API Reference

API:

• 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__()
      • 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.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.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.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.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()
      • make_filled()
      • make_obj_tree()
      • make_str_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.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()
      • 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
      • init_var()
      • parse_var()
    • 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