├── .dockerignore ├── .gitignore ├── Dockerfile ├── LICENSE ├── Lilly_Medchem_Rules.rb ├── Makefile ├── Molecule ├── ISIS_Atom_List.cc ├── Makefile ├── aromatic.cc ├── aromatic.h ├── atom.cc ├── atom.h ├── atom_alias.cc ├── atom_alias.h ├── bond.cc ├── bond.h ├── bond_list.cc ├── bond_list.h ├── careful_frag.cc ├── careful_frag.h ├── charge_assigner.cc ├── charge_assigner.h ├── charge_calculation.h ├── chiral_centre.cc ├── chiral_centre.h ├── cis_trans_bond.cc ├── cis_trans_bond.h ├── collection_template.h ├── coordinates.cc ├── coordinates.h ├── csubstructure.cc ├── demerit.cc ├── demerit.h ├── dihedral.cc ├── dihedral.h ├── donor_acceptor.cc ├── donor_acceptor.h ├── element.cc ├── element.h ├── element_hits_needed.cc ├── ematch.cc ├── ematch.h ├── etrans.cc ├── etrans.h ├── frag.cc ├── is_actually_chiral.cc ├── is_actually_chiral.h ├── isis_link_atom.cc ├── istream_and_type.h ├── iwdemerit.cc ├── iwmtypes.h ├── iwqry_wstats.cc ├── iwrcb.cc ├── iwrcb.h ├── iwrnm.cc ├── iwrnm.h ├── iwstandard.h ├── iwsubstructure.cc ├── jibomolecule.h ├── mc_first_pass.cc ├── mc_summarise.cc ├── mdl.cc ├── mdl.h ├── mdl_atom_record.cc ├── mdl_atom_record.h ├── mdl_file_data.cc ├── mdl_file_data.h ├── mdl_molecule.cc ├── mdl_molecule.h ├── mdl_v30.cc ├── misc2.cc ├── misc2.h ├── molecule.cc ├── molecule.h ├── molecule_arom.h ├── molecule_ctb.h ├── molecule_main.h ├── molecule_marvin.h ├── molecule_mdl.h ├── molecule_smarts.cc ├── molecule_smarts.h ├── molecule_smi.h ├── molecule_to_query.cc ├── molecule_to_query.h ├── molecule_tripos.h ├── moleculeb.cc ├── moleculed.cc ├── moleculed.h ├── moleculeh.cc ├── moleculeh.h ├── moleculer.cc ├── numass.cc ├── numass.h ├── ostream_and_type.cc ├── ostream_and_type.h ├── output.cc ├── output.h ├── parse_smarts_tmp.cc ├── parse_smarts_tmp.h ├── path.cc ├── path.h ├── path_scoring.cc ├── path_scoring.h ├── pearlman.cc ├── pearlman.h ├── qry_and_demerit.h ├── qry_wstats.h ├── readmdl.h ├── ring_bond_iterator.cc ├── rmele.cc ├── rmele.h ├── rwmolecule.cc ├── rwmolecule.h ├── rwsubstructure.cc ├── rwsubstructure.h ├── set_of_atoms.cc ├── set_of_atoms.h ├── skeleton.cc ├── smi.cc ├── smiles.cc ├── smiles.h ├── smiles_support.cc ├── space_vector.h ├── ss_atom_env.cc ├── ss_bonds.cc ├── ss_ring.cc ├── ss_ring_base.cc ├── ss_ring_sys.cc ├── standardise.cc ├── substructure.h ├── substructure_a.cc ├── substructure_chiral.cc ├── substructure_demerits.cc ├── substructure_demerits.h ├── substructure_env.cc ├── substructure_nmab.cc ├── substructure_results.cc ├── substructure_spec.cc ├── symm_class_can_rank.cc ├── target.cc ├── target.h ├── temp_detach_atoms.cc ├── temp_detach_atoms.h ├── tmpsmi.h ├── tmpsssr.h ├── toggle_kekule_form.cc ├── toggle_kekule_form.h ├── tokenise_atomic_smarts.cc ├── tokenise_atomic_smarts.h ├── tsmiles.cc ├── tsubstructure.cc └── unique.cc ├── NEWS.md ├── README.md ├── README_Docker.md ├── README_cygwin.md ├── README_ubuntu.md ├── charge_assigner ├── 4_amino_pyridine.qry ├── N_acylpyrazolidinone.qry ├── N_acylsulfonamide.qry ├── acid.qry ├── aliphatic_amine_restricted.qry ├── amidine.qry ├── amino_terminal_restricted.qry ├── carboxylic_acid.qry ├── guanidine.qry ├── imidazole_basic.qry ├── negative ├── phenolate.qry ├── phosphonate.qry ├── positive ├── pyrazolidinone.qry ├── queries ├── sulfonic_acid.qry ├── tetrazole.qry └── thiazolidinedione.qry ├── doc_support ├── Wikipedia_WikiProject_Pharmacology_Top_200_US_Prescriptions_2011.csv └── table_S3.csv ├── documentation.md ├── include ├── accumulator.h ├── cmdline.h ├── grep-2.5.config.h ├── grep-2.5.posix.regex.h ├── grep-2.5.regex.h ├── iw_auto_array.h ├── iw_stl_hash_map.h ├── iw_stl_hash_multimap.h ├── iw_stl_hash_set.h ├── iw_tdt.h ├── iwaray.h ├── iwarchive.h ├── iwbits.h ├── iwconfig.h ├── iwcrex.h ├── iwgrep-2.5.h ├── iwhash.h ├── iwlregex.h ├── iwminmax.h ├── iwqsort.h ├── iwrandom.h ├── iwstring.h ├── iwstring_data_source.h ├── iwzlib.h ├── kahan_sum.h ├── logical_expression.h ├── minmaxspc.h ├── misc.h ├── msi_object.h ├── mtrand.h ├── new_array_.h ├── primes.h ├── report_progress.h ├── set_or_unset.h ├── string_data_source.h └── timsort.hpp ├── preamble ├── queries ├── 3_valent_halogen.qry ├── 4_valent_sulphur_2_connections.qry ├── 4amino_pyrazole.qry ├── 6_membered_aromatic_sulfur.qry ├── 8_aminoquinoline.qry ├── 8_hydroxyquinoline.qry ├── 9_aminoacridine.qry ├── O_alkyl_hydroxylamine.qry ├── acetal_1_in_ring.qry ├── acetal_acyclic.qry ├── acetal_both_in_ring.qry ├── acetate_ester.qry ├── acetylene.qry ├── acetylene_heteroatom.qry ├── acid_halide.qry ├── activated_ester.qry ├── activated_phthalimide.qry ├── acyl_amide_acyclic.qry ├── acyl_amide_cyclic.qry ├── acyl_arom_n.qry ├── acyl_aromatic_nn.qry ├── acyl_enol.qry ├── acyl_hydrazone_cyclic.qry ├── acyl_hydroxamate.qry ├── acyl_hydroxamate_2.qry ├── acyl_hydroxamate_3.qry ├── acyl_isoamide_aromatic.qry ├── acyl_oxime.qry ├── acyl_sulfonamide.qry ├── acyl_thiohydroxamate.qry ├── acylated_enol.qry ├── acylated_halo_phenol.qry ├── acylurea.qry ├── adamantane.qry ├── adamantane_sub.qry ├── aldehyde.qry ├── alkyl_fluoride_activated.qry ├── alkyl_iodide.qry ├── alkyl_sulfite.qry ├── alkylthio_N_aromatic.qry ├── alkyne_michael.qry ├── alkynylsulfone.qry ├── allene.qry ├── aminal_acyclic.qry ├── amino_ester.qry ├── amino_naphthalene.qry ├── aminomethyl_ketone_peptide.qry ├── aminophenol.qry ├── anhydride.qry ├── aniline_acyl_ewd.qry ├── aniline_acyl_newd.qry ├── aniline_h_ewd.qry ├── aniline_h_newd.qry ├── aniline_no_h_ewd.qry ├── aniline_no_h_newd.qry ├── anthra_ketone.qry ├── anthracene_het.qry ├── anthracene_phenanthrene.qry ├── aromatic_iodide.qry ├── azapteridine.qry ├── aziridine.qry ├── benzocyclopentenone.qry ├── beta_lactone.qry ├── biguanide.qry ├── biotin.qry ├── bis_aryl_maleimide.qry ├── boc.qry ├── bromine.qry ├── catechol.qry ├── ccl3.qry ├── cf3.qry ├── charged_halide.qry ├── chlorine.qry ├── conjugated_triene_acyclic_2.qry ├── coumarin.qry ├── cplus.qry ├── crown_2_2_acyclic.qry ├── crown_2_2_cyclic.qry ├── crown_2_3_acyclic.qry ├── crown_2_3_cyclic.qry ├── crown_3_3_acyclic.qry ├── crown_3_3_cyclic.qry ├── cyanine_dye.qry ├── cyano.qry ├── cyano_amine.qry ├── cyano_methyl_amine.qry ├── cyano_methyl_sulfide.qry ├── cyanohydrin.qry ├── cyclobutadiene.qry ├── cyclohexane.qry ├── demerits ├── di_thio_acetal_acyclic.qry ├── diacylhydrazide.qry ├── dialkylsulfate_cyclic.qry ├── diamidine.qry ├── diaminal_acyclic.qry ├── diazo_cyclic.qry ├── dicyanomethylene.qry ├── dienone.qry ├── dihalo_vinyl_1_2_dicarbonyl.qry ├── dihydro_124_triazine.qry ├── dihydro_pyrrolidone.qry ├── dinitro_methyl.qry ├── diphosphate.qry ├── dithio_olefin.qry ├── divinyl_carbonyl.qry ├── dna_intercalator_1.qry ├── enamine.qry ├── enamine_2.qry ├── enol_or_vinyl_ether.qry ├── ester.qry ├── ester_thione.qry ├── f2_c_o2.qry ├── five_connected_n_or_p.qry ├── five_valent_nitrogen.qry ├── fluorine.qry ├── fluoro_methyl_ketone.qry ├── fmoc.qry ├── formylated.qry ├── four_valent_s_h.qry ├── four_valent_sulphur.qry ├── fulvene.qry ├── furan.qry ├── fused_tetrahydroquinoline.qry ├── half_sulfur_peroxide.qry ├── halo_imine.qry ├── halo_next_to_aryl_n_w_ewg.qry ├── halo_phthalazine.qry ├── halogen_nps.qry ├── halogen_to_oxygen.qry ├── halogenated_aromatic.qry ├── halogenated_ring_system.qry ├── halomethyl_ketone.qry ├── hemiacetal_acyclic.qry ├── hemiaminal.qry ├── het_3mem_ring.qry ├── het_3mem_ring_fused.qry ├── hydrazide.qry ├── hydrazide_acyclic.qry ├── hydrazide_cyclic.qry ├── hydrazone.qry ├── iminal.qry ├── imine_aromatic.qry ├── imino_oxime.qry ├── isoamide_acyclic.qry ├── isocyano.qry ├── isodithiocarbamate.qry ├── isolated_aromatic.qry ├── isothiazole_carbonyl.qry ├── isothioamide_cyclic.qry ├── isothioamide_cyclicS.qry ├── isothiourea.qry ├── isothiourea_sulfonamide.qry ├── keto_carbonyl.qry ├── ketoamide_cyclic.qry ├── lucifer_yellow.qry ├── melamine.qry ├── menthol.qry ├── metanitro.qry ├── methylene_bis_sulfone.qry ├── methylene_bis_sulfone_diaryl.qry ├── michael_demerited.qry ├── michael_rejected.qry ├── michael_thione.qry ├── multiple_nitro.qry ├── n_double_s_double_n_ring.qry ├── n_hydroxy.qry ├── n_o_acyclic.qry ├── n_oxide.qry ├── n_s_acyclic.qry ├── naphthalene_singly_connected.qry ├── naphthalene_sulfonate.qry ├── naphthyl.qry ├── ncn.qry ├── nitro.qry ├── nitro_aliphatic.qry ├── nitro_alpha_hetero.qry ├── nitro_alpha_to_halogen.qry ├── nitro_phenol_or_aniline.qry ├── nitromethyl_sulfone.qry ├── nitrone.qry ├── nitrosamine.qry ├── nitroso.qry ├── nitrous_ester.qry ├── nitroxide.qry ├── nitroxyl.qry ├── no_rings.qry ├── non_ring_ketal.qry ├── nso_2.qry ├── o_or_s_plus.qry ├── orthonitropyridine.qry ├── oxime.qry ├── oxiridine.qry ├── penicillin_cephalosporin.qry ├── perchlorate.qry ├── perimidine.qry ├── peroxide.qry ├── phenanthrene_het.qry ├── phenol_phosphate_ester.qry ├── phenolate.qry ├── phenolic_ester_or_carbamate.qry ├── phenylenediamine.qry ├── phosphate_ester.qry ├── phosphoric_acid.qry ├── phthalimide.qry ├── po4.qry ├── polyphenol.qry ├── pyridazine_dione.qry ├── pyrrole.qry ├── pyrrole_vinylidene.qry ├── quat_n_heteroatom.qry ├── quat_schiff_base.qry ├── quaternary_amine.qry ├── quaternary_aryl.qry ├── queries ├── quinone_methide.qry ├── quinone_para.qry ├── reject1 ├── reject2 ├── reverse_michael.qry ├── reverse_michael_demerit.qry ├── reverse_michael_quat.qry ├── rhodanine.qry ├── ring_system_too_large.qry ├── ring_system_too_large_with_aromatic.qry ├── s_4_single_bonds.qry ├── scf3.qry ├── sch2s.qry ├── schiff_base.qry ├── scscs.qry ├── so.qry ├── ss.qry ├── steve1.qry ├── strongly_fused_ring_system.qry ├── sulfimine.qry ├── sulfonamide_methylene_sulfone.qry ├── sulfonic_acid.qry ├── sulfonium.qry ├── sulfonyl_ester.qry ├── sulfonyl_halide.qry ├── sulfonyl_hydrazone.qry ├── sulfonyl_imine.qry ├── sulfonyl_n_aromatic_edg.qry ├── sulfonyl_n_aromatic_nedg.qry ├── sulfonyl_urea.qry ├── sulfonylmichael.qry ├── sulfoxide_imine.qry ├── tbutyl.qry ├── thio_aminal_acyclic.qry ├── thio_ester_thione_acyclic.qry ├── thio_ester_thione_cyclic.qry ├── thio_oxime.qry ├── thioacetal_acyclic.qry ├── thioaminal_C_cyclic.qry ├── thioaminal_n_sub_cyclic_2.qry ├── thioaminal_n_unsub_cyclic_2.qry ├── thiocarbonyl_aromatic.qry ├── thiocarbonyl_diester.qry ├── thiocyanate.qry ├── thioester.qry ├── thioester_acyclic.qry ├── thioester_acyclic_aliphatic.qry ├── thioester_acyclic_aromatic.qry ├── thioester_cyclic.qry ├── thiohydrazide.qry ├── thiol.qry ├── thiomethyl_ketone.qry ├── thione.qry ├── thione_oxide.qry ├── thiophene_furan_n_acyl.qry ├── thiophene_furan_nh.qry ├── thiourea.qry ├── too_many_aromatic_rings_in_ring_system.qry ├── too_many_sulfonate.qry ├── too_many_sulphur.qry ├── triflate.qry ├── trifluoroacetate_ester.qry ├── trifluoroborate.qry ├── triphenylmethyl.qry ├── trivalent_phosphorus.qry ├── tropolone.qry ├── unsat_n_plus.qry ├── vinyl_cyano_2.qry ├── vinyl_cyano_het.qry ├── vinyl_disulfide.qry ├── vinyl_disulfone.qry ├── vinyl_disulfur.qry ├── vinyl_ether.qry ├── vinyl_ether_thioate_isoamide.qry ├── vinyl_halide_2_halogens.qry ├── vinyl_halide_3_halogens.qry ├── vinyl_nitro.qry ├── vinyl_sulfone_2.qry ├── vinyl_sulfone_3.qry ├── vinyl_sulfoxide.qry ├── vinyl_sulphide.qry └── vinyl_thioether.qry ├── ruby ├── bindir.rb └── iwcmdline.rb ├── run_from_docker_image.sh ├── supporting_libraries ├── IWString_class.cc ├── KahanSum.cc ├── Makefile ├── _extending_resizable_array_int.cc ├── bits_in_common.c ├── cmdline.cc ├── dash_f.cc ├── du_bin2ascii.cc ├── dy_fingerprint.h ├── grep-2.5.regex.c ├── int_comparator.cc ├── iw_stl_hash_map.cc ├── iw_tdt.cc ├── iwbits.cc ├── iwbits_support.h ├── iwgrep-2.5.cc ├── iwmmap.cc ├── iwmmap.h ├── iwstring.cc ├── iwstring_and_file_descriptor.cc ├── iwstring_data_source.cc ├── iwstrncasecmp.cc ├── iwwrite.cc ├── iwwrite_block.cc ├── iwzlib.cc ├── logical_expression.cc ├── msi_object.cc ├── mtrand.cc ├── new_int.cc ├── precompbit.h ├── should_match.cc ├── should_match.h ├── string_data_source.cc ├── tsclass.cc └── 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