lXtractor package

• lXtractor.core package
  • lXtractor.core.alignment module
    • Alignment
      • Alignment.__init__()
      • Alignment.add()
      • Alignment.align()
      • Alignment.annotate()
      • Alignment.filter()
      • Alignment.filter_gaps()
      • Alignment.itercols()
      • Alignment.make()
      • Alignment.map()
      • Alignment.read()
      • Alignment.read_make()
      • Alignment.realign()
      • Alignment.remove()
      • Alignment.slice()
      • Alignment.write()
      • Alignment.add_method
      • Alignment.align_method
      • Alignment.seqs
      • Alignment.shape
  • lXtractor.core.base module
    • AbstractResource
      • AbstractResource.__init__()
      • AbstractResource.dump()
      • AbstractResource.fetch()
      • AbstractResource.parse()
      • AbstractResource.read()
    • AddMethod
      • AddMethod.__call__()
      • AddMethod.__init__()
    • AlignMethod
      • AlignMethod.__call__()
      • AlignMethod.__init__()
    • ApplyT
      • ApplyT.__call__()
      • ApplyT.__init__()
    • ApplyTWithArgs
      • ApplyTWithArgs.__call__()
      • ApplyTWithArgs.__init__()
    • FilterT
      • FilterT.__call__()
      • FilterT.__init__()
    • NamedTupleT
      • NamedTupleT.__init__()
    • Ord
      • Ord.__init__()
    • ResNameDict
      • ResNameDict.__init__()
    • SeqFilter
      • SeqFilter.__call__()
      • SeqFilter.__init__()
    • SeqMapper
      • SeqMapper.__call__()
      • SeqMapper.__init__()
    • SeqReader
      • SeqReader.__call__()
      • SeqReader.__init__()
    • SeqWriter
      • SeqWriter.__call__()
      • SeqWriter.__init__()
    • SupportsLT
      • SupportsLT.__init__()
    • SupportsWrite
      • SupportsWrite.__init__()
      • SupportsWrite.write()
    • UrlGetter
      • UrlGetter.__call__()
      • UrlGetter.__init__()
  • lXtractor.core.config module
    • AtomMark
      • AtomMark.CARB
      • AtomMark.COVALENT
      • AtomMark.LIGAND
      • AtomMark.NUC
      • AtomMark.PEP
      • AtomMark.SOLVENT
      • AtomMark.UNK
    • Config
      • Config.__init__()
      • Config.clear_user_config()
      • Config.reload()
      • Config.reset_to_defaults()
      • Config.save()
      • Config.temporary_namespace()
      • Config.update_with()
    • serialize_json_value()
  • lXtractor.core.exceptions module
    • AmbiguousData
    • AmbiguousMapping
    • ConfigError
    • FailedCalculation
    • FormatError
    • InitError
    • LengthMismatch
    • MissingData
    • NoOverlap
    • OverlapError
    • ParsingError
  • lXtractor.core.segment module
    • Segment
      • Segment.__init__()
      • Segment.add_seq()
      • Segment.append()
      • Segment.bounded_by()
      • Segment.bounds()
      • Segment.id_strip_parents()
      • Segment.insert()
      • Segment.overlap()
      • Segment.overlap_with()
      • Segment.overlaps()
      • Segment.remove_seq()
      • Segment.sub()
      • Segment.sub_by()
      • Segment.children
      • Segment.end
      • Segment.id
      • Segment.is_empty
      • Segment.is_singleton
      • Segment.item_type
      • Segment.meta
      • Segment.name
      • Segment.parent
      • Segment.seq_names
      • Segment.start
      • Segment.variables
    • do_overlap()
    • map_segment_numbering()
    • resolve_overlaps()
    • segments2graph()
  • lXtractor.core.structure module
    • CarbohydrateStructure
      • CarbohydrateStructure.__init__()
    • GenericStructure
      • GenericStructure.__init__()
      • GenericStructure.extract_positions()
      • GenericStructure.extract_segment()
      • GenericStructure.get_sequence()
      • GenericStructure.make_empty()
      • GenericStructure.read()
      • GenericStructure.rm_solvent()
      • GenericStructure.split_altloc()
      • GenericStructure.split_chains()
      • GenericStructure.subset()
      • GenericStructure.superpose()
      • GenericStructure.write()
      • GenericStructure.altloc_ids
      • GenericStructure.array
      • GenericStructure.atom_marks
      • GenericStructure.chain_ids
      • GenericStructure.chain_ids_ligand
      • GenericStructure.chain_ids_polymer
      • GenericStructure.graph
      • GenericStructure.id
      • GenericStructure.is_empty
      • GenericStructure.is_empty_polymer
      • GenericStructure.is_singleton
      • GenericStructure.ligands
      • GenericStructure.mask
      • GenericStructure.name
    • Masks
      • Masks.__init__()
      • Masks.ligand
      • Masks.ligand_carb
      • Masks.ligand_covalent
      • Masks.ligand_nonpoly
      • Masks.ligand_nuc
      • Masks.ligand_pep
      • Masks.ligand_poly
      • Masks.primary_polymer
      • Masks.primary_polymer_modified
      • Masks.primary_polymer_ptm
      • Masks.solvent
      • Masks.unk
    • NucleotideStructure
      • NucleotideStructure.__init__()
    • ProteinStructure
      • ProteinStructure.__init__()
    • mark_atoms()
    • mark_atoms_g()
  • lXtractor.core.ligand module
    • Ligand
      • Ligand.__init__()
      • Ligand.is_locally_connected()
      • Ligand.summary()
      • Ligand.array
      • Ligand.chain_id
      • Ligand.contact_mask
      • Ligand.dist
      • Ligand.id
      • Ligand.is_polymer
      • Ligand.ligand_idx
      • Ligand.mask
      • Ligand.meta
      • Ligand.parent
      • Ligand.parent_contact_atoms
      • Ligand.parent_contact_chains
      • Ligand.res_id
      • Ligand.res_name
    • ligands_from_atom_marks()
    • make_ligand()
  • lXtractor.core.pocket module
    • Pocket
      • Pocket.__init__()
      • Pocket.is_connected()
      • Pocket.definition
      • Pocket.name
    • make_sel()
    • translate_definition()
  • lXtractor.core.interface module
    • AtomNode
      • AtomNode.__init__()
      • AtomNode.atom
      • AtomNode.has_edge
      • AtomNode.idx
    • ContactEdge
      • ContactEdge.__init__()
      • ContactEdge.from_node_indices()
      • ContactEdge.atom_a
      • ContactEdge.atom_b
      • ContactEdge.dist
    • Interface
      • Interface.__init__()
      • Interface.count_contact_atoms()
      • Interface.count_contact_residues()
      • Interface.count_contacts()
      • Interface.get_contact_atoms()
      • Interface.get_contact_atoms_mask()
      • Interface.get_contact_idx()
      • Interface.get_contact_idx_a()
      • Interface.get_contact_idx_b()
      • Interface.iter_ccs()
      • Interface.read()
      • Interface.sasa()
      • Interface.split_connected()
      • Interface.write()
      • Interface.G
      • Interface.id
      • Interface.mask_a
      • Interface.mask_b
      • Interface.parent_structure
      • Interface.partners_a
      • Interface.partners_b
      • Interface.partners_fmt
      • Interface.partners_joined
    • InterfaceComparator
      • InterfaceComparator.__init__()
      • InterfaceComparator.are_comparable()
      • InterfaceComparator.dockq()
      • InterfaceComparator.fnat()
      • InterfaceComparator.irmsd()
      • InterfaceComparator.lrmsd()
      • InterfaceComparator.rmsd_over()
      • InterfaceComparator.state_mob
      • InterfaceComparator.state_ref
      • InterfaceComparator.superpose_by
      • InterfaceComparator.superposed_mob
      • InterfaceComparator.superposed_rmsd
      • InterfaceComparator.transformation
    • InterfaceSASA
      • InterfaceSASA.__init__()
      • InterfaceSASA.as_record()
      • InterfaceSASA.a_complex
      • InterfaceSASA.a_free
      • InterfaceSASA.b_complex
      • InterfaceSASA.b_free
      • InterfaceSASA.bsa_a
      • InterfaceSASA.bsa_b
      • InterfaceSASA.bsa_complex
      • InterfaceSASA.complex
    • RetainCondition
      • RetainCondition.__call__()
      • RetainCondition.__init__()
      • RetainCondition.apply()
      • RetainCondition.min_atoms
      • RetainCondition.min_res
      • RetainCondition.selector
    • filter_edges_by_nodes()
    • parse_partner()
    • residue_count_disjoint()
    • split_atoms_by_chains()
• lXtractor.chain package
  • lXtractor.chain.base module
    • is_chain_type()
    • is_chain_type_iterable()
    • topo_iter()
  • lXtractor.chain.sequence module
    • ChainSequence
      • ChainSequence.apply_children()
      • ChainSequence.apply_to_map()
      • ChainSequence.as_chain()
      • ChainSequence.as_df()
      • ChainSequence.as_np()
      • ChainSequence.coverage()
      • ChainSequence.fill()
      • ChainSequence.filter_children()
      • ChainSequence.from_df()
      • ChainSequence.from_file()
      • ChainSequence.from_string()
      • ChainSequence.from_tuple()
      • ChainSequence.get_closest()
      • ChainSequence.get_item()
      • ChainSequence.get_map()
      • ChainSequence.iter_children()
      • ChainSequence.make_empty()
      • ChainSequence.map_boundaries()
      • ChainSequence.map_numbering()
      • ChainSequence.match()
      • ChainSequence.patch()
      • ChainSequence.read()
      • ChainSequence.relate()
      • ChainSequence.rename()
      • ChainSequence.spawn_child()
      • ChainSequence.summary()
      • ChainSequence.write()
      • ChainSequence.write_meta()
      • ChainSequence.write_seq()
      • ChainSequence.categories
      • ChainSequence.fields
      • ChainSequence.numbering
      • ChainSequence.seq
      • ChainSequence.seq1
      • ChainSequence.seq3
    • map_numbering_12many()
    • map_numbering_many2many()
  • lXtractor.chain.structure module
    • ChainStructure
      • ChainStructure.__init__()
      • ChainStructure.apply_children()
      • ChainStructure.filter_children()
      • ChainStructure.iter_children()
      • ChainStructure.make_empty()
      • ChainStructure.read()
      • ChainStructure.rm_solvent()
      • ChainStructure.spawn_child()
      • ChainStructure.summary()
      • ChainStructure.superpose()
      • ChainStructure.write()
      • ChainStructure.altloc
      • ChainStructure.array
      • ChainStructure.categories
      • ChainStructure.chain_id
      • ChainStructure.children
      • ChainStructure.end
      • ChainStructure.id
      • ChainStructure.is_empty
      • ChainStructure.ligands
      • ChainStructure.meta
      • ChainStructure.name
      • ChainStructure.parent
      • ChainStructure.seq
      • ChainStructure.start
      • ChainStructure.structure
      • ChainStructure.variables
    • filter_selection_extended()
    • subset_to_matching()
  • lXtractor.chain.chain module
    • Chain
      • Chain.__init__()
      • Chain.add_structure()
      • Chain.apply_children()
      • Chain.apply_structures()
      • Chain.filter_children()
      • Chain.filter_structures()
      • Chain.generate_patched_seqs()
      • Chain.iter_children()
      • Chain.make_empty()
      • Chain.read()
      • Chain.spawn_child()
      • Chain.summary()
      • Chain.transfer_seq_mapping()
      • Chain.write()
      • Chain.categories
      • Chain.children
      • Chain.end
      • Chain.id
      • Chain.meta
      • Chain.name
      • Chain.parent
      • Chain.seq
      • Chain.start
      • Chain.structures
  • lXtractor.chain.list module
    • ChainList
      • ChainList.__init__()
      • ChainList.apply()
      • ChainList.collapse()
      • ChainList.collapse_children()
      • ChainList.drop_duplicates()
      • ChainList.filter()
      • ChainList.filter_category()
      • ChainList.filter_pos()
      • ChainList.get_level()
      • ChainList.groupby()
      • ChainList.index()
      • ChainList.insert()
      • ChainList.iter_children()
      • ChainList.iter_ids()
      • ChainList.iter_sequences()
      • ChainList.iter_structure_sequences()
      • ChainList.iter_structures()
      • ChainList.sort()
      • ChainList.summary()
      • ChainList.to_fasta()
      • ChainList.categories
      • ChainList.ids
      • ChainList.sequences
      • ChainList.structure_sequences
      • ChainList.structures
    • add_category()
  • lXtractor.chain.io module
    • ChainIO
      • ChainIO.__init__()
      • ChainIO.read()
      • ChainIO.read_chain()
      • ChainIO.read_chain_seq()
      • ChainIO.read_chain_str()
      • ChainIO.write()
      • ChainIO.num_proc
      • ChainIO.tolerate_failures
      • ChainIO.verbose
    • ChainIOConfig
      • ChainIOConfig.__init__()
      • ChainIOConfig.num_proc
      • ChainIOConfig.tolerate_failures
      • ChainIOConfig.verbose
    • read_chains()
  • lXtractor.chain.initializer module
    • ChainInitializer
      • ChainInitializer.__init__()
      • ChainInitializer.from_iterable()
      • ChainInitializer.from_mapping()
      • ChainInitializer.supported_seq_ext
      • ChainInitializer.supported_str_ext
    • ItemCallback
      • ItemCallback.__call__()
      • ItemCallback.__init__()
    • SingletonCallback
      • SingletonCallback.__call__()
      • SingletonCallback.__init__()
  • lXtractor.chain.tree module
    • list_ancestors()
    • list_ancestors_names()
    • make_filled()
    • make_id_tree()
    • recover()
• lXtractor.ext package
  • lXtractor.ext.base module
    • ApiBase
      • ApiBase.__init__()
      • ApiBase.max_trials
      • ApiBase.num_threads
      • ApiBase.url_args
      • ApiBase.url_getters
      • ApiBase.url_names
      • ApiBase.verbose
    • StructureApiBase
      • StructureApiBase.fetch_info()
      • StructureApiBase.fetch_structures()
      • StructureApiBase.supported_str_formats
    • SupportsAnnotate
      • SupportsAnnotate.__init__()
      • SupportsAnnotate.annotate()
    • load_json_callback()
    • parse_structure_callback()
  • lXtractor.ext.hmm module
    • Pfam
      • Pfam.__init__()
      • Pfam.clean()
      • Pfam.dump()
      • Pfam.fetch()
      • Pfam.load_hmm()
      • Pfam.parse()
      • Pfam.read()
      • Pfam.dat_columns
      • Pfam.df
    • PyHMMer
      • PyHMMer.__init__()
      • PyHMMer.align()
      • PyHMMer.annotate()
      • PyHMMer.convert_seq()
      • PyHMMer.from_hmm_collection()
      • PyHMMer.from_msa()
      • PyHMMer.init_pipeline()
      • PyHMMer.search()
      • PyHMMer.hits_
      • PyHMMer.hmm
      • PyHMMer.pipeline
    • digitize_seq()
    • iter_hmm()
  • lXtractor.ext.pdb_ module
    • PDB
      • PDB.__init__()
      • PDB.fetch_obsolete()
      • PDB.supported_str_formats
    • filter_by_method()
    • url_getters()
  • lXtractor.ext.sifts module
    • Mapping
      • Mapping.__init__()
    • SIFTS
      • SIFTS.__init__()
      • SIFTS.dump()
      • SIFTS.fetch()
      • SIFTS.load()
      • SIFTS.map_id()
      • SIFTS.map_numbering()
      • SIFTS.parse()
      • SIFTS.prepare_mapping()
      • SIFTS.read()
      • SIFTS.pdb_chains
      • SIFTS.pdb_ids
      • SIFTS.uniprot_ids
    • wrap_into_segments()
  • lXtractor.ext.uniprot module
    • UniProt
      • UniProt.__init__()
      • UniProt.fetch_info()
      • UniProt.fetch_sequences()
    • fetch_uniprot()
    • make_url()
    • url_getters()
  • lXtractor.ext.dssp module
    • dssp_run()
    • dssp_set_ss_annotation()
    • dssp_to_df()
• lXtractor.util package
  • lXtractor.util.io module
    • fetch_chunks()
    • fetch_iterable()
    • fetch_text()
    • fetch_to_file()
    • fetch_urls()
    • get_dirs()
    • get_files()
    • parse_suffix()
    • path_tree()
    • read_n_col_table()
    • run_sp()
  • lXtractor.util.misc module
    • all_logging_disabled()
    • apply()
    • col2col()
    • get_cpu_count()
    • graph_reindex_nodes()
    • is_empty()
    • is_valid_field_name()
    • json_to_molgraph()
    • molgraph_to_json()
    • valgroup()
  • lXtractor.util.seq module
    • biotite_align()
    • mafft_add()
    • mafft_align()
    • map_pairs_numbering()
    • partition_gap_sequences()
    • read_fasta()
    • remove_gap_columns()
    • write_fasta()
  • lXtractor.util.structure module
    • calculate_dihedral()
    • compare_arrays()
    • compare_coord()
    • extend_residue_mask()
    • filter_any_polymer()
    • filter_ligand()
    • filter_polymer()
    • filter_selection()
    • filter_solvent_extended()
    • filter_to_common_atoms()
    • find_contacts()
    • find_first_polymer_type()
    • find_primary_polymer_type()
    • get_missing_atoms()
    • get_observed_atoms_frac()
    • iter_canonical()
    • iter_residue_masks()
    • load_structure()
    • mark_polymer_type()
    • save_structure()
    • to_graph()
• lXtractor.variables package
  • lXtractor.variables.base module
    • AbstractCalculator
      • AbstractCalculator.__call__()
      • AbstractCalculator.map()
      • AbstractCalculator.vmap()
    • AbstractVariable
      • AbstractVariable.calculate()
      • AbstractVariable.id
      • AbstractVariable.rtype
    • AggFn
      • AggFn.__call__()
      • AggFn.__init__()
    • LigandVariable
      • LigandVariable.calculate()
    • ProtFP
      • ProtFP.__init__()
    • SequenceVariable
      • SequenceVariable.calculate()
    • StructureVariable
      • StructureVariable.calculate()
    • Variables
      • Variables.as_df()
      • Variables.read()
      • Variables.write()
      • Variables.sequence
      • Variables.structure
  • lXtractor.variables.calculator module
    • GenericCalculator
      • GenericCalculator.__call__()
      • GenericCalculator.__init__()
      • GenericCalculator.map()
      • GenericCalculator.vmap()
      • GenericCalculator.apply_kwargs
      • GenericCalculator.num_proc
      • GenericCalculator.valid_exceptions
      • GenericCalculator.verbose
    • calculate()
  • lXtractor.variables.manager module
    • Manager
      • Manager.__init__()
      • Manager.aggregate_from_chains()
      • Manager.aggregate_from_it()
      • Manager.assign()
      • Manager.calculate()
      • Manager.remove()
      • Manager.reset()
      • Manager.stage()
      • Manager.verbose
    • find_structure()
    • get_mapping()
    • stage()
  • lXtractor.variables.parser module
  • lXtractor.variables.sequential module
    • PFP
      • PFP.__init__()
      • PFP.calculate()
      • PFP.i
      • PFP.p
      • PFP.rtype
    • SeqEl
      • SeqEl.__init__()
      • SeqEl.calculate()
      • SeqEl.p
      • SeqEl.rtype
      • SeqEl.seq_name
    • SliceTransformReduce
      • SliceTransformReduce.__init__()
      • SliceTransformReduce.calculate()
      • SliceTransformReduce.reduce()
      • SliceTransformReduce.transform()
      • SliceTransformReduce.seq_name
      • SliceTransformReduce.start
      • SliceTransformReduce.step
      • SliceTransformReduce.stop
    • make_str()
  • lXtractor.variables.structural module
    • AggDist
      • AggDist.__init__()
      • AggDist.calculate()
      • AggDist.key
      • AggDist.p1
      • AggDist.p2
      • AggDist.rtype
    • Chi1
      • Chi1.get_dihedrals()
    • Chi2
      • Chi2.get_dihedrals()
    • ClosestLigandContactsCount
      • ClosestLigandContactsCount.__init__()
      • ClosestLigandContactsCount.calculate()
      • ClosestLigandContactsCount.a
      • ClosestLigandContactsCount.p
      • ClosestLigandContactsCount.rtype
    • ClosestLigandDist
      • ClosestLigandDist.__init__()
      • ClosestLigandDist.calculate()
      • ClosestLigandDist.a
      • ClosestLigandDist.agg_lig
      • ClosestLigandDist.agg_res
      • ClosestLigandDist.p
      • ClosestLigandDist.rtype
    • ClosestLigandNames
      • ClosestLigandNames.__init__()
      • ClosestLigandNames.calculate()
      • ClosestLigandNames.a
      • ClosestLigandNames.p
      • ClosestLigandNames.rtype
    • Contacts
      • Contacts.__init__()
      • Contacts.calculate()
      • Contacts.p
      • Contacts.r
      • Contacts.rtype
    • Dihedral
      • Dihedral.__init__()
      • Dihedral.calculate()
      • Dihedral.a1
      • Dihedral.a2
      • Dihedral.a3
      • Dihedral.a4
      • Dihedral.atoms
      • Dihedral.name
      • Dihedral.p1
      • Dihedral.p2
      • Dihedral.p3
      • Dihedral.p4
      • Dihedral.positions
      • Dihedral.rtype
    • Dist
      • Dist.__init__()
      • Dist.calculate()
      • Dist.a1
      • Dist.a2
      • Dist.com
      • Dist.p1
      • Dist.p2
      • Dist.rtype
    • Omega
      • Omega.__init__()
      • Omega.p
    • Phi
      • Phi.__init__()
      • Phi.p
    • PseudoDihedral
      • PseudoDihedral.__init__()
    • Psi
      • Psi.__init__()
      • Psi.p
    • SASA
      • SASA.__init__()
      • SASA.calculate()
      • SASA.a
      • SASA.p
      • SASA.rtype
• lXtractor.protocols package
  • lXtractor.protocols.superpose module
    • SuperposeOutput
      • SuperposeOutput.Distance
      • SuperposeOutput.ID_fix
      • SuperposeOutput.ID_mob
      • SuperposeOutput.RmsdSuperpose
      • SuperposeOutput.Transformation
    • align_and_superpose_pair()
    • superpose_pair()
    • superpose_pairwise()
• lXtractor.collection package