Index

A

add_angles() (opencadd.structure.core.Structure method) add_bonds() (opencadd.structure.core.Structure method) add_dihedrals() (opencadd.structure.core.Structure method) add_impropers() (opencadd.structure.core.Structure method)

add_Residue() (opencadd.structure.core.Structure method) add_Segment() (opencadd.structure.core.Structure method) add_TopologyAttr() (opencadd.structure.core.Structure method) align() (in module opencadd.structure.superposition.api) angles (opencadd.structure.core.Structure property)

B

BaseAligner (class in opencadd.structure.superposition.engines.base)

bonds (opencadd.structure.core.Structure property)

C

calculate() (opencadd.structure.superposition.engines.base.BaseAligner method) (opencadd.structure.superposition.engines.mda.MDAnalysisAligner method) (opencadd.structure.superposition.engines.mmligner.MMLignerAligner method) (opencadd.structure.superposition.engines.theseus.TheseusAligner method)

configure_logger() (in module opencadd.structure.superposition.cli) converter() (opencadd.utils.EmojiPerLevelFormatter method) (opencadd.utils.PerLevelFormatter method) coord (opencadd.structure.core.Structure property) copy() (opencadd.structure.core.Structure method)

D

default_msec_format (opencadd.utils.EmojiPerLevelFormatter attribute) (opencadd.utils.PerLevelFormatter attribute) default_time_format (opencadd.utils.EmojiPerLevelFormatter attribute) (opencadd.utils.PerLevelFormatter attribute) del_TopologyAttr() (opencadd.structure.core.Structure method)

delete_angles() (opencadd.structure.core.Structure method) delete_bonds() (opencadd.structure.core.Structure method) delete_dihedrals() (opencadd.structure.core.Structure method) delete_impropers() (opencadd.structure.core.Structure method) dihedrals (opencadd.structure.core.Structure property) dimensions (opencadd.structure.core.Structure property)

E

EmojiPerLevelFormatter (class in opencadd.utils)

empty() (opencadd.structure.core.Structure class method) enter_temp_directory() (in module opencadd.utils)

F

fasta2select() (in module opencadd.structure.superposition.sequences) format() (opencadd.utils.EmojiPerLevelFormatter method) (opencadd.utils.PerLevelFormatter method) formatException() (opencadd.utils.EmojiPerLevelFormatter method) (opencadd.utils.PerLevelFormatter method) formatMessage() (opencadd.utils.EmojiPerLevelFormatter method) (opencadd.utils.PerLevelFormatter method) FORMATS (opencadd.utils.EmojiPerLevelFormatter attribute) (opencadd.utils.PerLevelFormatter attribute)

formatStack() (opencadd.utils.EmojiPerLevelFormatter method) (opencadd.utils.PerLevelFormatter method) formatTime() (opencadd.utils.EmojiPerLevelFormatter method) (opencadd.utils.PerLevelFormatter method) from_atomgroup() (opencadd.structure.core.Structure class method) from_pdbid() (opencadd.structure.core.Structure class method) from_smiles() (opencadd.structure.core.Structure class method) from_string() (opencadd.structure.core.Structure class method)

G

greeting() (in module opencadd.structure.superposition.cli)

I

impropers (opencadd.structure.core.Structure property)

ivalue() (opencadd.structure.superposition.engines.mmligner.MMLignerAligner method)

K

kwargs (opencadd.structure.core.Structure property)

L

load_new() (opencadd.structure.core.Structure method)

M

main() (in module opencadd.structure.superposition.cli) matching_selection() (opencadd.structure.superposition.engines.mda.MDAnalysisAligner method) matrices() (in module opencadd.structure.superposition.sequences) MDAnalysisAligner (class in opencadd.structure.superposition.engines.mda) MMLignerAligner (class in opencadd.structure.superposition.engines.mmligner) models (opencadd.structure.core.Structure property) module opencadd opencadd.structure.core opencadd.structure.superposition opencadd.structure.superposition.api opencadd.structure.superposition.cli opencadd.structure.superposition.engines.base opencadd.structure.superposition.engines.mda opencadd.structure.superposition.engines.mmligner opencadd.structure.superposition.engines.theseus opencadd.structure.superposition.sequences opencadd.utils

O

opencadd module opencadd.structure.core module opencadd.structure.superposition module opencadd.structure.superposition.api module opencadd.structure.superposition.cli module opencadd.structure.superposition.engines.base module

opencadd.structure.superposition.engines.mda module opencadd.structure.superposition.engines.mmligner module opencadd.structure.superposition.engines.theseus module opencadd.structure.superposition.sequences module opencadd.utils module

P

parse_cli() (in module opencadd.structure.superposition.cli) parse_method_options() (in module opencadd.structure.superposition.cli)

parse_selection() (in module opencadd.structure.superposition.cli) PerLevelFormatter (class in opencadd.utils)

S

select_atoms() (opencadd.structure.core.Structure method)

sequence_alignment() (in module opencadd.structure.superposition.sequences) Structure (class in opencadd.structure.core)

T

TheseusAligner (class in opencadd.structure.superposition.engines.theseus)

trajectory (opencadd.structure.core.Structure property) transfer_to_memory() (opencadd.structure.core.Structure method)

U

universe (opencadd.structure.core.Structure property)

usesTime() (opencadd.utils.EmojiPerLevelFormatter method) (opencadd.utils.PerLevelFormatter method)

W

write() (opencadd.structure.core.Structure method)