rdkit.Chem.fmcs package

Submodules

• rdkit.Chem.fmcs.fmcs module
  • Atom
    • Atom.atom_smarts
    • Atom.bond_indices
    • Atom.is_in_ring
    • Atom.real_atom
  • AtomSmartsNoAromaticity
  • Bond
    • Bond.atom_indices
    • Bond.bond_smarts
    • Bond.canonical_bondtype
    • Bond.is_in_ring
    • Bond.real_bond
  • CachingTargetsMatcher
    • CachingTargetsMatcher.shift_targets()
  • CangenNode
    • CangenNode.atom_smarts
    • CangenNode.index
    • CangenNode.neighbors
    • CangenNode.outgoing_edges
    • CangenNode.rank
    • CangenNode.value
  • Default
    • Default.atomCompare
    • Default.bondCompare
    • Default.completeRingsOnly
    • Default.matchValences
    • Default.maximize
    • Default.ringMatchesRingOnly
    • Default.timeout
    • Default.timeoutString
  • DirectedEdge
    • DirectedEdge.bond_index
    • DirectedEdge.end_atom_index
  • EnumerationMolecule
  • FragmentedTypedMolecule
  • MATCH()
  • MCSResult
  • OutgoingEdge
    • OutgoingEdge.bond_index
    • OutgoingEdge.bond_smarts
    • OutgoingEdge.from_atom_index
    • OutgoingEdge.other_node
    • OutgoingEdge.other_node_idx
  • SingleBestAtoms
    • SingleBestAtoms.add_new_match()
  • SingleBestAtomsCompleteRingsOnly
    • SingleBestAtomsCompleteRingsOnly.add_new_match()
  • SingleBestBonds
    • SingleBestBonds.add_new_match()
  • SingleBestBondsCompleteRingsOnly
    • SingleBestBondsCompleteRingsOnly.add_new_match()
  • Subgraph
    • Subgraph.atom_indices
    • Subgraph.bond_indices
  • Timer
    • Timer.mark()
  • TypedFragment
  • TypedMolecule
  • Uniquer
  • VerboseCachingTargetsMatcher
    • VerboseCachingTargetsMatcher.report()
    • VerboseCachingTargetsMatcher.shift_targets()
  • VerboseHeapOps
    • VerboseHeapOps.heappop()
    • VerboseHeapOps.heappush()
    • VerboseHeapOps.report()
    • VerboseHeapOps.trigger_report()
  • all_subgraph_extensions()
  • assign_isotopes_from_class_tag()
  • atom_typer_any()
  • atom_typer_elements()
  • atom_typer_isotopes()
  • bond_typer_any()
  • bond_typer_bondtypes()
  • canon()
  • check_completeRingsOnly()
  • compute_mcs()
  • convert_input_to_typed_molecules()
  • default_atom_typer()
  • default_bond_typer()
  • enumerate_subgraphs()
  • find_duplicates()
  • find_extension_size()
  • find_extensions()
  • find_upper_fragment_size_limits()
  • fmcs()
  • fragmented_mol_to_enumeration_mols()
  • gen_primes()
  • generate_smarts()
  • get_canonical_bondtype_counts()
  • get_canonical_bondtypes()
  • get_closure_label()
  • get_counts()
  • get_initial_cangen_nodes()
  • get_isotopes()
  • get_selected_atom_classes()
  • get_specified_types()
  • get_typed_fragment()
  • get_typed_molecule()
  • intersect_counts()
  • main()
  • make_arbitrary_smarts()
  • make_canonical_smarts()
  • make_complete_sdf()
  • make_fragment_sdf()
  • make_fragment_smiles()
  • make_structure_format()
  • nonempty_powerset()
  • parse_num_atoms()
  • parse_select()
  • parse_threshold()
  • parse_timeout()
  • powerset()
  • prune_maximize_atoms()
  • prune_maximize_bonds()
  • remove_unknown_bondtypes()
  • rerank()
  • restore_isotopes()
  • save_atom_classes()
  • save_isotopes()
  • set_isotopes()
  • starting_from
  • subgraph_to_fragment()
  • tiebreaker()

Module contents

Actual implementation of the FMCS algorithm This code should be used by importing rdkit.Chem.MCS