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
- lXtractor.core.config module
- lXtractor.core.exceptions module
- lXtractor.core.ligand module
- lXtractor.core.pocket module
- 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
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
NucleotideStructure
ProteinStructure
mark_atoms()
mark_atoms_g()
- lXtractor.core.alignment module
- lXtractor.chain package
- lXtractor.chain.base module
- 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
- lXtractor.chain.initializer module
- lXtractor.chain.tree module
- lXtractor.ext package
- lXtractor.util package
- lXtractor.util.io module
- lXtractor.util.misc module
- lXtractor.util.seq module
- 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
- lXtractor.variables.calculator module
- lXtractor.variables.manager module
- lXtractor.variables.parser module
- lXtractor.variables.sequential module
- lXtractor.variables.structural module
- lXtractor.protocols package
- lXtractor.collection package