Index

A

add_atom() (chemper.graphs.cluster_graph.ClusterGraph.AtomStorage method) add_bond() (chemper.graphs.cluster_graph.ClusterGraph.BondStorage method) add_mol() (chemper.graphs.cluster_graph.ClusterGraph method) as_smirks() (chemper.graphs.cluster_graph.ClusterGraph method) (chemper.graphs.cluster_graph.ClusterGraph.AtomStorage method) (chemper.graphs.cluster_graph.ClusterGraph.BondStorage method)

atom (chemper.mol_toolkits.adapters.AtomAdapter attribute) Atom (class in chemper.mol_toolkits.cp_openeye) (class in chemper.mol_toolkits.cp_rdk) AtomAdapter (class in chemper.mol_toolkits.adapters) atomic_number() (chemper.mol_toolkits.adapters.AtomAdapter method) (chemper.mol_toolkits.cp_openeye.Atom method) (chemper.mol_toolkits.cp_rdk.Atom method)

B

bond (chemper.mol_toolkits.adapters.BondAdapter attribute) Bond (class in chemper.mol_toolkits.cp_openeye) (class in chemper.mol_toolkits.cp_rdk)

BondAdapter (class in chemper.mol_toolkits.adapters)

C

chemper.graphs.cluster_graph module chemper.mol_toolkits.adapters module chemper.mol_toolkits.cp_openeye module chemper.mol_toolkits.cp_rdk module chemper.smirksify module

cluster_dict (chemper.smirksify.Reducer attribute) ClusterGraph (class in chemper.graphs.cluster_graph) ClusterGraph.AtomStorage (class in chemper.graphs.cluster_graph) ClusterGraph.BondStorage (class in chemper.graphs.cluster_graph) ClusteringError compare_atom() (chemper.graphs.cluster_graph.ClusterGraph.AtomStorage method) compare_bond() (chemper.graphs.cluster_graph.ClusterGraph.BondStorage method) connectivity() (chemper.mol_toolkits.adapters.AtomAdapter method) (chemper.mol_toolkits.cp_openeye.Atom method) (chemper.mol_toolkits.cp_rdk.Atom method) current_smirks (chemper.smirksify.Reducer attribute)

D

degree() (chemper.mol_toolkits.adapters.AtomAdapter method) (chemper.mol_toolkits.cp_openeye.Atom method) (chemper.mol_toolkits.cp_rdk.Atom method)

F

find_pairs() (chemper.graphs.cluster_graph.ClusterGraph method) formal_charge() (chemper.mol_toolkits.adapters.AtomAdapter method) (chemper.mol_toolkits.cp_openeye.Atom method) (chemper.mol_toolkits.cp_rdk.Atom method)

from_smiles() (chemper.mol_toolkits.adapters.MolAdapter class method) (chemper.mol_toolkits.cp_openeye.Mol class method) (chemper.mol_toolkits.cp_rdk.Mol class method)

G

get_atom_by_index() (chemper.mol_toolkits.adapters.MolAdapter method) (chemper.mol_toolkits.cp_openeye.Mol method) (chemper.mol_toolkits.cp_rdk.Mol method) get_atoms() (chemper.mol_toolkits.adapters.BondAdapter method) (chemper.mol_toolkits.adapters.MolAdapter method) (chemper.mol_toolkits.cp_openeye.Bond method) (chemper.mol_toolkits.cp_openeye.Mol method) (chemper.mol_toolkits.cp_rdk.Bond method) (chemper.mol_toolkits.cp_rdk.Mol method) get_bond_by_atoms() (chemper.mol_toolkits.adapters.MolAdapter method) (chemper.mol_toolkits.cp_openeye.Mol method) (chemper.mol_toolkits.cp_rdk.Mol method) get_bond_by_index() (chemper.mol_toolkits.adapters.MolAdapter method) (chemper.mol_toolkits.cp_openeye.Mol method) (chemper.mol_toolkits.cp_rdk.Mol method) get_bonds() (chemper.mol_toolkits.adapters.AtomAdapter method) (chemper.mol_toolkits.adapters.MolAdapter method) (chemper.mol_toolkits.cp_openeye.Atom method) (chemper.mol_toolkits.cp_openeye.Mol method) (chemper.mol_toolkits.cp_rdk.Atom method) (chemper.mol_toolkits.cp_rdk.Mol method)

get_index() (chemper.mol_toolkits.adapters.AtomAdapter method) (chemper.mol_toolkits.adapters.BondAdapter method) (chemper.mol_toolkits.cp_openeye.Atom method) (chemper.mol_toolkits.cp_openeye.Bond method) (chemper.mol_toolkits.cp_rdk.Atom method) (chemper.mol_toolkits.cp_rdk.Bond method) get_molecule() (chemper.mol_toolkits.adapters.AtomAdapter method) (chemper.mol_toolkits.adapters.BondAdapter method) (chemper.mol_toolkits.cp_openeye.Atom method) (chemper.mol_toolkits.cp_openeye.Bond method) (chemper.mol_toolkits.cp_rdk.Atom method) (chemper.mol_toolkits.cp_rdk.Bond method) get_neighbors() (chemper.mol_toolkits.adapters.AtomAdapter method) (chemper.mol_toolkits.cp_openeye.Atom method) (chemper.mol_toolkits.cp_rdk.Atom method) get_order() (chemper.mol_toolkits.adapters.BondAdapter method) (chemper.mol_toolkits.cp_openeye.Bond method) (chemper.mol_toolkits.cp_rdk.Bond method) get_smiles() (chemper.mol_toolkits.adapters.MolAdapter method) (chemper.mol_toolkits.cp_openeye.Mol method) (chemper.mol_toolkits.cp_rdk.Mol method) get_symmetry_funct() (chemper.graphs.cluster_graph.ClusterGraph method)

H

hydrogen_count() (chemper.mol_toolkits.adapters.AtomAdapter method) (chemper.mol_toolkits.cp_openeye.Atom method) (chemper.mol_toolkits.cp_rdk.Atom method)

I

is_aromatic() (chemper.mol_toolkits.adapters.AtomAdapter method) (chemper.mol_toolkits.adapters.BondAdapter method) (chemper.mol_toolkits.cp_openeye.Atom method) (chemper.mol_toolkits.cp_openeye.Bond method) (chemper.mol_toolkits.cp_rdk.Atom method) (chemper.mol_toolkits.cp_rdk.Bond method) is_connected_to() (chemper.mol_toolkits.adapters.AtomAdapter method) (chemper.mol_toolkits.cp_openeye.Atom method) (chemper.mol_toolkits.cp_rdk.Atom method) is_double() (chemper.mol_toolkits.adapters.BondAdapter method) (chemper.mol_toolkits.cp_openeye.Bond method) (chemper.mol_toolkits.cp_rdk.Bond method)

is_ring() (chemper.mol_toolkits.adapters.BondAdapter method) (chemper.mol_toolkits.cp_openeye.Bond method) (chemper.mol_toolkits.cp_rdk.Bond method) is_single() (chemper.mol_toolkits.adapters.BondAdapter method) (chemper.mol_toolkits.cp_openeye.Bond method) (chemper.mol_toolkits.cp_rdk.Bond method) is_triple() (chemper.mol_toolkits.adapters.BondAdapter method) (chemper.mol_toolkits.cp_openeye.Bond method) (chemper.mol_toolkits.cp_rdk.Bond method)

M

make_atom_decorators() (chemper.graphs.cluster_graph.ClusterGraph.AtomStorage method) make_smirks() (chemper.smirksify.SMIRKSifier method) min_ring_size() (chemper.mol_toolkits.adapters.AtomAdapter method) (chemper.mol_toolkits.cp_openeye.Atom method) (chemper.mol_toolkits.cp_rdk.Atom method) module chemper.graphs.cluster_graph chemper.mol_toolkits.adapters chemper.mol_toolkits.cp_openeye chemper.mol_toolkits.cp_rdk chemper.smirksify

mol (chemper.mol_toolkits.adapters.MolAdapter attribute) Mol (class in chemper.mol_toolkits.cp_openeye) (class in chemper.mol_toolkits.cp_rdk) MolAdapter (class in chemper.mol_toolkits.adapters) mols (chemper.smirksify.Reducer attribute) mols_from_file() (in module chemper.mol_toolkits.cp_openeye) mols_from_mol2() (in module chemper.mol_toolkits.cp_rdk)

P

print_smirks() (in module chemper.smirksify)

R

reduce() (chemper.smirksify.SMIRKSifier method) Reducer (class in chemper.smirksify) remove_all_bases() (chemper.smirksify.Reducer method) remove_all_dec_type() (chemper.smirksify.Reducer method) remove_and() (chemper.smirksify.Reducer method) remove_decorator() (chemper.smirksify.Reducer method) remove_one_sub_dec() (chemper.smirksify.Reducer method)

remove_or() (chemper.smirksify.Reducer method) remove_or_atom() (chemper.smirksify.Reducer method) remove_ref() (chemper.smirksify.Reducer method) remove_ref_sub_decs() (chemper.smirksify.Reducer method) ring_connectivity() (chemper.mol_toolkits.adapters.AtomAdapter method) (chemper.mol_toolkits.cp_openeye.Atom method) (chemper.mol_toolkits.cp_rdk.Atom method) run() (chemper.smirksify.Reducer method)

S

set_aromaticity_mdl() (chemper.mol_toolkits.adapters.MolAdapter method) (chemper.mol_toolkits.cp_openeye.Mol method) (chemper.mol_toolkits.cp_rdk.Mol method)

smirks_search() (chemper.mol_toolkits.adapters.MolAdapter method) (chemper.mol_toolkits.cp_openeye.Mol method) (chemper.mol_toolkits.cp_rdk.Mol method) SMIRKSifier (class in chemper.smirksify)

T

types_match_reference() (chemper.smirksify.SMIRKSifier method)

V

valence() (chemper.mol_toolkits.adapters.AtomAdapter method) (chemper.mol_toolkits.cp_openeye.Atom method) (chemper.mol_toolkits.cp_rdk.Atom method)