SMARTS_InteLigand from Open Babel

# 
#              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