RubyGems - lazar - Versions diffs - 0.0.7 → 0.0.9 - Mend

lazar 0.0.7 → 0.0.9

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (61) hide show

checksums.yaml +4 -4
data/.gitignore +3 -0
data/README.md +2 -1
data/VERSION +1 -1
data/ext/lazar/extconf.rb +15 -76
data/ext/lazar/rinstall.R +9 -0
data/lazar.gemspec +7 -7
data/lib/classification.rb +5 -78
data/lib/compound.rb +201 -44
data/lib/crossvalidation.rb +224 -121
data/lib/dataset.rb +83 -93
data/lib/error.rb +1 -1
data/lib/experiment.rb +99 -0
data/lib/feature.rb +2 -54
data/lib/lazar.rb +47 -34
data/lib/leave-one-out-validation.rb +205 -0
data/lib/model.rb +131 -76
data/lib/opentox.rb +2 -2
data/lib/overwrite.rb +37 -0
data/lib/physchem.rb +133 -0
data/lib/regression.rb +117 -189
data/lib/rest-client-wrapper.rb +4 -5
data/lib/unique_descriptors.rb +6 -7
data/lib/validation.rb +63 -69
data/test/all.rb +2 -2
data/test/classification.rb +41 -0
data/test/compound.rb +116 -7
data/test/data/LOAEL_log_mg_corrected_smiles.csv +567 -567
data/test/data/LOAEL_log_mmol_corrected_smiles.csv +566 -566
data/test/data/LOAEL_mmol_corrected_smiles.csv +568 -0
data/test/data/batch_prediction.csv +25 -0
data/test/data/batch_prediction_inchi_small.csv +4 -0
data/test/data/batch_prediction_smiles_small.csv +4 -0
data/test/data/hamster_carcinogenicity.json +3 -0
data/test/data/loael.csv +568 -0
data/test/dataset-long.rb +5 -8
data/test/dataset.rb +31 -11
data/test/default_environment.rb +11 -0
data/test/descriptor.rb +26 -41
data/test/error.rb +1 -3
data/test/experiment.rb +301 -0
data/test/feature.rb +22 -10
data/test/lazar-long.rb +43 -23
data/test/lazar-physchem-short.rb +19 -16
data/test/prediction_models.rb +20 -0
data/test/regression.rb +43 -0
data/test/setup.rb +3 -1
data/test/test_environment.rb +10 -0
data/test/validation.rb +92 -26
metadata +64 -38
data/lib/SMARTS_InteLigand.txt +0 -983
data/lib/bbrc.rb +0 -165
data/lib/descriptor.rb +0 -247
data/lib/neighbor.rb +0 -25
data/lib/similarity.rb +0 -58
data/mongoid.yml +0 -8
data/test/descriptor-long.rb +0 -26
data/test/fminer-long.rb +0 -38
data/test/fminer.rb +0 -52
data/test/lazar-fminer.rb +0 -50
data/test/lazar-regression.rb +0 -27

data/lib/SMARTS_InteLigand.txt DELETED Viewed

@@ -1,983 +0,0 @@
-#
-#              SMARTS Patterns for Functional Group Classification
-#
-#              written by Christian Laggner
-#              Copyright 2005 Inte:Ligand Software-Entwicklungs und Consulting GmbH
-#
-#              Released under the Lesser General Public License (LGPL license)
-#              see http://www.gnu.org/copyleft/lesser.html
-#              Modified from Version 221105
-#####################################################################################################
-# General Stuff:
-# These patters were written in an attempt to represent the classification of organic compounds
-# from the viewpoint of an organic chemist.
-# They are often very restrictive. This may be generally a good thing, but it also takes some time
-# for filtering/indexing large compound sets.
-# For filtering undesired groups (in druglike compounds) one will want to have more general patterns
-# (e.g. you don't want *any* halide of *any* acid, *neither* aldehyde *nor* formyl esters and amides, ...).
-#
-# Part I: Carbon
-# ==============
-# I.1: Carbon-Carbon Bonds
-# ------------------------
-# I.1.1 Alkanes:
-Primary_carbon: [CX4H3][#6]
-Secondary_carbon: [CX4H2]([#6])[#6]
-Tertiary_carbon: [CX4H1]([#6])([#6])[#6]
-Quaternary_carbon: [CX4]([#6])([#6])([#6])[#6]
-# I.1.2 C-C double and Triple Bonds
-Alkene: [CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]=[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]
-# sp2 C may be substituted only by C or H -
-# does not hit ketenes and allenes, nor enamines, enols and the like
-Alkyne: [CX2]#[CX2]
-# non-carbon substituents (e.g. alkynol ethers) are rather rare, thus no further discrimination
-Allene: [CX3]=[CX2]=[CX3]
-# I.2: One Carbon-Hetero Bond
-# ---------------------------
-# I.2.1 Alkyl Halogenides
-Alkylchloride: [ClX1][CX4]
-# will also hit chloromethylethers and the like, but no chloroalkenes, -alkynes or -aromats
-# a more restrictive version can be obtained by modifying the Alcohol string.
-Alkylfluoride: [FX1][CX4]
-Alkylbromide: [BrX1][CX4]
-Alkyliodide: [IX1][CX4]
-# I.2.2 Alcohols and Ethers
-Alcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])]
-# nonspecific definition, no acetals, aminals, and the like
-Primary_alcohol: [OX2H][CX4H2;!$(C([OX2H])[O,S,#7,#15])]
-Secondary_alcohol: [OX2H][CX4H;!$(C([OX2H])[O,S,#7,#15])]
-Tertiary_alcohol: [OX2H][CX4D4;!$(C([OX2H])[O,S,#7,#15])]
-Dialkylether: [OX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]
-# no acetals and the like; no enolethers
-Dialkylthioether: [SX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]
-# no acetals and the like; no enolethers
-Alkylarylether: [OX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]
-# no acetals and the like; no enolethers
-Diarylether: [c][OX2][c]
-Alkylarylthioether: [SX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]
-Diarylthioether: [c][SX2][c]
-Oxonium: [O+;!$([O]~[!#6]);!$([S]*~[#7,#8,#15,#16])]
-# can't be aromatic, thus O and not #8
-# I.2.3 Amines
-Amine: [NX3+0,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])]
-# hits all amines (prim/sec/tert/quart), including ammonium salts, also enamines, but not amides, imides, aminals, ...
-# the following amines include also the protonated forms
-Primary_aliph_amine: [NX3H2+0,NX4H3+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
-Secondary_aliph_amine: [NX3H1+0,NX4H2+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
-Tertiary_aliph_amine: [NX3H0+0,NX4H1+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
-Quaternary_aliph_ammonium: [NX4H0+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
-Primary_arom_amine: [NX3H2+0,NX4H3+]c
-Secondary_arom_amine: [NX3H1+0,NX4H2+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
-Tertiary_arom_amine: [NX3H0+0,NX4H1+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
-Quaternary_arom_ammonium: [NX4H0+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
-Secondary_mixed_amine: [NX3H1+0,NX4H2+;$([N]([c])[C]);!$([N]*~[#7,#8,#15,#16])]
-Tertiary_mixed_amine: [NX3H0+0,NX4H1+;$([N]([c])([C])[#6]);!$([N]*~[#7,#8,#15,#16])]
-Quaternary_mixed_ammonium: [NX4H0+;$([N]([c])([C])[#6][#6]);!$([N]*~[#7,#8,#15,#16])]
-Ammonium: [N+;!$([N]~[!#6]);!$(N=*);!$([N]*~[#7,#8,#15,#16])]
-# only C and H substituents allowed. Quaternary or protonated amines
-# NX4+ or Nv4+ is not recognized by Daylight's depictmatch if less than four C are present
-# I.2.4 Others
-Alkylthiol: [SX2H][CX4;!$(C([SX2H])~[O,S,#7,#15])]
-Dialkylthioether: [SX2]([CX4;!$(C([SX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([SX2])[O,S,#7,#15])]
-Alkylarylthioether: [SX2](c)[CX4;!$(C([SX2])[O,S,#7,#15])]
-Disulfide: [SX2D2][SX2D2]
-1,2-Aminoalcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15,F,Cl,Br,I])][CX4;!$(C([N])[O,S,#7,#15])][NX3;!$(NC=[O,S,N])]
-# does not hit alpha-amino acids, enaminoalcohols, 1,2-aminoacetals, o-aminophenols, etc.
-1,2-Diol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])][CX4;!$(C([OX2H])[O,S,#7,#15])][OX2H]
-# does not hit alpha-hydroxy acids, enolalcohols, 1,2-hydroxyacetals, 1,2-diphenols, etc.
-1,1-Diol: [OX2H][CX4;!$(C([OX2H])([OX2H])[O,S,#7,#15])][OX2H]
-Hydroperoxide: [OX2H][OX2]
-#does not neccessarily have to be connected to a carbon atom, includes also hydrotrioxides
-Peroxo: [OX2D2][OX2D2]
-Organolithium_compounds: [LiX1][#6,#14]
-Organomagnesium_compounds: [MgX2][#6,#14]
-# not restricted to Grignard compounds, also dialkyl Mg
-Organometallic_compounds: [!#1;!#5;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#33;!#34;!#35;!#52;!#53;!#85]~[#6;!-]
-# very general, includes all metals covalently bound to carbon
-# I.3: Two Carbon-Hetero Bonds (Carbonyl and Derivatives)
-# ----------------------------
-# I.3.1 Double Bond to Hetero
-Aldehyde: [$([CX3H][#6]),$([CX3H2])]=[OX1]
-# hits aldehydes including formaldehyde
-Ketone: [#6][CX3](=[OX1])[#6]
-# does not include oxo-groups connected to a (hetero-) aromatic ring
-Thioaldehyde: [$([CX3H][#6]),$([CX3H2])]=[SX1]
-Thioketone: [#6][CX3](=[SX1])[#6]
-# does not include thioxo-groups connected to a (hetero-) aromatic ring
-Imine: [NX2;$([N][#6]),$([NH]);!$([N][CX3]=[#7,#8,#15,#16])]=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])]
-# nitrogen is not part of an amidelike strukture, nor of an aromatic ring, but can be part of an aminal or similar
-Immonium: [NX3+;!$([N][!#6]);!$([N][CX3]=[#7,#8,#15,#16])]
-Oxime: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2H]
-Oximether: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2][#6;!$(C=[#7,#8])]
-# ether, not ester or amide; does not hit isoxazole
-# I.3.2. Two Single Bonds to Hetero
-Acetal: [OX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]
-# does not hit hydroxy-methylesters, ketenacetals, hemiacetals, orthoesters, etc.
-Hemiacetal: [OX2H][CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]
-Aminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][NX3v3;!$(NC=[#7,#8,#15,#16])][#6]
-# Ns are not part of an amide or similar. v3 ist to exclude nitro and similar groups
-Hemiaminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][OX2H]
-Thioacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][SX2][#6;!$(C=[O,S,N])]
-Thiohemiacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][OX2H]
-Halogen_acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]
-# hits chloromethylenethers and other reactive alkylating agents
-Acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]
-# includes all of the above and other combinations (S-C-N, hydrates, ...), but still no aminomethylenesters and similar
-Halogenmethylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]
-# also reactive alkylating agents. Acid does not have to be carboxylic acid, also S- and P-based acids allowed
-NOS_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]
-# Same as above, but N,O or S instead of halogen. Ester/amide allowed only on one side
-Hetero_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]
-# Combination of the last two patterns
-Cyanhydrine: [NX1]#[CX2][CX4;$([CH2]),$([CH]([CX2])[#6]),$(C([CX2])([#6])[#6])][OX2H]
-# I.3.3 Single Bond to Hetero, C=C Double Bond (Enols and Similar)
-Chloroalkene: [ClX1][CX3]=[CX3]
-Fluoroalkene: [FX1][CX3]=[CX3]
-Bromoalkene: [BrX1][CX3]=[CX3]
-Iodoalkene: [IX1][CX3]=[CX3]
-Enol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3]
-# no phenols
-Endiol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3;$([H1]),$(C[#6])][OX2H]
-# no 1,2-diphenols, ketenacetals, ...
-Enolether: [OX2]([#6;!$(C=[N,O,S])])[CX3;$([H0][#6]),$([H1])]=[CX3]
-# finds also endiodiethers, but not enolesters, no aromats
-Enolester: [OX2]([CX3]=[OX1])[#6X3;$([#6][#6]),$([H1])]=[#6X3;!$(C[OX2H])]
-Enamine: [NX3;$([NH2][CX3]),$([NH1]([CX3])[#6]),$([N]([CX3])([#6])[#6]);!$([N]*=[#7,#8,#15,#16])][CX3;$([CH]),$([C][#6])]=[CX3]
-# does not hit amines attached to aromatic rings, nor may the nitrogen be aromatic
-Thioenol: [SX2H][CX3;$([H1]),$(C[#6])]=[CX3]
-Thioenolether: [SX2]([#6;!$(C=[N,O,S])])[CX3;$(C[#6]),$([CH])]=[CX3]
-# I.4: Three Carbon-Hetero Bonds (Carboxyl and Derivatives)
-# ------------------------------
-Acylchloride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[ClX1]
-Acylfluoride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1]
-Acylbromide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[BrX1]
-Acyliodide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[IX1]
-Acylhalide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1,ClX1,BrX1,IX1]
-# all of the above
-# The following contains all simple carboxylic combinations of O, N, S, & Hal -
-# - acids, esters, amides, ... as well as a few extra cases (anhydride, hydrazide...)
-# Cyclic structures (including aromats) like lactones, lactames, ... got their own
-# definitions. Structures where both heteroatoms are part of an aromatic ring
-# (oxazoles, imidazoles, ...) were excluded.
-Carboxylic_acid: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[$([OX2H]),$([OX1-])]
-# includes carboxylate anions
-Carboxylic_ester:  [CX3;$([R0][#6]),$([H1R0])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
-# does not hit anhydrides or lactones
-Lactone: [#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])]
-# may also be aromatic
-Carboxylic_anhydride: [CX3;$([H0][#6]),$([H1])](=[OX1])[#8X2][CX3;$([H0][#6]),$([H1])](=[OX1])
-# anhydride formed by two carboxylic acids, no mixed anhydrides (e.g. between carboxylic acid and sulfuric acid); may be part of a ring, even aromatic
-Carboxylic_acid_derivative: [$([#6X3H0][#6]),$([#6X3H])](=[!#6])[!#6]
-# includes most of the structures of I.4 and many more, also 1,3-heteroaromatics such as isoxazole
-Carbothioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[OX1])[$([SX2H]),$([SX1-])]),$([C](=[SX1])[$([OX2H]),$([OX1-])])]
-# hits both tautomeric forms, as well as anions
-Carbothioic_S_ester: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[SX2][#6;!$(C=[O,N,S])]
-Carbothioic_S_lactone: [#6][#6X3R](=[OX1])[#16X2][#6;!$(C=[O,N,S])]
-# may also be aromatic
-Carbothioic_O_ester: [CX3;$([H0][#6]),$([H1])](=[SX1])[OX2][#6;!$(C=[O,N,S])]
-Carbothioic_O_lactone: [#6][#6X3R](=[SX1])[#8X2][#6;!$(C=[O,N,S])]
-Carbothioic_halide: [CX3;$([H0][#6]),$([H1])](=[SX1])[FX1,ClX1,BrX1,IX1]
-Carbodithioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2H])]
-Carbodithioic_ester: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2][#6;!$(C=[O,N,S])])]
-Carbodithiolactone: [#6][#6X3R](=[SX1])[#16X2][#6;!$(C=[O,N,S])]
-Amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-# does not hit lactames
-Primary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[NX3H2]
-Secondary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])]
-Tertiary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])]
-Lactam: [#6R][#6X3R](=[OX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-# cyclic amides, may also be aromatic
-Alkyl_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])
-# may be part of a ring, even aromatic. only C allowed at central N. May also be triacyl amide
-N_hetero_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([!#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])
-# everything else than H or C at central N
-Imide_acidic: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H1][#6X3;$([H0][#6]),$([H1])](=[OX1])
-# can be deprotonated
-Thioamide: [$([CX3;!R][#6]),$([CX3H;!R])](=[SX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-# does not hit thiolactames
-Thiolactam: [#6R][#6X3R](=[SX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-# cyclic thioamides, may also be aromatic
-Oximester: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#8X2][#7X2]=,:[#6X3;$([H0]([#6])[#6]),$([H1][#6]),$([H2])]
-# may also be part of a ring / aromatic
-Amidine: [NX3;!$(NC=[O,S])][CX3;$([CH]),$([C][#6])]=[NX2;!$(NC=[O,S])]
-# only basic amidines, not as part of aromatic ring (e.g. imidazole)
-Hydroxamic_acid: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][$([OX2H]),$([OX1-])]
-Hydroxamic_acid_ester: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][OX2][#6;!$(C=[O,N,S])]
-# does not hit anhydrides of carboxylic acids withs hydroxamic acids
-Imidoacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
-# not cyclic
-Imidoacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
-# the enamide-form of lactames. may be aromatic like 2-hydroxypyridine
-Imidoester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]
-# esters of the above structures. no anhydrides.
-Imidolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]
-# no oxazoles and similar
-Imidothioacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]
-# not cyclic
-Imidothioacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]
-# the enamide-form of thiolactames. may be aromatic like 2-thiopyridine
-Imidothioester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]
-# thioesters of the above structures. no anhydrides.
-Imidothiolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]
-# no thioxazoles and similar
-Amidine: [#7X3v3;!$(N([#6X3]=[#7X2])C=[O,S])][CX3R0;$([H1]),$([H0][#6])]=[NX2v3;!$(N(=[#6X3][#7X3])C=[O,S])]
-# only basic amidines, not substituted by carbonyl or thiocarbonyl, not as part of a ring
-Imidolactam: [#6][#6X3R;$([H0](=[NX2;!$(N(=[#6X3][#7X3])C=[O,S])])[#7X3;!$(N([#6X3]=[#7X2])C=[O,S])]),$([H0](-[NX3;!$(N([#6X3]=[#7X2])C=[O,S])])=,:[#7X2;!$(N(=[#6X3][#7X3])C=[O,S])])]
-# one of the two C~N bonds is part of a ring (may be aromatic), but not both - thus no imidazole
-Imidoylhalide: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]
-# not cyclic
-Imidoylhalide_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]
-# may also be aromatic
-# may be ring, aromatic, substituted with carbonyls, hetero, ...
-# (everything else would get too complicated)
-Amidrazone: [$([$([#6X3][#6]),$([#6X3H])](=[#7X2v3])[#7X3v3][#7X3v3]),$([$([#6X3][#6]),$([#6X3H])]([#7X3v3])=[#7X2v3][#7X3v3])]
-# hits both tautomers. as above, it may be ring, aromatic, substituted with carbonyls, hetero, ...
-Alpha_aminoacid: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[OX2H,OX1-]
-# N may be alkylated, but not part of an amide (as in peptides), ionic forms are included
-# includes also non-natural aminoacids with double-bonded or two aliph./arom. substituents at alpha-C
-# N may not be aromatic as in 1H-pyrrole-2-carboxylic acid
-Alpha_hydroxyacid: [OX2H][C][CX3](=[OX1])[OX2H,OX1-]
-Peptide_middle: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]
-# finds peptidic structures which are neither C- nor N-terminal. Both neighbours must be amino-acids/peptides
-Peptide_C_term: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[OX2H,OX1-]
-# finds C-terminal amino acids
-Peptide_N_term: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]
-# finds N-terminal amino acids. As above, N may be substituted, but not part of an amide-bond.
-Carboxylic_orthoester: [#6][OX2][CX4;$(C[#6]),$([CH])]([OX2][#6])[OX2][#6]
-# hits also anhydride like struktures (e. g. HC(OMe)2-OC=O residues)
-Ketene: [CX3]=[CX2]=[OX1]
-Ketenacetal: [#7X2,#8X3,#16X2;$(*[#6,#14])][#6X3]([#7X2,#8X3,#16X2;$(*[#6,#14])])=[#6X3]
-# includes aminals, silylacetals, ketenesters, etc. C=C DB is not aromatic, everything else may be
-Nitrile: [NX1]#[CX2]
-# includes cyanhydrines
-Isonitrile: [CX1-]#[NX2+]
-Vinylogous_carbonyl_or_carboxyl_derivative: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7,#8,#16,F,Cl,Br,I]
-# may be part of a ring, even aromatic
-Vinylogous_acid: [#6X3](=[OX1])[#6X3]=,:[#6X3][$([OX2H]),$([OX1-])]
-Vinylogous_ester: [#6X3](=[OX1])[#6X3]=,:[#6X3][#6;!$(C=[O,N,S])]
-Vinylogous_amide: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Vinylogous_halide: [#6X3](=[OX1])[#6X3]=,:[#6X3][FX1,ClX1,BrX1,IX1]
-# I.5: Four Carbon-Hetero Bonds (Carbonic Acid and Derivatives)
-# -----------------------------
-Carbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[OX1])[#8X2][#6;!$(C=[O,N,S])]
-# may be part of a ring, even aromatic
-Carbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[OX2][FX1,ClX1,BrX1,IX1]
-Carbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[$([OX2H]),$([OX1-])]
-# unstable
-Carbonic_acid_derivatives: [!#6][#6X3](=[!#6])[!#6]
-Thiocarbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[SX1])[#8X2][#6;!$(C=[O,N,S])]
-# may be part of a ring, even aromatic
-Thiocarbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[OX2][FX1,ClX1,BrX1,IX1]
-Thiocarbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[$([OX2H]),$([OX1-])]
-Urea:[#7X3;!$([#7][!#6])][#6X3](=[OX1])[#7X3;!$([#7][!#6])]
-# no check whether part of imide, biuret, etc. Aromatic structures are only hit if
-# both N share no double bonds, like in the dioxo-form of uracil
-Thiourea: [#7X3;!$([#7][!#6])][#6X3](=[SX1])[#7X3;!$([#7][!#6])]
-Isourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#8X2&!$([#8][!#6]),OX1-])[#7X3;!$([#7][!#6])]
-# O may be substituted. no check whether further amide-like bonds are present. Aromatic
-# structures are only hit if single bonded N shares no additional double bond, like in
-# the 1-hydroxy-3-oxo form of uracil
-Isothiourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#16X2&!$([#16][!#6]),SX1-])[#7X3;!$([#7][!#6])]
-Guanidine: [N;v3X3,v4X4+][CX3](=[N;v3X2,v4X3+])[N;v3X3,v4X4+]
-# also hits guanidinium salts. v3 and v4 to avoid nitroamidines
-Carbaminic_acid: [NX3]C(=[OX1])[O;X2H,X1-]
-# quite unstable, unlikely to be found. Also hits salts
-Urethan: [#7X3][#6](=[OX1])[#8X2][#6]
-# also hits when part of a ring, no check whether the last C is part of carbonyl
-Biuret: [#7X3][#6](=[OX1])[#7X3][#6](=[OX1])[#7X3]
-Semicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]
-Carbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[OX1]
-Semicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]
-Carbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[OX1]
-Thiosemicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]
-Thiocarbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[SX1]
-Thiosemicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]
-Thiocarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[SX1]
-Isocyanate: [NX2]=[CX2]=[OX1]
-Cyanate: [OX2][CX2]#[NX1]
-Isothiocyanate: [NX2]=[CX2]=[SX1]
-Thiocyanate: [SX2][CX2]#[NX1]
-Carbodiimide: [NX2]=[CX2]=[NX2]
-Orthocarbonic_derivatives: [CX4H0]([O,S,#7])([O,S,#7])([O,S,#7])[O,S,#7,F,Cl,Br,I]
-# halogen allowed just once, to avoid mapping to -OCF3 and similar groups (much more
-# stable as for example C(OCH3)4)
-# I.6 Aromatics
-# -------------
-# I know that this classification is not very logical, arylamines are found under I.2 ...
-Phenol: [OX2H][c]
-1,2-Diphenol: [OX2H][c][c][OX2H]
-Arylchloride: [Cl][c]
-Arylfluoride: [F][c]
-Arylbromide: [Br][c]
-Aryliodide: [I][c]
-Arylthiol: [SX2H][c]
-Iminoarene: [c]=[NX2;$([H1]),$([H0][#6;!$([C]=[N,S,O])])]
-# N may be substituted with H or C, but not carbonyl or similar
-# aromatic atom is always C, not S or P (these are not planar when substituted)
-Oxoarene: [c]=[OX1]
-Thioarene: [c]=[SX1]
-Hetero_N_basic_H: [nX3H1+0]
-# as in pyrole. uncharged to exclude pyridinium ions
-Hetero_N_basic_no_H: [nX3H0+0]
-# as in N-methylpyrole. uncharged to exclude pyridinium ions
-Hetero_N_nonbasic: [nX2,nX3+]
-# as in pyridine, pyridinium
-Hetero_O: [o]
-Hetero_S: [sX2]
-# X2 because Daylight's depictmatch falsely describes C1=CS(=O)C=C1 as aromatic
-# (is not planar because of lonepair at S)
-Heteroaromatic: [a;!c]
-# Part II: N, S, P, Si, B
-# =======================
-# II.1 Nitrogen
-# -------------
-Nitrite: [NX2](=[OX1])[O;$([X2]),$([X1-])]
-# hits nitrous acid, its anion, esters, and other O-substituted derivatives
-Thionitrite: [SX2][NX2]=[OX1]
-Nitrate: [$([NX3](=[OX1])(=[OX1])[O;$([X2]),$([X1-])]),$([NX3+]([OX1-])(=[OX1])[O;$([X2]),$([X1-])])]
-# hits nitric acid, its anion, esters, and other O-substituted derivatives
-Nitro: [$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]
-# hits nitro groups attached to C,N, ... but not nitrates
-Nitroso: [NX2](=[OX1])[!#7;!#8]
-# no nitrites, no nitrosamines
-Azide: [NX1]~[NX2]~[NX2,NX1]
-# hits both mesomeric forms, also anion
-Acylazide: [CX3](=[OX1])[NX2]~[NX2]~[NX1]
-Diazo: [$([#6]=[NX2+]=[NX1-]),$([#6-]-[NX2+]#[NX1])]
-Diazonium: [#6][NX2+]#[NX1]
-Nitrosamine: [#7;!$(N*=O)][NX2]=[OX1]
-Nitrosamide: [NX2](=[OX1])N-*=O
-# includes nitrososulfonamides
-N-Oxide: [$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])]
-# Hits both forms. Won't hit azoxy, nitro, nitroso, or nitrate.
-Hydrazine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])]
-# no hydrazides
-Hydrazone: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX2]=[#6]
-Hydroxylamine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][OX2;$([H1]),$(O[#6;!$(C=[N,O,S])])]
-# no discrimination between O-, N-, and O,N-substitution
-# II.2 Sulfur
-# -----------
-Sulfon: [$([SX4](=[OX1])(=[OX1])([#6])[#6]),$([SX4+2]([OX1-])([OX1-])([#6])[#6])]
-# can't be aromatic, thus S and not #16
-Sulfoxide: [$([SX3](=[OX1])([#6])[#6]),$([SX3+]([OX1-])([#6])[#6])]
-Sulfonium: [S+;!$([S]~[!#6]);!$([S]*~[#7,#8,#15,#16])]
-# can't be aromatic, thus S and not #16
-Sulfuric_acid: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
-# includes anions
-Sulfuric_monoester: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
-Sulfuric_diester: [SX4](=[OX1])(=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
-Sulfuric_monoamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
-Sulfuric_diamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Sulfuric_esteramide: [SX4](=[OX1])(=[OX1])([#7X3][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
-Sulfuric_derivative: [SX4D4](=[!#6])(=[!#6])([!#6])[!#6]
-# everything else (would not be a "true" derivative of sulfuric acid, if one of the substituents were less electronegative
-# than sulfur, but this should be very very rare, anyway)
-#### sulfurous acid and derivatives missing!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-Sulfonic_acid: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[$([OX2H]),$([OX1-])]
-Sulfonamide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Sulfonic_ester: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[OX2][#6;!$(C=[O,N,S])]
-Sulfonic_halide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[FX1,ClX1,BrX1,IX1]
-Sulfonic_derivative: [SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6])[!#6]
-# includes all of the above and many more
-# for comparison: this is what "all sulfonic derivatives but not the ones above" would look like:
-# [$([SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6;!O])[!#6]),$([SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[!$([FX1,ClX1,BrX1,IX1]);!$([#6]);!$([OX2H]);!$([OX1-]);!$([OX2][#6;!$(C=[O,N,S])]);!$([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])])]
-Sulfinic_acid: [SX3;$([H1]),$([H0][#6])](=[OX1])[$([OX2H]),$([OX1-])]
-Sulfinic_amide: [SX3;$([H1]),$([H0][#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Sulfinic_ester: [SX3;$([H1]),$([H0][#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
-Sulfinic_halide: [SX3;$([H1]),$([H0][#6])](=[OX1])[FX1,ClX1,BrX1,IX1]
-Sulfinic_derivative: [SX3;$([H1]),$([H0][#6])](=[!#6])[!#6]
-Sulfenic_acid: [SX2;$([H1]),$([H0][#6])][$([OX2H]),$([OX1-])]
-Sulfenic_amide: [SX2;$([H1]),$([H0][#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Sulfenic_ester: [SX2;$([H1]),$([H0][#6])][OX2][#6;!$(C=[O,N,S])]
-Sulfenic_halide: [SX2;$([H1]),$([H0][#6])][FX1,ClX1,BrX1,IX1]
-Sulfenic_derivative: [SX2;$([H1]),$([H0][#6])][!#6]
-# II.3 Phosphorous
-# ----------------
-Phosphine: [PX3;$([H3]),$([H2][#6]),$([H1]([#6])[#6]),$([H0]([#6])([#6])[#6])]
-# similar to amine, but less restrictive: includes also amide- and aminal-analogues
-Phosphine_oxide: [PX4;$([H3]=[OX1]),$([H2](=[OX1])[#6]),$([H1](=[OX1])([#6])[#6]),$([H0](=[OX1])([#6])([#6])[#6])]
-Phosphonium: [P+;!$([P]~[!#6]);!$([P]*~[#7,#8,#15,#16])]
-# similar to Ammonium
-Phosphorylen: [PX4;$([H3]=[CX3]),$([H2](=[CX3])[#6]),$([H1](=[CX3])([#6])[#6]),$([H0](=[CX3])([#6])([#6])[#6])]
-# conventions for the following acids and derivatives:
-# acids find protonated and deprotonated acids
-# esters do not find mixed anhydrides ( ...P-O-C(=O))
-# derivatives: subtituents which go in place of the OH and =O are not H or C (may also be O,
-# thus including acids and esters)
-Phosphonic_acid: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
-# includes anions
-Phosphonic_monoester: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
-Phosphonic_diester: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
-Phosphonic_monoamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Phosphonic_diamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Phosphonic_esteramide: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Phosphonic_acid_derivative: [PX4;$([H1]),$([H0][#6])](=[!#6])([!#6])[!#6]
-# all of the above and much more
-Phosphoric_acid: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
-# includes anions
-Phosphoric_monoester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
-Phosphoric_diester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
-Phosphoric_triester: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
-Phosphoric_monoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Phosphoric_diamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Phosphoric_triamide: [PX4D4](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Phosphoric_monoestermonoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Phosphoric_diestermonoamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Phosphoric_monoesterdiamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Phosphoric_acid_derivative: [PX4D4](=[!#6])([!#6])([!#6])[!#6]
-Phosphinic_acid: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[$([OX2H]),$([OX1-])]
-Phosphinic_ester: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
-Phosphinic_amide: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Phosphinic_acid_derivative: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[!#6])[!#6]
-Phosphonous_acid: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
-Phosphonous_monoester: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
-Phosphonous_diester: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
-Phosphonous_monoamide: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Phosphonous_diamide: [PX3;$([H1]),$([H0][#6])]([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Phosphonous_esteramide: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Phosphonous_derivatives: [PX3;$([D2]),$([D3][#6])]([!#6])[!#6]
-Phosphinous_acid: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][$([OX2H]),$([OX1-])]
-Phosphinous_ester: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][OX2][#6;!$(C=[O,N,S])]
-Phosphinous_amide: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
-Phosphinous_derivatives: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][!#6]
-# II.4 Silicon
-# ------------
-Quart_silane: [SiX4]([#6])([#6])([#6])[#6]
-# four C-substituents. non-reactive, non-toxic, in experimental phase for drug development
-Non-quart_silane: [SiX4;$([H1]([#6])([#6])[#6]),$([H2]([#6])[#6]),$([H3][#6]),$([H4])]
-# has 1-4 hydride(s), reactive. Daylight's depictmatch does not add hydrogens automatically to
-# the free positions at Si, thus Hs had to be added implicitly
-Silylmonohalide: [SiX4]([FX1,ClX1,BrX1,IX1])([#6])([#6])[#6]
-# reagents for inserting protection groups
-Het_trialkylsilane: [SiX4]([!#6])([#6])([#6])[#6]
-# mostly acid-labile protection groups such as trimethylsilyl-ethers
-Dihet_dialkylsilane: [SiX4]([!#6])([!#6])([#6])[#6]
-Trihet_alkylsilane: [SiX4]([!#6])([!#6])([!#6])[#6]
-Silicic_acid_derivative: [SiX4]([!#6])([!#6])([!#6])[!#6]
-# four substituent which are neither C nor H
-# II.5 Boron
-# ----------
-Trialkylborane: [BX3]([#6])([#6])[#6]
-# also carbonyls allowed
-Boric_acid_derivatives: [BX3]([!#6])([!#6])[!#6]
-# includes acids, esters, amides, ... H-substituent at B is very rare.
-Boronic_acid_derivative: [BX3]([!#6])([!#6])[!#6]
-# # includes acids, esters, amides, ...
-Borohydride: [BH1,BH2,BH3,BH4]
-# at least one H attached to B
-Quaternary_boron: [BX4]
-# mostly borates (negative charge), in complex with Lewis-base
-# Part III: Some Special Patterns
-# ===============================
-# III.1 Chains
-# ------------
-# some simple chains
-# III.2 Rings
-# -----------
-Aromatic: a
-Heterocyclic: [!#6;!R0]
-# may be aromatic or not
-Epoxide: [OX2r3]1[#6r3][#6r3]1
-# toxic/reactive. may be annelated to aromat, but must not be aromatic itself (oxirane-2,3-dione)
-NH_aziridine: [NX3H1r3]1[#6r3][#6r3]1
-# toxic/reactive according to Maybridge's garbage filter
-Spiro: [D4R;$(*(@*)(@*)(@*)@*)]
-# at least two different rings can be found which are sharing just one atom.
-# these two rings can be connected by a third ring, so it matches also some
-# bridged systems, like morphine
-Annelated_rings: [R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]
-# two different rings sharing exactly two atoms
-Bridged_rings: [R;$(*(@*)(@*)@*);!$([D4R;$(*(@*)(@*)(@*)@*)]);!$([R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])])]
-# part of two or more rings, not spiro, not annelated -> finds bridgehead atoms,
-# but only if they are not annelated at the same time - otherwise impossible (?)
-# to distinguish from non-bridgehead annelated atoms
-# some basic ring-patterns (just size, no other information):
-# III.3 Sugars and Nucleosides/Nucleotides, Steroids
-# --------------------------------------------------
-# because of the large variety of sugar derivatives, different patterns can be applied.
-# The choice of patterns and their combinations will depend on the contents of the database
-# e.g. natural products, nucleoside analoges with modified sugars, ... as well as on the
-# desired restriction
-Sugar_pattern_1: [OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)]
-# 5 or 6-membered ring containing one O and at least one (r5) or two (r6) oxygen-substituents.
-Sugar_pattern_2: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
-# 5 or 6-membered ring containing one O and an acetal-like bond at postion 2.
-Sugar_pattern_combi: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C(O)@C1)]
-# combination of the two above
-Sugar_pattern_2_reducing: [OX2;$([r5]1@C(!@[OX2H1])@C@C@C1),$([r6]1@C(!@[OX2H1])@C@C@C@C1)]
-# 5 or 6-membered cyclic hemi-acetal
-Sugar_pattern_2_alpha: [OX2;$([r5]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
-# 5 or 6-membered cyclic hemi-acetal
-Sugar_pattern_2_beta: [OX2;$([r5]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
-# 5 or 6-membered cyclic hemi-acetal
-##Poly_sugar_1: ([OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)].[OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)])
-# pattern1 occours more than once (in same molecule, but moieties don't have to be adjacent!)
-##Poly_sugar_2: ([OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)].[OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)])
-# pattern2 occours more than once (in same molecule, but moieties don't have to be adjacent!)
-# III.4 Everything else...
-# ------------------------
-Conjugated_double_bond: *=*[*]=,#,:[*]
-Conjugated_tripple_bond: *#*[*]=,#,:[*]
-Cis_double_bond: */[D2]=[D2]\*
-# only one single-bonded substituent on each DB-atom. no aromats.
-# only found when character of DB is explicitely stated.
-Trans_double_bond: */[D2]=[D2]/*
-# analog
-Mixed_anhydrides: [$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))][#8X2][$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))]
-# should hits all combinations of two acids
-Halogen_on_hetero: [FX1,ClX1,BrX1,IX1][!#6]
-Halogen_multi_subst: [F,Cl,Br,I;!$([X1]);!$([X0-])]
-# Halogen which is not mono-substituted nor an anion, e.g. chlorate.
-# Most of these cases should be also filtered by Halogen_on_hetero.
-Trifluoromethyl: [FX1][CX4;!$([H0][Cl,Br,I]);!$([F][C]([F])([F])[F])]([FX1])([FX1])
-# C with three F attached, connected to anything which is not another halogen
-C_ONS_bond: [#6]~[#7,#8,#16]
-# probably all drug-like molecules have at least one O, N, or S connected to a C -> nice filter
-## Mixture: (*).(*)
-# two or more seperate parts, may also be salt
-# component-level grouping is not yet supported in Open Babel Version 2.0
-Charged: [!+0]
-Anion: [-1,-2,-3,-4,-5,-6,-7]
-Kation: [+1,+2,+3,+4,+5,+6,+7]
-Salt: ([-1,-2,-3,-4,-5,-6,-7]).([+1,+2,+3,+4,+5,+6,+7])
-# two or more seperate components with opposite charges
-##Zwitterion: ([-1,-2,-3,-4,-5,-6,-7].[+1,+2,+3,+4,+5,+6,+7])
-# both negative and positive charges somewhere within the same molecule.
-1,3-Tautomerizable: [$([#7X2,OX1,SX1]=*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=*),$([#7X3,OX2,SX2;!H0]*:n)]
-# 1,3 migration of H allowed. Includes keto/enol and amide/enamide.
-# Aromatic rings must stay aromatic - no keto form of phenol
-1,5-Tautomerizable: [$([#7X2,OX1,SX1]=,:**=,:*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=**=*),$([#7X3,OX2,SX2;!H0]*=,:**:n)]
-Rotatable_bond: [!$(*#*)&!D1]-!@[!$(*#*)&!D1]
-# taken from http://www.daylight.com/support/contrib/smarts/content.html
-Michael_acceptor: [CX3]=[CX3][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-])]
-# the classical case: C=C near carbonyl, nitrile, nitro, or similar
-# Oxo-heteroaromats and similar are not included.
-Dicarbodiazene: [CX3](=[OX1])[NX2]=[NX2][CX3](=[OX1])
-# Michael-like acceptor, see Mitsunobu reaction
-# H-Bond_donor:
-# H-Bond_acceptor:
-# Pos_ionizable:
-# Neg_ionizable:
-# Unlikely_ions:
-# O+,N-,C+,C-, ...
-CH-acidic: [$([CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]),$([CX4;!$([H0])]1[CX3]=[CX3][CX3]=[CX3]1)]
-# C-H alpha to carbony, nitro or similar, C is not double-bonded, only C, H, S,P=O and nitro substituents allowed.
-# pentadiene is included. acids, their salts, prim./sec. amides, and imides are excluded.
-# hits also CH-acidic_strong
-CH-acidic_strong: [CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])]([$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])])[$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]
-# same as above (without pentadiene), but carbonyl or similar on two or three sides
-Chiral_center_specified: [$([*@](~*)(~*)(*)*),$([*@H](*)(*)*),$([*@](~*)(*)*),$([*@H](~*)~*)]
-# Hits atoms with tetrahedral chirality, if chiral center is specified in the SMILES string
-# depictmach does not find oxonium, sulfonium, or sulfoxides!
-# Chiral_center_unspecified: [$([*@?](~*)(~*)(*)*),$([*@?H](*)(*)*),$([*@?](~*)(*)*),$([*@?H](~*)~*)]
-# Hits atoms with tetrahedral chirality, if chiral center is not specified in the SMILES string
-# "@?" (unspecified chirality) is not yet supported in Open Babel Version 2.0