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

lazar 0.0.7 → 0.0.9

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