumberedSequence attribute) (antibody_utils.numbering.NumberedSequence attribute) (antibody_utils.structure.AntibodyChain property) (antibody_utils.structure.Fv property) (antibody_utils.structure.models.AntibodyChain property) (antibody_utils.structure.models.Fv property) number() (in module antibody_utils.numbering) (in module antibody_utils.numbering.anarcii) number_sequence() (in module antibody_utils.numbering) (in module antibody_utils.numbering.anarcii)

numbered (antibody_utils.structure.AntibodyChain property) (antibody_utils.structure.Fv property) (antibody_utils.structure.models.AntibodyChain property) (antibody_utils.structure.models.Fv property) NumberedSequence (class in antibody_utils.numbering) (class in antibody_utils.numbering.anarcii) numbering (antibody_utils.numbering.anarcii.NumberedSequence property) (antibody_utils.numbering.NumberedSequence property) NumberingError, [1]

O

orientation_rmsd() (in module antibody_utils.geometry) (in module antibody_utils.geometry.superposition) OrientationAngles (class in antibody_utils.geometry) (class in antibody_utils.geometry.orientation)

other_chains (antibody_utils.structure.AntibodyStructure property) (antibody_utils.structure.models.AntibodyStructure property)

P

parse() (antibody_utils.numbering.Position class method) (antibody_utils.numbering.positions.Position class method) parse_chain_position() (in module antibody_utils.numbering) (in module antibody_utils.numbering.positions)

Position (class in antibody_utils.numbering) (class in antibody_utils.numbering.positions) positions (antibody_utils.liabilities.Liability attribute) (antibody_utils.numbering.anarcii.NumberedSequence attribute) (antibody_utils.numbering.NumberedSequence attribute)

R

read_structure() (in module antibody_utils.structure) (in module antibody_utils.structure.parser) Region (class in antibody_utils.regions) REGION_GROUPS (in module antibody_utils.regions) region_residues() (antibody_utils.structure.AntibodyChain method) (antibody_utils.structure.Fv method) (antibody_utils.structure.models.AntibodyChain method) (antibody_utils.structure.models.Fv method) region_rmsd() (in module antibody_utils.geometry) (in module antibody_utils.geometry.superposition)

region_sequences() (in module antibody_utils.sequence) RegionSelector (class in antibody_utils.regions) residues (antibody_utils.liabilities.Liability attribute) (antibody_utils.structure.AntibodyChain property) (antibody_utils.structure.models.AntibodyChain property) rmsd (antibody_utils.geometry.Superposition attribute) (antibody_utils.geometry.superposition.Superposition attribute) rmsd() (in module antibody_utils.geometry) (in module antibody_utils.geometry.superposition) rotation (antibody_utils.geometry.Superposition attribute) (antibody_utils.geometry.superposition.Superposition attribute)

S

scheme (antibody_utils.numbering.anarcii.NumberedSequence attribute) (antibody_utils.numbering.NumberedSequence attribute) (antibody_utils.structure.AntibodyChain property) (antibody_utils.structure.AntibodyStructure attribute) (antibody_utils.structure.Fv property) (antibody_utils.structure.models.AntibodyChain property) (antibody_utils.structure.models.AntibodyStructure attribute) (antibody_utils.structure.models.Fv property) Scheme (class in antibody_utils.numbering) (class in antibody_utils.numbering.positions) score (antibody_utils.numbering.anarcii.NumberedSequence attribute) (antibody_utils.numbering.NumberedSequence attribute) select() (in module antibody_utils.structure) (in module antibody_utils.structure.selection)

sequence (antibody_utils.numbering.anarcii.NumberedSequence attribute) (antibody_utils.numbering.NumberedSequence attribute) similarity() (in module antibody_utils.sequence) start (antibody_utils.liabilities.Liability attribute) (antibody_utils.numbering.anarcii.NumberedSequence attribute) (antibody_utils.numbering.NumberedSequence attribute) structure (antibody_utils.structure.AntibodyStructure attribute) (antibody_utils.structure.models.AntibodyStructure attribute) superpose() (in module antibody_utils.geometry) (in module antibody_utils.geometry.superposition) Superposition (class in antibody_utils.geometry) (class in antibody_utils.geometry.superposition)

T

to_tuple() (antibody_utils.numbering.Position method) (antibody_utils.numbering.positions.Position method)

translation (antibody_utils.geometry.Superposition attribute) (antibody_utils.geometry.superposition.Superposition attribute)