Index

_

__call__() (glypy.io.glyspace.BoundURIRef method) (glypy.utils.enum.EnumMeta method) __eq__() (glypy.algorithms.database.GlycanRecord method) (glypy.composition.glycan_composition.MonosaccharideResidue method) (glypy.io.glyspace.BoundURIRef method) (glypy.structure.glycan.Glycan method) (glypy.structure.link.Link method) (glypy.structure.monosaccharide.Monosaccharide method) __getattr__() (glypy.io.glyspace.BoundURIRef method) __getitem__() (glypy.algorithms.database.RecordDatabase method) (glypy.composition.glycan_composition.GlycanComposition method) (glypy.io.glyspace.GlySpaceRDFClient method) (glypy.structure.glycan.Glycan method) (glypy.structure.link.Link method) (glypy.structure.monosaccharide.Monosaccharide method) __hash__() (glypy.composition.glycan_composition.MonosaccharideResidue method) (glypy.composition.glycan_composition.SubstituentResidue method) __init__() (glypy.composition.composition.PComposition method) (glypy.io.glycoct.GlycoCTReader method) (glypy.structure.glycan.Glycan method) (glypy.structure.link.Link method) __iter__() (glypy.algorithms.database.RecordDatabase method) (glypy.io.glycoct.GlycoCTReader method) (glypy.structure.link.Link method) (glypy.utils.multimap.OrderedMultiMap method) __len__() (glypy.algorithms.database.RecordDatabase method) (glypy.structure.glycan.Glycan method) (glypy.utils.multimap.MultiMap method) __next__() (glypy.io.glycoct.GlycoCTReader method) __setattr__() (glypy.utils.enum.EnumMeta method) __setitem__() (glypy.composition.glycan_composition.GlycanComposition method) __setstate__() (glypy.structure.monosaccharide.Monosaccharide method) _derivatize_monosaccharide() (in module glypy.composition.composition_transform)

_extract_maximum_common_subgraph() (in module glypy.algorithms.subtree_search) _fast_reduce() (glypy.structure.monosaccharide.Monosaccharide method) _find_max_of_matrix() (in module glypy.algorithms.subtree_search) _flat_equality() (glypy.structure.monosaccharide.Monosaccharide method) _get_standard_composition() (in module glypy.structure.monosaccharide) _glycoct_sigils() (glypy.structure.link.Link method) _make_isotope_string() (in module glypy.composition.composition) _match_substituents() (glypy.structure.monosaccharide.Monosaccharide method) _parse_isotope_string() (in module glypy.composition.composition) _patch_querymethods() (glypy.algorithms.database.RecordDatabase method) _resolve_column_data_mro() (in module glypy.algorithms.database) _traverse_debug() (in module glypy.structure.monosaccharide)

A

a (glypy.structure.constants.Modification attribute) accession_to_uriref() (glypy.io.glyspace.RDFClientBase method) add_column_data() (glypy.algorithms.database.GlycanRecord method) add_index() (glypy.algorithms.database.GlycanRecord class method) add_modification() (glypy.structure.monosaccharide.Monosaccharide method) add_monosaccharide() (glypy.structure.monosaccharide.Monosaccharide method) add_substituent() (glypy.structure.monosaccharide.Monosaccharide method) (glypy.structure.substituent.Substituent method) aldi (glypy.structure.constants.Modification attribute)

all (glypy.structure.constants.Stem attribute) alpha (glypy.structure.constants.Anomer attribute) alt (glypy.structure.constants.Stem attribute) Anomer (class in glypy.structure.constants) apply() (glypy.structure.link.Link method) apply_indices() (glypy.algorithms.database.RecordDatabase method) apply_schema() (glypy.algorithms.database.RecordDatabase method) ara (glypy.structure.constants.Stem attribute)

B

beta (glypy.structure.constants.Anomer attribute) BoundURIRef (class in glypy.io.glyspace) breadth_first_traversal() (glypy.structure.glycan.Glycan method)

break_link() (glypy.structure.link.Link method) break_links_subtrees() (glypy.structure.glycan.Glycan method) build_unique_index_pairs() (in module glypy.algorithms.similarity)

C

calculate_mass() (in module glypy.composition.composition) ChainFunctionDict (class in glypy.io.glyspace) children() (glypy.structure.monosaccharide.Monosaccharide method) (glypy.structure.substituent.Substituent method) classproperty() (in module glypy.utils.base) ClassPropertyDescriptor (class in glypy.utils.base) clone() (glypy.structure.glycan.Glycan method) (glypy.structure.link.Link method) (glypy.structure.monosaccharide.Monosaccharide method) (glypy.structure.substituent.Substituent method) collapse() (glypy.composition.glycan_composition.GlycanComposition method) column_data() (in module glypy.algorithms.database) commit() (glypy.algorithms.database.RecordDatabase method)

compare_nodes() (in module glypy.algorithms.subtree_search) Composition (in module glypy.composition.composition) conf_stem_pattern (in module glypy.io.glycoct) Configuration (class in glypy.structure.constants) count_branches() (glypy.structure.glycan.Glycan method) create() (glypy.algorithms.database.RecordDatabase method) crossring_subtrees() (glypy.structure.glycan.Glycan method) cyclewarning() (in module glypy.utils.base)

D

d (glypy.structure.constants.Configuration attribute) (glypy.structure.constants.Modification attribute) dbopen (in module glypy.algorithms.database) dec (glypy.structure.constants.SuperClass attribute) decorate_tree() (in module glypy.io.glycoct) decorated_value() (in module glypy.io.glycoct) deindex() (glypy.structure.glycan.Glycan method) depth() (in module glypy.structure.monosaccharide) depth_first_traversal() (glypy.structure.glycan.Glycan method)

derivatize() (in module glypy.composition.composition_transform) distinct_fragments() (in module glypy.algorithms.subtree_search) drop_modification() (glypy.structure.monosaccharide.Monosaccharide method) drop_monosaccharide() (glypy.structure.monosaccharide.Monosaccharide method) drop_substituent() (glypy.structure.monosaccharide.Monosaccharide method) dump() (in module glypy.io.glycoct) dumps() (in module glypy.io.linear_code)

E

en (glypy.structure.constants.Modification attribute) Enum (class in glypy.utils.enum) EnumMeta (class in glypy.utils.enum) EnumValue (class in glypy.utils.enum) ery (glypy.structure.constants.Stem attribute) exact_ordering_equality() (glypy.structure.glycan.Glycan method) (glypy.structure.monosaccharide.Monosaccharide method)

exact_ordering_inclusion() (in module glypy.algorithms.subtree_search) execute() (glypy.algorithms.database.RecordDatabase method) executemany() (glypy.algorithms.database.RecordDatabase method) executescript() (glypy.algorithms.database.RecordDatabase method) extract_composition() (in module glypy.algorithms.database)

F

fragment_to_substructure() (in module glypy.structure.glycan) fragments() (glypy.structure.glycan.Glycan method) from_glycan() (glypy.composition.glycan_composition.GlycanComposition class method) (in module glypy.composition.glycan_composition) from_iupac() (in module glypy.io.iupac) from_iupac_lite() (in module glypy.composition.glycan_composition)

from_monosaccharide() (glypy.composition.glycan_composition.MonosaccharideResidue class method) from_sql() (glypy.algorithms.database.GlycanRecord method) (glypy.algorithms.database.RecordDatabase method) from_taxon() (glypy.io.glyspace.GlySpaceRDFClient method) furanose (glypy.structure.constants.RingType attribute)

G

gal (glypy.structure.constants.Stem attribute) geminal (glypy.structure.constants.Modification attribute) get() (glypy.io.glycomedb.GlycomeDBSearchMatch method) (glypy.io.glyspace.BoundURIRef method) (glypy.io.glyspace.GlySpaceRDFClient method) (glypy.io.glyspace.RDFClientBase method) (in module glypy.io.glycomedb) get_decorated() (in module glypy.io.glycoct) get_metadata() (glypy.algorithms.database.RecordDatabase method) get_preferred_name() (in module glypy.io.nomenclature.identity) get_record() (glypy.io.glycomedb.GlycomeDBSearchMatch method) (in module glypy.io.glycomedb) get_relevant_substituents() (in module glypy.io.linear_code) glc (glypy.structure.constants.Stem attribute) Glycan (class in glypy.structure.glycan) glycan_record_from_xml() (in module glypy.io.glycomedb) glycan_to_linear_code() (in module glypy.io.linear_code) GlycanComposition (class in glypy.composition.glycan_composition) GlycanRecord (class in glypy.algorithms.database) GlycoCT (in module glypy.io.glycoct) GlycoCTReader (class in glypy.io.glycoct) GlycomeDBSearchMatch (class in glypy.io.glycomedb) glypy.algorithms.database (module) glypy.algorithms.similarity (module) glypy.algorithms.subtree_search (module)

glypy.composition.composition (module) glypy.composition.composition_transform (module) glypy.io.glycoct (module) glypy.io.glycomedb (module) glypy.io.linear_code (module) glypy.io.nomenclature.identity (module) glypy.io.nomenclature.synonyms (module) glypy.structure.constants (module) glypy.structure.glycan (module) glypy.structure.link (module) glypy.structure.monosaccharide (module) glypy.structure.substituent (module) glypy.utils.base (module) glypy.utils.enum (module) glypy.utils.multimap (module) GlySpaceRDFClient (class in glypy.io.glyspace) graph_clone() (in module glypy.structure.monosaccharide) gro (glypy.structure.constants.Stem attribute) gul (glypy.structure.constants.Stem attribute)

H

handle_linkage() (glypy.io.glycoct.GlycoCTReader method) handle_residue_line() (glypy.io.glycoct.GlycoCTReader method) handle_residue_substituent() (glypy.io.glycoct.GlycoCTReader method)

hep (glypy.structure.constants.SuperClass attribute) hex (glypy.structure.constants.SuperClass attribute)

I

identify() (in module glypy.io.nomenclature.identity) ido (glypy.structure.constants.Stem attribute) internal_link_pattern (in module glypy.io.glycoct) is_a() (in module glypy.io.nomenclature.identity) is_attached() (glypy.structure.link.Link method) is_child() (glypy.structure.link.Link method) is_n_glycan (glypy.algorithms.database.GlycanRecord attribute) is_n_glycan() (in module glypy.algorithms.database)

is_occupied() (glypy.structure.monosaccharide.Monosaccharide method) (glypy.structure.substituent.Substituent method) is_parent() (glypy.structure.link.Link method) is_substituent_link() (glypy.structure.link.Link method) isotopic_composition_abundance() (in module glypy.composition.composition) items() (glypy.utils.multimap.MultiMap method) (glypy.utils.multimap.OrderedMultiMap method) iterlinks() (glypy.structure.glycan.Glycan method) iternodes() (glypy.structure.glycan.Glycan method)

K

keto (glypy.structure.constants.Modification attribute)

keys() (glypy.utils.multimap.MultiMap method) (glypy.utils.multimap.OrderedMultiMap method)

L

l (glypy.structure.constants.Configuration attribute) label_branches() (glypy.structure.glycan.Glycan method) leaves() (glypy.structure.glycan.Glycan method) Link (class in glypy.structure.link) link_pattern (in module glypy.io.glycoct)

LinkMaskContext (class in glypy.structure.link) load_data() (glypy.algorithms.database.RecordDatabase method) loads() (glypy.io.glycoct.GlycoCTReader class method) (in module glypy.io.glycoct) (in module glypy.io.linear_code) lyx (glypy.structure.constants.Stem attribute)

M

make_counter() (in module glypy.utils.base) make_entries() (in module glypy.io.glycomedb) make_struct() (in module glypy.utils.base) man (glypy.structure.constants.Stem attribute) mask() (glypy.structure.link.LinkMaskContext method) mass() (glypy.algorithms.database.GlycanRecord method) (glypy.structure.glycan.Glycan method) (glypy.structure.monosaccharide.Monosaccharide method) (glypy.structure.substituent.Substituent method) maximum_common_subgraph() (in module glypy.algorithms.subtree_search) MaximumCommonSubtreeResults (class in glypy.algorithms.subtree_search) Modification (class in glypy.structure.constants) modification_pattern (in module glypy.io.glycoct)

Monosaccharide (class in glypy.structure.monosaccharide) monosaccharide_from_linear_code() (in module glypy.io.linear_code) monosaccharide_similarity() (in module glypy.algorithms.similarity) monosaccharide_to_linear_code() (in module glypy.io.linear_code) MonosaccharideResidue (class in glypy.composition.glycan_composition) monosaccharides (glypy.algorithms.database.GlycanRecord attribute) (in module glypy.io.nomenclature.synonyms) monosaccharides_from (in module glypy.io.linear_code) monosaccharides_to (in module glypy.io.linear_code) most_probable_isotopic_composition() (in module glypy.composition.composition) MultiMap (class in glypy.utils.multimap)

N

n_saccharide_similarity() (in module glypy.algorithms.subtree_search) naive_name_monosaccharide() (in module glypy.io.nomenclature.identity) name_fragment() (glypy.structure.glycan.Glycan method)

next() (glypy.io.glycoct.GlycoCTReader method) non (glypy.structure.constants.SuperClass attribute)

O

oct (glypy.structure.constants.SuperClass attribute) open (glypy.structure.constants.RingType attribute) open_attachment_sites() (glypy.structure.monosaccharide.Monosaccharide method) opener() (in module glypy.utils.base)

optimal_assignment() (in module glypy.algorithms.similarity) order() (glypy.structure.glycan.Glycan method) (glypy.structure.monosaccharide.Monosaccharide method) OrderedMultiMap (class in glypy.utils.multimap)

P

parents() (glypy.structure.monosaccharide.Monosaccharide method) (glypy.structure.substituent.Substituent method) parse() (glypy.io.glycoct.GlycoCTReader method) (in module glypy.composition.glycan_composition) parse_linear_code() (in module glypy.io.linear_code) pcalculate_mass() (in module glypy.composition.composition) PComposition (class in glypy.composition.composition) pen (glypy.structure.constants.SuperClass attribute)

pop() (glypy.utils.multimap.MultiMap method) postprocess() (glypy.io.glycoct.GlycoCTReader method) ppm_match_tolerance_search() (glypy.algorithms.database.RecordDatabase method) priority() (in module glypy.io.linear_code) pyranose (glypy.structure.constants.RingType attribute)

Q

query() (glypy.io.glyspace.GlySpaceRDFClient method)

querymethod() (in module glypy.algorithms.database)

R

RDFClientBase (class in glypy.io.glyspace) read() (in module glypy.io.glycoct) reconnect() (glypy.structure.link.Link method) RecordDatabase (class in glypy.algorithms.database) reducing_end (glypy.structure.glycan.Glycan attribute) (glypy.structure.monosaccharide.Monosaccharide attribute) ReferenceEntity (class in glypy.io.glyspace) refund() (glypy.structure.link.Link method) register() (glypy.structure.substituent.Substituent static method) (in module glypy.structure.substituent) register_predicate_processor() (glypy.io.glyspace.RDFClientBase class method) reindex() (glypy.structure.glycan.Glycan method)

release() (in module glypy.structure.monosaccharide) rep_header_pattern (in module glypy.io.glycoct) reroot() (glypy.structure.glycan.Glycan method) res_pattern (in module glypy.io.glycoct) rib (glypy.structure.constants.Stem attribute) ring_type (glypy.structure.monosaccharide.Monosaccharide attribute) RingType (class in glypy.structure.constants) rollback() (glypy.algorithms.database.RecordDatabase method) root() (in module glypy.utils.base)

S

s11 (glypy.structure.constants.SuperClass attribute) s12 (glypy.structure.constants.SuperClass attribute) s13 (glypy.structure.constants.SuperClass attribute) s14 (glypy.structure.constants.SuperClass attribute) s15 (glypy.structure.constants.SuperClass attribute) s16 (glypy.structure.constants.SuperClass attribute) s17 (glypy.structure.constants.SuperClass attribute) s18 (glypy.structure.constants.SuperClass attribute) s19 (glypy.structure.constants.SuperClass attribute) s20 (glypy.structure.constants.SuperClass attribute) search_by_species() (in module glypy.io.glycomedb) search_minimum_common_substructure() (in module glypy.io.glycomedb) search_substructure() (in module glypy.io.glycomedb) set_cache() (in module glypy.io.glycomedb) set_metadata() (glypy.algorithms.database.RecordDatabase method) set_reducing_end() (glypy.structure.glycan.Glycan method) sigil (glypy.composition.glycan_composition.SubstituentResidue attribute) sp (glypy.structure.constants.Modification attribute) sp2 (glypy.structure.constants.Modification attribute)

Stem (class in glypy.structure.constants) Stereocoding (class in glypy.structure.constants) stn() (glypy.algorithms.database.RecordDatabase method) strip_derivatization() (in module glypy.composition.composition_transform) StructurePrecisionEnum (class in glypy.io.glycoct) structures_with_motif() (glypy.io.glyspace.GlySpaceRDFClient method) sub_table_name() (glypy.algorithms.database.RecordDatabase method) Substituent (class in glypy.structure.substituent) substituent_to_linear_code() (in module glypy.io.linear_code) SubstituentResidue (class in glypy.composition.glycan_composition) substituents() (glypy.structure.monosaccharide.Monosaccharide method) substituents_from (in module glypy.io.linear_code) substituents_to (in module glypy.io.linear_code) substructures() (glypy.structure.glycan.Glycan method) subtree_of() (in module glypy.algorithms.subtree_search) subtrees() (glypy.structure.glycan.Glycan method) sug (glypy.structure.constants.SuperClass attribute) SuperClass (class in glypy.structure.constants)

T

tal (glypy.structure.constants.Stem attribute) tet (glypy.structure.constants.SuperClass attribute) to() (glypy.structure.link.Link method) to_iupac() (in module glypy.io.iupac) to_iupac_lite() (in module glypy.composition.glycan_composition) to_linear_code() (in module glypy.io.linear_code) toggle() (in module glypy.structure.monosaccharide) topological_equality() (glypy.structure.glycan.Glycan method) (glypy.structure.monosaccharide.Monosaccharide method) topological_inclusion() (in module glypy.algorithms.subtree_search)

total_composition() (glypy.structure.glycan.Glycan method) (glypy.structure.monosaccharide.Monosaccharide method) (glypy.structure.substituent.Substituent method) translate() (glypy.utils.enum.EnumMeta method) traverse() (in module glypy.structure.monosaccharide) tre (glypy.structure.constants.Stem attribute) tree() (in module glypy.utils.base) tri (glypy.structure.constants.SuperClass attribute) triples() (glypy.io.glyspace.GlySpaceRDFClient method) try_apply() (glypy.structure.link.Link method) try_break_link() (glypy.structure.link.Link method)

U

uncyclized (glypy.structure.constants.Anomer attribute) undecorate_tree() (in module glypy.io.glycoct)

unmask() (glypy.structure.link.LinkMaskContext method) unregister() (glypy.structure.substituent.Substituent static method) (in module glypy.structure.substituent)

V

values() (glypy.utils.multimap.MultiMap method)

X

x (glypy.structure.constants.Anomer attribute) (glypy.structure.constants.RingType attribute) (glypy.structure.constants.Stem attribute) (glypy.structure.constants.SuperClass attribute)

xyl (glypy.structure.constants.Stem attribute)