Index

_

__call__() (lXtractor.chain.initializer.ItemCallback method) (lXtractor.chain.initializer.SingletonCallback method) (lXtractor.core.base.AddMethod method) (lXtractor.core.base.AlignMethod method) (lXtractor.core.base.ApplyT method) (lXtractor.core.base.ApplyTWithArgs method) (lXtractor.core.base.FilterT method) (lXtractor.core.base.SeqFilter method) (lXtractor.core.base.SeqMapper method) (lXtractor.core.base.SeqReader method) (lXtractor.core.base.SeqWriter method) (lXtractor.core.base.UrlGetter method) (lXtractor.variables.base.AbstractCalculator method) (lXtractor.variables.base.AggFn method) (lXtractor.variables.calculator.GenericCalculator method) __init__() (lXtractor.chain.chain.Chain method) (lXtractor.chain.initializer.ChainInitializer method) (lXtractor.chain.initializer.ItemCallback method) (lXtractor.chain.initializer.SingletonCallback method) (lXtractor.chain.io.ChainIO method) (lXtractor.chain.io.ChainIOConfig method) (lXtractor.chain.list.ChainList method) (lXtractor.chain.structure.ChainStructure method) (lXtractor.core.alignment.Alignment method) (lXtractor.core.base.AbstractResource method) (lXtractor.core.base.AddMethod method) (lXtractor.core.base.AlignMethod method) (lXtractor.core.base.ApplyT method) (lXtractor.core.base.ApplyTWithArgs method) (lXtractor.core.base.FilterT method) (lXtractor.core.base.NamedTupleT method) (lXtractor.core.base.Ord method) (lXtractor.core.base.ResNameDict method) (lXtractor.core.base.SeqFilter method) (lXtractor.core.base.SeqMapper method) (lXtractor.core.base.SeqReader method) (lXtractor.core.base.SeqWriter method) (lXtractor.core.base.SupportsWrite method) (lXtractor.core.base.UrlGetter method) (lXtractor.core.config.Config method) (lXtractor.core.ligand.Ligand method) (lXtractor.core.pocket.Pocket method) (lXtractor.core.segment.Segment method) (lXtractor.core.structure.CarbohydrateStructure method) (lXtractor.core.structure.GenericStructure method) (lXtractor.core.structure.Masks method) (lXtractor.core.structure.NucleotideStructure method) (lXtractor.core.structure.ProteinStructure method) (lXtractor.ext.base.ApiBase method) (lXtractor.ext.base.SupportsAnnotate method) (lXtractor.ext.hmm.Pfam method) (lXtractor.ext.hmm.PyHMMer method) (lXtractor.ext.pdb_.PDB method) (lXtractor.ext.sifts.Mapping method) (lXtractor.ext.sifts.SIFTS method) (lXtractor.ext.uniprot.UniProt method) (lXtractor.variables.base.AggFn method) (lXtractor.variables.base.ProtFP method) (lXtractor.variables.calculator.GenericCalculator method) (lXtractor.variables.manager.Manager method) (lXtractor.variables.sequential.PFP method) (lXtractor.variables.sequential.SeqEl method) (lXtractor.variables.sequential.SliceTransformReduce method) (lXtractor.variables.structural.AggDist method) (lXtractor.variables.structural.ClosestLigandContactsCount method) (lXtractor.variables.structural.ClosestLigandDist method) (lXtractor.variables.structural.ClosestLigandNames method) (lXtractor.variables.structural.Contacts method) (lXtractor.variables.structural.Dihedral method) (lXtractor.variables.structural.Dist method) (lXtractor.variables.structural.Omega method) (lXtractor.variables.structural.Phi method) (lXtractor.variables.structural.PseudoDihedral method) (lXtractor.variables.structural.Psi method) (lXtractor.variables.structural.SASA method)

A

a (lXtractor.variables.structural.ClosestLigandContactsCount attribute) (lXtractor.variables.structural.ClosestLigandDist attribute) (lXtractor.variables.structural.ClosestLigandNames attribute) (lXtractor.variables.structural.SASA attribute) a1 (lXtractor.variables.structural.Dihedral attribute) (lXtractor.variables.structural.Dist attribute) a2 (lXtractor.variables.structural.Dihedral attribute) (lXtractor.variables.structural.Dist attribute) a3 (lXtractor.variables.structural.Dihedral attribute) a4 (lXtractor.variables.structural.Dihedral attribute) AbstractCalculator (class in lXtractor.variables.base) AbstractResource (class in lXtractor.core.base) AbstractVariable (class in lXtractor.variables.base) add() (lXtractor.core.alignment.Alignment method) add_category() (in module lXtractor.chain.list) add_method (lXtractor.core.alignment.Alignment attribute) add_seq() (lXtractor.core.segment.Segment method) add_structure() (lXtractor.chain.chain.Chain method) AddMethod (class in lXtractor.core.base) agg_lig (lXtractor.variables.structural.ClosestLigandDist attribute) agg_res (lXtractor.variables.structural.ClosestLigandDist attribute) AggDist (class in lXtractor.variables.structural) AggFn (class in lXtractor.variables.base) aggregate_from_chains() (lXtractor.variables.manager.Manager method) aggregate_from_it() (lXtractor.variables.manager.Manager method) align() (lXtractor.core.alignment.Alignment method) (lXtractor.ext.hmm.PyHMMer method) align_and_superpose_pair() (in module lXtractor.protocols.superpose) align_method (lXtractor.core.alignment.Alignment attribute) Alignment (class in lXtractor.core.alignment) AlignMethod (class in lXtractor.core.base)

all_logging_disabled() (in module lXtractor.util.misc) altloc (lXtractor.chain.structure.ChainStructure property) altloc_ids (lXtractor.core.structure.GenericStructure property) AmbiguousData AmbiguousMapping annotate() (lXtractor.core.alignment.Alignment method) (lXtractor.ext.base.SupportsAnnotate method) (lXtractor.ext.hmm.PyHMMer method) ApiBase (class in lXtractor.ext.base) append() (lXtractor.core.segment.Segment method) apply() (in module lXtractor.util.misc) (lXtractor.chain.list.ChainList method) apply_children() (lXtractor.chain.chain.Chain method) (lXtractor.chain.sequence.ChainSequence method) (lXtractor.chain.structure.ChainStructure method) apply_kwargs (lXtractor.variables.calculator.GenericCalculator attribute) apply_structures() (lXtractor.chain.chain.Chain method) apply_to_map() (lXtractor.chain.sequence.ChainSequence method) ApplyT (class in lXtractor.core.base) ApplyTWithArgs (class in lXtractor.core.base) array (lXtractor.chain.structure.ChainStructure property) (lXtractor.core.ligand.Ligand property) (lXtractor.core.structure.GenericStructure property) as_chain() (lXtractor.chain.sequence.ChainSequence method) as_df() (lXtractor.chain.sequence.ChainSequence method) (lXtractor.variables.base.Variables method) as_np() (lXtractor.chain.sequence.ChainSequence method) assign() (lXtractor.variables.manager.Manager method) atom_marks (lXtractor.core.structure.GenericStructure property) AtomMark (class in lXtractor.core.config) atoms (lXtractor.variables.structural.Dihedral property)

B

biotite_align() (in module lXtractor.util.seq)

bounded_by() (lXtractor.core.segment.Segment method) bounds() (lXtractor.core.segment.Segment method)

C

calculate() (in module lXtractor.variables.calculator) (lXtractor.variables.base.AbstractVariable method) (lXtractor.variables.base.LigandVariable method) (lXtractor.variables.base.SequenceVariable method) (lXtractor.variables.base.StructureVariable method) (lXtractor.variables.manager.Manager method) (lXtractor.variables.sequential.PFP method) (lXtractor.variables.sequential.SeqEl method) (lXtractor.variables.sequential.SliceTransformReduce method) (lXtractor.variables.structural.AggDist method) (lXtractor.variables.structural.ClosestLigandContactsCount method) (lXtractor.variables.structural.ClosestLigandDist method) (lXtractor.variables.structural.ClosestLigandNames method) (lXtractor.variables.structural.Contacts method) (lXtractor.variables.structural.Dihedral method) (lXtractor.variables.structural.Dist method) (lXtractor.variables.structural.SASA method) calculate_dihedral() (in module lXtractor.util.structure) CARB (lXtractor.core.config.AtomMark attribute) CarbohydrateStructure (class in lXtractor.core.structure) categories (lXtractor.chain.chain.Chain property) (lXtractor.chain.list.ChainList property) (lXtractor.chain.sequence.ChainSequence property) (lXtractor.chain.structure.ChainStructure property) Chain (class in lXtractor.chain.chain) chain_id (lXtractor.chain.structure.ChainStructure property) (lXtractor.core.ligand.Ligand property) chain_ids (lXtractor.core.structure.GenericStructure property) chain_ids_ligand (lXtractor.core.structure.GenericStructure property)

chain_ids_polymer (lXtractor.core.structure.GenericStructure property) ChainInitializer (class in lXtractor.chain.initializer) ChainIO (class in lXtractor.chain.io) ChainIOConfig (class in lXtractor.chain.io) ChainList (class in lXtractor.chain.list) ChainSequence (class in lXtractor.chain.sequence) ChainStructure (class in lXtractor.chain.structure) Chi1 (class in lXtractor.variables.structural) Chi2 (class in lXtractor.variables.structural) children (lXtractor.chain.chain.Chain attribute) (lXtractor.chain.structure.ChainStructure attribute) (lXtractor.core.segment.Segment attribute) clean() (lXtractor.ext.hmm.Pfam method) clear_user_config() (lXtractor.core.config.Config method) ClosestLigandContactsCount (class in lXtractor.variables.structural) ClosestLigandDist (class in lXtractor.variables.structural) ClosestLigandNames (class in lXtractor.variables.structural) col2col() (in module lXtractor.util.misc) collapse() (lXtractor.chain.list.ChainList method) collapse_children() (lXtractor.chain.list.ChainList method) com (lXtractor.variables.structural.Dist attribute) compare_arrays() (in module lXtractor.util.structure) compare_coord() (in module lXtractor.util.structure) Config (class in lXtractor.core.config) ConfigError contact_mask (lXtractor.core.ligand.Ligand attribute) Contacts (class in lXtractor.variables.structural) convert_seq() (lXtractor.ext.hmm.PyHMMer method) COVALENT (lXtractor.core.config.AtomMark attribute) coverage() (lXtractor.chain.sequence.ChainSequence method)

D

dat_columns (lXtractor.ext.hmm.Pfam property) definition (lXtractor.core.pocket.Pocket attribute) df (lXtractor.ext.hmm.Pfam property) digitize_seq() (in module lXtractor.ext.hmm) Dihedral (class in lXtractor.variables.structural) Dist (class in lXtractor.variables.structural)

dist (lXtractor.core.ligand.Ligand attribute) Distance (lXtractor.protocols.superpose.SuperposeOutput attribute) do_overlap() (in module lXtractor.core.segment) drop_duplicates() (lXtractor.chain.list.ChainList method) dump() (lXtractor.core.base.AbstractResource method) (lXtractor.ext.hmm.Pfam method) (lXtractor.ext.sifts.SIFTS method)

E

end (lXtractor.chain.chain.Chain property) (lXtractor.chain.structure.ChainStructure property) (lXtractor.core.segment.Segment property)

extend_residue_mask() (in module lXtractor.util.structure) extract_positions() (lXtractor.core.structure.GenericStructure method) extract_segment() (lXtractor.core.structure.GenericStructure method)

F

FailedCalculation fetch() (lXtractor.core.base.AbstractResource method) (lXtractor.ext.hmm.Pfam method) (lXtractor.ext.sifts.SIFTS method) fetch_chunks() (in module lXtractor.util.io) fetch_info() (lXtractor.ext.base.StructureApiBase method) (lXtractor.ext.uniprot.UniProt method) fetch_iterable() (in module lXtractor.util.io) fetch_obsolete() (lXtractor.ext.pdb_.PDB static method) fetch_sequences() (lXtractor.ext.uniprot.UniProt method) fetch_structures() (lXtractor.ext.base.StructureApiBase method) fetch_text() (in module lXtractor.util.io) fetch_to_file() (in module lXtractor.util.io) fetch_uniprot() (in module lXtractor.ext.uniprot) fetch_urls() (in module lXtractor.util.io) fields (lXtractor.chain.sequence.ChainSequence property) fill() (lXtractor.chain.sequence.ChainSequence method) filter() (lXtractor.chain.list.ChainList method) (lXtractor.core.alignment.Alignment method) filter_any_polymer() (in module lXtractor.util.structure) filter_by_method() (in module lXtractor.ext.pdb_) filter_category() (lXtractor.chain.list.ChainList method) filter_children() (lXtractor.chain.chain.Chain method) (lXtractor.chain.sequence.ChainSequence method) (lXtractor.chain.structure.ChainStructure method)

filter_gaps() (lXtractor.core.alignment.Alignment method) filter_ligand() (in module lXtractor.util.structure) filter_polymer() (in module lXtractor.util.structure) filter_pos() (lXtractor.chain.list.ChainList method) filter_selection() (in module lXtractor.util.structure) filter_selection_extended() (in module lXtractor.chain.structure) filter_solvent_extended() (in module lXtractor.util.structure) filter_structures() (lXtractor.chain.chain.Chain method) filter_to_common_atoms() (in module lXtractor.util.structure) FilterT (class in lXtractor.core.base) find_contacts() (in module lXtractor.util.structure) find_first_polymer_type() (in module lXtractor.util.structure) find_primary_polymer_type() (in module lXtractor.util.structure) find_structure() (in module lXtractor.variables.manager) FormatError from_df() (lXtractor.chain.sequence.ChainSequence class method) from_file() (lXtractor.chain.sequence.ChainSequence class method) from_hmm_collection() (lXtractor.ext.hmm.PyHMMer class method) from_iterable() (lXtractor.chain.initializer.ChainInitializer method) from_mapping() (lXtractor.chain.initializer.ChainInitializer method) from_msa() (lXtractor.ext.hmm.PyHMMer class method) from_string() (lXtractor.chain.sequence.ChainSequence class method) from_tuple() (lXtractor.chain.sequence.ChainSequence class method)

G

generate_patched_seqs() (lXtractor.chain.chain.Chain method) GenericCalculator (class in lXtractor.variables.calculator) GenericStructure (class in lXtractor.core.structure) get_closest() (lXtractor.chain.sequence.ChainSequence method) get_cpu_count() (in module lXtractor.util.misc) get_dihedrals() (lXtractor.variables.structural.Chi1 static method) (lXtractor.variables.structural.Chi2 static method) get_dirs() (in module lXtractor.util.io) get_files() (in module lXtractor.util.io)

get_item() (lXtractor.chain.sequence.ChainSequence method) get_level() (lXtractor.chain.list.ChainList method) get_map() (lXtractor.chain.sequence.ChainSequence method) get_mapping() (in module lXtractor.variables.manager) get_missing_atoms() (in module lXtractor.util.structure) get_observed_atoms_frac() (in module lXtractor.util.structure) get_sequence() (lXtractor.core.structure.GenericStructure method) graph (lXtractor.core.structure.GenericStructure property) graph_reindex_nodes() (in module lXtractor.util.misc) groupby() (lXtractor.chain.list.ChainList method)

H

hits_ (lXtractor.ext.hmm.PyHMMer attribute)

hmm (lXtractor.ext.hmm.PyHMMer attribute)

I

i (lXtractor.variables.sequential.PFP attribute) id (lXtractor.chain.chain.Chain property) (lXtractor.chain.structure.ChainStructure property) (lXtractor.core.ligand.Ligand property) (lXtractor.core.segment.Segment property) (lXtractor.core.structure.GenericStructure property) (lXtractor.variables.base.AbstractVariable property) ID_fix (lXtractor.protocols.superpose.SuperposeOutput attribute) ID_mob (lXtractor.protocols.superpose.SuperposeOutput attribute) id_strip_parents() (lXtractor.core.segment.Segment method) ids (lXtractor.chain.list.ChainList property) index() (lXtractor.chain.list.ChainList method) init_pipeline() (lXtractor.ext.hmm.PyHMMer method) init_var() (in module lXtractor.variables.parser) InitError insert() (lXtractor.chain.list.ChainList method) (lXtractor.core.segment.Segment method) is_chain_type() (in module lXtractor.chain.base) is_chain_type_iterable() (in module lXtractor.chain.base) is_connected() (lXtractor.core.pocket.Pocket method) is_empty (lXtractor.chain.structure.ChainStructure property) (lXtractor.core.segment.Segment property) (lXtractor.core.structure.GenericStructure property)

is_empty() (in module lXtractor.util.misc) is_empty_polymer (lXtractor.core.structure.GenericStructure property) is_locally_connected() (lXtractor.core.ligand.Ligand method) is_polymer (lXtractor.core.ligand.Ligand attribute) is_singleton (lXtractor.core.segment.Segment property) (lXtractor.core.structure.GenericStructure property) is_valid_field_name() (in module lXtractor.util.misc) item_type (lXtractor.core.segment.Segment property) ItemCallback (class in lXtractor.chain.initializer) iter_canonical() (in module lXtractor.util.structure) iter_children() (lXtractor.chain.chain.Chain method) (lXtractor.chain.list.ChainList method) (lXtractor.chain.sequence.ChainSequence method) (lXtractor.chain.structure.ChainStructure method) iter_hmm() (in module lXtractor.ext.hmm) iter_ids() (lXtractor.chain.list.ChainList method) iter_residue_masks() (in module lXtractor.util.structure) iter_sequences() (lXtractor.chain.list.ChainList method) iter_structure_sequences() (lXtractor.chain.list.ChainList method) iter_structures() (lXtractor.chain.list.ChainList method) itercols() (lXtractor.core.alignment.Alignment method)

J

json_to_molgraph() (in module lXtractor.util.misc)

K

key (lXtractor.variables.structural.AggDist attribute)

L

LengthMismatch Ligand (class in lXtractor.core.ligand) LIGAND (lXtractor.core.config.AtomMark attribute) ligand (lXtractor.core.structure.Masks attribute) ligand_carb (lXtractor.core.structure.Masks attribute) ligand_covalent (lXtractor.core.structure.Masks attribute) ligand_idx (lXtractor.core.ligand.Ligand attribute) ligand_nonpoly (lXtractor.core.structure.Masks attribute) ligand_nuc (lXtractor.core.structure.Masks attribute) ligand_pep (lXtractor.core.structure.Masks attribute) ligand_poly (lXtractor.core.structure.Masks attribute) ligands (lXtractor.chain.structure.ChainStructure property) (lXtractor.core.structure.GenericStructure property) ligands_from_atom_marks() (in module lXtractor.core.ligand) LigandVariable (class in lXtractor.variables.base) list_ancestors() (in module lXtractor.chain.tree) list_ancestors_names() (in module lXtractor.chain.tree) load() (lXtractor.ext.sifts.SIFTS static method) load_hmm() (lXtractor.ext.hmm.Pfam method) load_json_callback() (in module lXtractor.ext.base) load_structure() (in module lXtractor.util.structure) lXtractor.chain.base module lXtractor.chain.chain module lXtractor.chain.initializer module lXtractor.chain.io module lXtractor.chain.list module lXtractor.chain.sequence module lXtractor.chain.structure module lXtractor.chain.tree module lXtractor.collection module lXtractor.core.alignment module lXtractor.core.base module

lXtractor.core.config module lXtractor.core.exceptions module lXtractor.core.ligand module lXtractor.core.pocket module lXtractor.core.segment module lXtractor.core.structure module lXtractor.ext.base module lXtractor.ext.hmm module lXtractor.ext.pdb_ module lXtractor.ext.sifts module lXtractor.ext.uniprot module lXtractor.protocols.superpose module lXtractor.util.io module lXtractor.util.misc module lXtractor.util.seq module lXtractor.util.structure module lXtractor.variables.base module lXtractor.variables.calculator module lXtractor.variables.manager module lXtractor.variables.parser module lXtractor.variables.sequential module lXtractor.variables.structural module

M

mafft_add() (in module lXtractor.util.seq) mafft_align() (in module lXtractor.util.seq) make() (in module lXtractor.chain.tree) (lXtractor.core.alignment.Alignment class method) make_empty() (lXtractor.chain.chain.Chain class method) (lXtractor.chain.sequence.ChainSequence class method) (lXtractor.chain.structure.ChainStructure class method) (lXtractor.core.structure.GenericStructure class method) make_filled() (in module lXtractor.chain.tree) make_ligand() (in module lXtractor.core.ligand) make_obj_tree() (in module lXtractor.chain.tree) make_sel() (in module lXtractor.core.pocket) make_str() (in module lXtractor.variables.sequential) make_str_tree() (in module lXtractor.chain.tree) make_url() (in module lXtractor.ext.uniprot) Manager (class in lXtractor.variables.manager) map() (lXtractor.core.alignment.Alignment method) (lXtractor.variables.base.AbstractCalculator method) (lXtractor.variables.calculator.GenericCalculator method) map_boundaries() (lXtractor.chain.sequence.ChainSequence method) map_id() (lXtractor.ext.sifts.SIFTS method) map_numbering() (lXtractor.chain.sequence.ChainSequence method) (lXtractor.ext.sifts.SIFTS method) map_numbering_12many() (in module lXtractor.chain.sequence) map_numbering_many2many() (in module lXtractor.chain.sequence) map_pairs_numbering() (in module lXtractor.util.seq) map_segment_numbering() (in module lXtractor.core.segment) Mapping (class in lXtractor.ext.sifts) mark_atoms() (in module lXtractor.core.structure) mark_atoms_g() (in module lXtractor.core.structure) mark_polymer_type() (in module lXtractor.util.structure) mask (lXtractor.core.ligand.Ligand attribute) (lXtractor.core.structure.GenericStructure property) Masks (class in lXtractor.core.structure) match() (lXtractor.chain.sequence.ChainSequence method) max_trials (lXtractor.ext.base.ApiBase attribute) meta (lXtractor.chain.chain.Chain property) (lXtractor.chain.structure.ChainStructure property) (lXtractor.core.ligand.Ligand attribute) (lXtractor.core.segment.Segment attribute)

MissingData module lXtractor.chain.base lXtractor.chain.chain lXtractor.chain.initializer lXtractor.chain.io lXtractor.chain.list lXtractor.chain.sequence lXtractor.chain.structure lXtractor.chain.tree lXtractor.collection lXtractor.core.alignment lXtractor.core.base lXtractor.core.config lXtractor.core.exceptions lXtractor.core.ligand lXtractor.core.pocket lXtractor.core.segment lXtractor.core.structure lXtractor.ext.base lXtractor.ext.hmm lXtractor.ext.pdb_ lXtractor.ext.sifts lXtractor.ext.uniprot lXtractor.protocols.superpose lXtractor.util.io lXtractor.util.misc lXtractor.util.seq lXtractor.util.structure lXtractor.variables.base lXtractor.variables.calculator lXtractor.variables.manager lXtractor.variables.parser lXtractor.variables.sequential lXtractor.variables.structural

N

name (lXtractor.chain.chain.Chain property) (lXtractor.chain.structure.ChainStructure property) (lXtractor.core.pocket.Pocket attribute) (lXtractor.core.segment.Segment property) (lXtractor.core.structure.GenericStructure property) (lXtractor.variables.structural.Dihedral attribute) NamedTupleT (class in lXtractor.core.base)

NoOverlap NUC (lXtractor.core.config.AtomMark attribute) NucleotideStructure (class in lXtractor.core.structure) num_proc (lXtractor.chain.io.ChainIO attribute) (lXtractor.chain.io.ChainIOConfig attribute) (lXtractor.variables.calculator.GenericCalculator attribute) num_threads (lXtractor.ext.base.ApiBase attribute) numbering (lXtractor.chain.sequence.ChainSequence property)

O

Omega (class in lXtractor.variables.structural) Ord (class in lXtractor.core.base) overlap() (lXtractor.core.segment.Segment method)

overlap_with() (lXtractor.core.segment.Segment method) OverlapError overlaps() (lXtractor.core.segment.Segment method)

P

p (lXtractor.variables.sequential.PFP attribute) (lXtractor.variables.sequential.SeqEl attribute) (lXtractor.variables.structural.ClosestLigandContactsCount attribute) (lXtractor.variables.structural.ClosestLigandDist attribute) (lXtractor.variables.structural.ClosestLigandNames attribute) (lXtractor.variables.structural.Contacts attribute) (lXtractor.variables.structural.Omega attribute) (lXtractor.variables.structural.Phi attribute) (lXtractor.variables.structural.Psi attribute) (lXtractor.variables.structural.SASA attribute) p1 (lXtractor.variables.structural.AggDist attribute) (lXtractor.variables.structural.Dihedral attribute) (lXtractor.variables.structural.Dist attribute) p2 (lXtractor.variables.structural.AggDist attribute) (lXtractor.variables.structural.Dihedral attribute) (lXtractor.variables.structural.Dist attribute) p3 (lXtractor.variables.structural.Dihedral attribute) p4 (lXtractor.variables.structural.Dihedral attribute) parent (lXtractor.chain.chain.Chain property) (lXtractor.chain.structure.ChainStructure property) (lXtractor.core.ligand.Ligand attribute) (lXtractor.core.segment.Segment property) parent_contact_atoms (lXtractor.core.ligand.Ligand property) parent_contact_chains (lXtractor.core.ligand.Ligand property) parse() (lXtractor.core.base.AbstractResource method) (lXtractor.ext.hmm.Pfam method) (lXtractor.ext.sifts.SIFTS method)

parse_structure_callback() (in module lXtractor.ext.base) parse_suffix() (in module lXtractor.util.io) parse_var() (in module lXtractor.variables.parser) ParsingError partition_gap_sequences() (in module lXtractor.util.seq) patch() (lXtractor.chain.sequence.ChainSequence method) path_tree() (in module lXtractor.util.io) PDB (class in lXtractor.ext.pdb_) pdb_chains (lXtractor.ext.sifts.SIFTS property) pdb_ids (lXtractor.ext.sifts.SIFTS property) PEP (lXtractor.core.config.AtomMark attribute) Pfam (class in lXtractor.ext.hmm) PFP (class in lXtractor.variables.sequential) Phi (class in lXtractor.variables.structural) pipeline (lXtractor.ext.hmm.PyHMMer attribute) Pocket (class in lXtractor.core.pocket) positions (lXtractor.variables.structural.Dihedral property) prepare_mapping() (lXtractor.ext.sifts.SIFTS method) primary_polymer (lXtractor.core.structure.Masks attribute) primary_polymer_modified (lXtractor.core.structure.Masks attribute) primary_polymer_ptm (lXtractor.core.structure.Masks attribute) ProteinStructure (class in lXtractor.core.structure) ProtFP (class in lXtractor.variables.base) PseudoDihedral (class in lXtractor.variables.structural) Psi (class in lXtractor.variables.structural) PyHMMer (class in lXtractor.ext.hmm)

R

r (lXtractor.variables.structural.Contacts attribute) read() (lXtractor.chain.chain.Chain class method) (lXtractor.chain.io.ChainIO method) (lXtractor.chain.sequence.ChainSequence class method) (lXtractor.chain.structure.ChainStructure class method) (lXtractor.core.alignment.Alignment class method) (lXtractor.core.base.AbstractResource method) (lXtractor.core.structure.GenericStructure class method) (lXtractor.ext.hmm.Pfam method) (lXtractor.ext.sifts.SIFTS method) (lXtractor.variables.base.Variables class method) read_chain() (lXtractor.chain.io.ChainIO method) read_chain_seq() (lXtractor.chain.io.ChainIO method) read_chain_str() (lXtractor.chain.io.ChainIO method) read_chains() (in module lXtractor.chain.io) read_fasta() (in module lXtractor.util.seq) read_make() (lXtractor.core.alignment.Alignment class method) read_n_col_table() (in module lXtractor.util.io) realign() (lXtractor.core.alignment.Alignment method) recover() (in module lXtractor.chain.tree) reduce() (lXtractor.variables.sequential.SliceTransformReduce static method) relate() (lXtractor.chain.sequence.ChainSequence method) reload() (lXtractor.core.config.Config method) remove() (lXtractor.core.alignment.Alignment method) (lXtractor.variables.manager.Manager method)

remove_gap_columns() (in module lXtractor.util.seq) remove_seq() (lXtractor.core.segment.Segment method) rename() (lXtractor.chain.sequence.ChainSequence method) res_id (lXtractor.core.ligand.Ligand property) res_name (lXtractor.core.ligand.Ligand property) reset() (lXtractor.variables.manager.Manager method) reset_to_defaults() (lXtractor.core.config.Config method) ResNameDict (class in lXtractor.core.base) resolve_overlaps() (in module lXtractor.core.segment) rm_solvent() (lXtractor.chain.structure.ChainStructure method) (lXtractor.core.structure.GenericStructure method) RmsdSuperpose (lXtractor.protocols.superpose.SuperposeOutput attribute) rtype (lXtractor.variables.base.AbstractVariable property) (lXtractor.variables.sequential.PFP property) (lXtractor.variables.sequential.SeqEl property) (lXtractor.variables.structural.AggDist property) (lXtractor.variables.structural.ClosestLigandContactsCount property) (lXtractor.variables.structural.ClosestLigandDist property) (lXtractor.variables.structural.ClosestLigandNames property) (lXtractor.variables.structural.Contacts property) (lXtractor.variables.structural.Dihedral property) (lXtractor.variables.structural.Dist property) (lXtractor.variables.structural.SASA property) run_sp() (in module lXtractor.util.io)

S

SASA (class in lXtractor.variables.structural) save() (lXtractor.core.config.Config method) save_structure() (in module lXtractor.util.structure) search() (lXtractor.ext.hmm.PyHMMer method) Segment (class in lXtractor.core.segment) segments2graph() (in module lXtractor.core.segment) seq (lXtractor.chain.chain.Chain property) (lXtractor.chain.sequence.ChainSequence property) (lXtractor.chain.structure.ChainStructure property) seq1 (lXtractor.chain.sequence.ChainSequence property) seq3 (lXtractor.chain.sequence.ChainSequence property) seq_name (lXtractor.variables.sequential.SeqEl attribute) (lXtractor.variables.sequential.SliceTransformReduce attribute) seq_names (lXtractor.core.segment.Segment property) SeqEl (class in lXtractor.variables.sequential) SeqFilter (class in lXtractor.core.base) SeqMapper (class in lXtractor.core.base) SeqReader (class in lXtractor.core.base) seqs (lXtractor.core.alignment.Alignment attribute) sequence (lXtractor.variables.base.Variables property) sequences (lXtractor.chain.list.ChainList property) SequenceVariable (class in lXtractor.variables.base) SeqWriter (class in lXtractor.core.base) serialize_json_value() (in module lXtractor.core.config) shape (lXtractor.core.alignment.Alignment property) SIFTS (class in lXtractor.ext.sifts) SingletonCallback (class in lXtractor.chain.initializer) slice() (lXtractor.core.alignment.Alignment method) SliceTransformReduce (class in lXtractor.variables.sequential) SOLVENT (lXtractor.core.config.AtomMark attribute) solvent (lXtractor.core.structure.Masks attribute) sort() (lXtractor.chain.list.ChainList method) spawn_child() (lXtractor.chain.chain.Chain method) (lXtractor.chain.sequence.ChainSequence method) (lXtractor.chain.structure.ChainStructure method) split_altloc() (lXtractor.core.structure.GenericStructure method)

split_chains() (lXtractor.core.structure.GenericStructure method) stage() (in module lXtractor.variables.manager) (lXtractor.variables.manager.Manager method) start (lXtractor.chain.chain.Chain property) (lXtractor.chain.structure.ChainStructure property) (lXtractor.core.segment.Segment property) (lXtractor.variables.sequential.SliceTransformReduce attribute) step (lXtractor.variables.sequential.SliceTransformReduce attribute) stop (lXtractor.variables.sequential.SliceTransformReduce attribute) structure (lXtractor.chain.structure.ChainStructure property) (lXtractor.variables.base.Variables property) structure_sequences (lXtractor.chain.list.ChainList property) StructureApiBase (class in lXtractor.ext.base) structures (lXtractor.chain.chain.Chain attribute) (lXtractor.chain.list.ChainList property) StructureVariable (class in lXtractor.variables.base) sub() (lXtractor.core.segment.Segment method) sub_by() (lXtractor.core.segment.Segment method) subset() (lXtractor.core.structure.GenericStructure method) subset_to_matching() (in module lXtractor.chain.structure) summary() (lXtractor.chain.chain.Chain method) (lXtractor.chain.list.ChainList method) (lXtractor.chain.sequence.ChainSequence method) (lXtractor.chain.structure.ChainStructure method) (lXtractor.core.ligand.Ligand method) superpose() (lXtractor.chain.structure.ChainStructure method) (lXtractor.core.structure.GenericStructure method) superpose_pair() (in module lXtractor.protocols.superpose) superpose_pairwise() (in module lXtractor.protocols.superpose) SuperposeOutput (class in lXtractor.protocols.superpose) supported_seq_ext (lXtractor.chain.initializer.ChainInitializer property) supported_str_ext (lXtractor.chain.initializer.ChainInitializer property) supported_str_formats (lXtractor.ext.base.StructureApiBase property) (lXtractor.ext.pdb_.PDB property) SupportsAnnotate (class in lXtractor.ext.base) SupportsWrite (class in lXtractor.core.base)

T

temporary_namespace() (lXtractor.core.config.Config method) to_graph() (in module lXtractor.util.structure) tolerate_failures (lXtractor.chain.io.ChainIO attribute) (lXtractor.chain.io.ChainIOConfig attribute)

topo_iter() (in module lXtractor.chain.base) transfer_seq_mapping() (lXtractor.chain.chain.Chain method) transform() (lXtractor.variables.sequential.SliceTransformReduce static method) Transformation (lXtractor.protocols.superpose.SuperposeOutput attribute) translate_definition() (in module lXtractor.core.pocket)

U

UniProt (class in lXtractor.ext.uniprot) uniprot_ids (lXtractor.ext.sifts.SIFTS property) UNK (lXtractor.core.config.AtomMark attribute) unk (lXtractor.core.structure.Masks attribute) update_with() (lXtractor.core.config.Config method)

url_args (lXtractor.ext.base.ApiBase property) url_getters (lXtractor.ext.base.ApiBase attribute) url_getters() (in module lXtractor.ext.pdb_) (in module lXtractor.ext.uniprot) url_names (lXtractor.ext.base.ApiBase property) UrlGetter (class in lXtractor.core.base)

V

valgroup() (in module lXtractor.util.misc) valid_exceptions (lXtractor.variables.calculator.GenericCalculator attribute) Variables (class in lXtractor.variables.base) variables (lXtractor.chain.structure.ChainStructure attribute) (lXtractor.core.segment.Segment attribute) verbose (lXtractor.chain.io.ChainIO attribute) (lXtractor.chain.io.ChainIOConfig attribute) (lXtractor.ext.base.ApiBase attribute) (lXtractor.variables.calculator.GenericCalculator attribute) (lXtractor.variables.manager.Manager attribute)

vmap() (lXtractor.variables.base.AbstractCalculator method) (lXtractor.variables.calculator.GenericCalculator method)

W

wrap_into_segments() (in module lXtractor.ext.sifts) write() (lXtractor.chain.chain.Chain method) (lXtractor.chain.io.ChainIO method) (lXtractor.chain.sequence.ChainSequence method) (lXtractor.chain.structure.ChainStructure method) (lXtractor.core.alignment.Alignment method) (lXtractor.core.base.SupportsWrite method) (lXtractor.core.structure.GenericStructure method) (lXtractor.variables.base.Variables method)

write_fasta() (in module lXtractor.util.seq) write_meta() (lXtractor.chain.sequence.ChainSequence method) write_seq() (lXtractor.chain.sequence.ChainSequence method)