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smart_search_strings.yml
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smart_search_strings.yml
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---
#:ester:
# - "[#6][CX3](=O)[OX2H0][#6]" #also hits anhydrides but not formic anhydrides
:ester_terminal:
- "[#6][CX3](=O)[OX2H1]"
:ester_internal:
- "[#6][CX3](=O)[OX2][#6]"
:ester_excludes_anhydrides:
- "[CX4]([!O])[CX3](=O)[OX2][CX4]([!O])"
:ketone:
- "[#6][CX3](=O)[#6]"
:ether:
- "[OD2]([#6])[#6]"
:amide:
- "[NX3][CX3](=[OX1])[#6]"
:vinylic_carbon:
- "[$([CX3]=[CX3])]"
:proton:
- "[H+]"
:cyano:
- "[CX2]#[NX1]"
:alkyl_carbon:
- "[CX4]"
:allenic_carbon:
- "[$([CX2](=C)=C)]"
:acetylenic_carbon:
- "[$([CX2]#C)]"
:carbonyl:
- "[CX3]=[OX1]" #Hits carboxylic acid, ester, ketone, aldehyde, carbonic acid/ester,anhydride, carbamic acid/ester, acyl halide, amide
- "[$([CX3]=[OX1]),$([CX3+]-[OX1-])]" #Hits either resonance structure
:carbonyl_with_carbon:
- "[CX3](=[OX1])C" #Hits aldehyde, ketone, carboxylic acid (except formic), anhydride (except formic), acyl halides (acid halides). Won't hit carbamic acid/ester, carbonic acid/ester
:carbonyl_with_nitrogen:
- "[OX1]=CN" #Hits amide, carbamic acid/ester, poly peptide
:carbonyl_with_oxygen:
- "[CX3](=[OX1])O" #Hits ester, carboxylic acid, carbonic acid or ester, carbamic acid or ester, anhydride Won't hit aldehyde or ketone
:acyl_halide:
- "[CX3](=[OX1])[F,Cl,Br,I]" #acid halide, -oyl halide
:aldehyde:
- "[CX3H1](=O)[#6]"
:anhydride:
- "[CX3](=[OX1])[OX2][CX3](=[OX1])"
:amidinium:
- "[NX3][CX3]=[NX3+]"
:carbamate:
- "[NX3,NX4+][CX3](=[OX1])[OX2,OX1-]" #Hits carbamic esters, acids, and zwitterions
:carbamic_ester:
- "[NX3][CX3](=[OX1])[OX2H0]"
:carbamic_acid:
- "[NX3,NX4+][CX3](=[OX1])[OX2H,OX1-]" #Hits carbamic acids and zwitterions.
:carboxylate_ion:
- "[CX3](=O)[O-]" #Hits conjugate bases of carboxylic, carbamic, and carbonic acids.
:carbonic_acid_or_ester:
- "[CX3](=[OX1])(O)O" #Carbonic Acid, Carbonic Ester, or combination
:carbonic_acid_or_carbonic_acid_ester:
- "[CX3](=[OX1])([OX2])[OX2H,OX1H0-1]" #Hits acid and conjugate base. Won't hit carbonic acid diester
:carbonic_ester:
- "C[OX2][CX3](=[OX1])[OX2]C" #(carbonic acid diester), Won't hit carbonic acid or combination carbonic acid/ester
:carboxylic_acid:
- "[CX3](=O)[OX2H1]" #-oic acid, COOH
:carboxylic_acid_or_conjugate_base:
- "[CX3](=O)[OX1H0-,OX2H1]"
:cyanamide:
- "[NX3][CX2]#[NX1]"
:hydrogen_atom:
- "[H]" #Hits SMILES that are hydrogen atoms: [H+] [2H] [H][H]
:not_hydrogen:
- "[!#1]" #Hits SMILES that are not hydrogen atoms
:mono_hydrogenated_cation:
- "[+H]" #Hits atoms that have a positive charge and exactly one attached hydrogen: F[C+](F)[H]
:not_mono_hydrogenated:
- "[!H]" #Hits atoms that don't have exactly one attached hydrogen
- "[!H1]" #Hits atoms that don't have exactly one attached hydrogen
#:primary_or_secondary_amine_not_amide: ## NOTE
# - "[NX3;H2,H1;!$(NC=O)]" #not ammonium ion (N must be 3-connected), not ammonia (H count can't be 3). Primary or secondary is specified by N's H-count (H2 & H1 respectively). Also note that "&" (and) is the dafault opperator and is higher precedence that "," (or), which is higher precedence than ";" (and). Will hit cyanamides and thioamides
:enamine:
- "[NX3][CX3]=[CX3]"
:primary_amine_not_amide:
- "[NX3;H2;!$(NC=[!#6]);!$(NC#[!#6])][#6]" #Not amide (C not double bonded to a hetero-atom), not ammonium ion (N must be 3-connected), not ammonia (N's H-count can't be 3), not cyanamide (C not triple bonded to a hetero-atom)
#:two_primary_or_secondary_amines: ### NOTE to fix!
# - "[NX3;H2,H1;!$(NC=O)].[NX3;H2,H1;!$(NC=O)]" #Here we use the disconnection symbol (".") to match two separate unbonded identical patterns.
:enamine_or_aniline_nitrogen:
- "[NX3][$(C=C),$(cc)]"
:azide_group:
- "[$(*-[NX2-]-[NX2+]#[NX1]),$(*-[NX2]=[NX2+]=[NX1-])]" #Hits any atom with an attached azide.
:azide_ion:
- "[$([NX1-]=[NX2+]=[NX1-]),$([NX1]#[NX2+]-[NX1-2])]" #Hits N in azide ion
:nitrogen:
- "[#7]" #Nitrogen in N-containing compound. aromatic or aliphatic. Most general interpretation of "azo"
:azo_nitrogen_lowspec:
- "[NX2]=N" #Low specificity. Hits diazene, azoxy and some diazo structures
:azo_nitrogen_diazene:
- "[NX2]=[NX2]" #(diaza alkene)
:azoxy_nitrogen:
- "[$([NX2]=[NX3+]([O-])[#6]),$([NX2]=[NX3+0](=[O])[#6])]"
:diazo_nitrogen:
- "[$([#6]=[N+]=[N-]),$([#6-]-[N+]#[N])]"
:azole:
- "[$([nr5]:[nr5,or5,sr5]),$([nr5]:[cr5]:[nr5,or5,sr5])]" #5 member aromatic heterocycle w/ 2double bonds. contains N & another non C (N,O,S) subclasses are furo-, thio-, pyrro- (replace CH o' furfuran, thiophene, pyrrol w/ N)
:hydrazine:
- "[NX3][NX3]" #H2NNH2
:hydrazone:
- "[NX3][NX2]=[*]" #C=NNH2
:substituted_imine:
- "[CX3;$([C]([#6])[#6]),$([CH][#6])]=[NX2][#6]" #Schiff base
:substituted_or_unsubstituted_imine:
- "[$([CX3]([#6])[#6]),$([CX3H][#6])]=[$([NX2][#6]),$([NX2H])]"
:iminium:
- "[NX3+]=[CX3]"
:unsubstituted_dicarboximide:
- "[CX3](=[OX1])[NX3H][CX3](=[OX1])"
:substituted_dicarboximide:
- "[CX3](=[OX1])[NX3H0]([#6])[CX3](=[OX1])"
:dicarboxdiimide:
- "[CX3](=[OX1])[NX3H0]([NX3H0]([CX3](=[OX1]))[CX3](=[OX1]))[CX3](=[OX1])"
:nitrate_group:
- "[$([NX3](=[OX1])(=[OX1])O),$([NX3+]([OX1-])(=[OX1])O)]" #Also hits nitrate anion
:nitrate_anion:
- "[$([OX1]=[NX3](=[OX1])[OX1-]),$([OX1]=[NX3+]([OX1-])[OX1-])]"
:nitrile:
- "[NX1]#[CX2]"
:isonitrile:
- "[CX1-]#[NX2+]"
:nitro_group:
- "[$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]" #Hits both forms
#:two_nitro_groups: ## NOTE
# - "[$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8].[$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]"
:nitroso_group:
- "[NX2]=[OX1]"
:n_oxide:
- "[$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])]" #Hits both forms. Won't hit azoxy, nitro, nitroso,or nitrate.
:hydroxyl:
- "[OX2H]"
:hydroxyl_in_alcohol:
- "[#6][OX2H]"
:hydroxyl_in_carboxylic_acid:
- "[OX2H][CX3]=[OX1]"
:hydroxyl_in_h_o_p:
- "[OX2H]P"
:hydroxyl_acidic:
- "[$([OH]-*=[!#6])]" #An acidic hydroxyl is a hydroxyl bonded to an atom which is multiply bonded to a hetero atom, this includes carboxylic, sulphur, phosphorous, halogen and nitrogen oxyacids
:enol:
- "[OX2H][#6X3]=[#6]"
:phenol:
- "[OX2H][cX3]:[c]"
:enol_or_phenol:
- "[OX2H][$(C=C),$(cc)]"
:peroxide_groups:
- "[OX2,OX1-][OX2,OX1-]" #Also hits anions
:phosphoric_acid_groups:
- "[$(P(=[OX1])([$([OX2H]),$([OX1-]),$([OX2]P)])([$([OX2H]),$([OX1-]),$([OX2]P)])[$([OX2H]),$([OX1-]),$([OX2]P)]),$([P+]([OX1-])([$([OX2H]),$([OX1-]),$([OX2]P)])([$([OX2H]),$([OX1-]),$([OX2]P)])[$([OX2H]),$([OX1-]),$([OX2]P)])]" #Hits both depiction forms. Hits orthophosphoric acid and polyphosphoric acid anhydrides. Doesn't hit monophosphoric acid anhydride esters (including acidic mono- & di- esters) but will hit some polyphosphoric acid anhydride esters (mono- esters on pyrophosphoric acid and longer, di- esters on linear triphosphoric acid and longer)
:phosphoric_ester_groups:
- "[$(P(=[OX1])([OX2][#6])([$([OX2H]),$([OX1-]),$([OX2][#6])])[$([OX2H]),$([OX1-]),$([OX2][#6]),$([OX2]P)]),$([P+]([OX1-])([OX2][#6])([$([OX2H]),$([OX1-]),$([OX2][#6])])[$([OX2H]),$([OX1-]),$([OX2][#6]),$([OX2]P)])]" #Hits both depiction forms. Doesn't hit non-ester phosphoric_acid groups
:carbo_thiocarboxylate:
- "[S-][CX3](=S)[#6]"
:carbo_thioester:
- "S([#6])[CX3](=O)[#6]"
:thio_analog_of_carbonyl:
- "[#6X3](=[SX1])([!N])[!N]" #Where S replaces O. Not a thioamide
:thiol_sulfide_or_disulfide_sulfur:
- "[SX2]"
:thiol:
- "[#16X2H]"
:sulfur_with_atleast_one_hydrogen:
- "[#16!H0]"
:thioamide:
- "[NX3][CX3]=[SX1]"
:sulfide:
- "[#16X2H0]" #-alkylthio - hits disulfides. Won't hit thiols
:mono_sulfide:
- "[#16X2H0][!#16]" #alkylthio- or alkoxy- Won't hit thiols. Won't hit disulfides.
:disulfide:
- "[#16X2H0][#16X2H0]" #Won't hit thiols. Won't hit mono-sulfides
#:two_sulfides: ## NOTE
# - "[#16X2H0][!#16].[#16X2H0][!#16]" #Won't hit thiols. Won't hit mono-sulfides. Won't hit disulfides.
:sulfinate:
- "[$([#16X3](=[OX1])[OX2H0]),$([#16X3+]([OX1-])[OX2H0])]" #Won't hit Sulfinic Acid. Hits Both Depiction Forms.
:sulfinic_acid:
- "[$([#16X3](=[OX1])[OX2H,OX1H0-]),$([#16X3+]([OX1-])[OX2H,OX1H0-])]" #Won't hit substituted Sulfinates. Hits Both Depiction Forms. Hits acid and conjugate base (sulfinate).
:sulfone_low_specificity:
- "[$([#16X4](=[OX1])=[OX1]),$([#16X4+2]([OX1-])[OX1-])]" #Hits all sulfones, including heteroatom-substituted sulfones: sulfonic acid, sulfonate, sulfuric acid mono- & di- esters, sulfamic acid, sulfamate, sulfonamide... Hits Both Depiction Forms.
:sulfone_high_specificity:
- "[$([#16X4](=[OX1])(=[OX1])([#6])[#6]),$([#16X4+2]([OX1-])([OX1-])([#6])[#6])]" #Only hits carbo- sulfones (Won't hit herteroatom-substituted molecules). Hits Both Depiction Forms.
:sulfonic_acid_high_specificity:
- "[$([#16X4](=[OX1])(=[OX1])([#6])[OX2H,OX1H0-]),$([#16X4+2]([OX1-])([OX1-])([#6])[OX2H,OX1H0-])]" #Only hits carbo- sulfonic acids (Won't hit herteroatom-substituted molecules). Hits acid and conjugate base. Hits Both Depiction Forms. Hits Arene sulfonic acids.
:sulfonate:
- "[$([#16X4](=[OX1])(=[OX1])([#6])[OX2H0]),$([#16X4+2]([OX1-])([OX1-])([#6])[OX2H0])]" #(sulfonic ester) Only hits carbon-substituted sulfur (Oxygen may be herteroatom-substituted). Hits Both Depiction Forms.
:sulfonamide:
- "[$([#16X4]([NX3])(=[OX1])(=[OX1])[#6]),$([#16X4+2]([NX3])([OX1-])([OX1-])[#6])]" #Only hits carbo- sulfonamide. Hits Both Depiction Forms.
:carbo_azosulfone:
- "[SX4](C)(C)(=O)=N" #Partial N-Analog of Sulfone
:sulfonamide:
- "[$([SX4](=[OX1])(=[OX1])([!O])[NX3]),$([SX4+2]([OX1-])([OX1-])([!O])[NX3])]" #(sulf drugs) Won't hit sulfamic acid or sulfamate. Hits Both Depiction Forms.
:sulfoxide_low_specificity:
- "[$([#16X3]=[OX1]),$([#16X3+][OX1-])]" #( sulfinyl, thionyl ) Analog of carbonyl where S replaces C. Hits all sulfoxides, including heteroatom-substituted sulfoxides, dialkylsulfoxides carbo-sulfoxides, sulfinate, sulfinic acids... Hits Both Depiction Forms. Won't hit sulfones.
:sulfoxide_high_specificity:
- "[$([#16X3](=[OX1])([#6])[#6]),$([#16X3+]([OX1-])([#6])[#6])]" #(sulfinyl, thionyl) Analog of carbonyl where S replaces C. Only hits carbo-sulfoxides (Won't hit herteroatom-substituted molecules). Hits Both Depiction Forms. Won't hit sulfones.
:sulfate:
- "[$([#16X4](=[OX1])(=[OX1])([OX2H,OX1H0-])[OX2][#6]),$([#16X4+2]([OX1-])([OX1-])([OX2H,OX1H0-])[OX2][#6])]" #(sulfuric acid monoester) Only hits when oxygen is carbon-substituted. Hits acid and conjugate base. Hits Both Depiction Forms.
:sulfuric_acid_ester_low_specificity:
- "[$([SX4](=O)(=O)(O)O),$([SX4+2]([O-])([O-])(O)O)]" #(sulfate ester); Hits sulfuric acid, sulfuric acid monoesters (sulfuric acids) and diesters (sulfates). Hits acid and conjugate base. Hits Both Depiction Forms.
:sulfuric_acid_diester:
- "[$([#16X4](=[OX1])(=[OX1])([OX2][#6])[OX2][#6]),$([#16X4](=[OX1])(=[OX1])([OX2][#6])[OX2][#6])]" #Only hits when oxygen is carbon-substituted. Hits Both Depiction Forms.
:sulfamate:
- "[$([#16X4]([NX3])(=[OX1])(=[OX1])[OX2][#6]),$([#16X4+2]([NX3])([OX1-])([OX1-])[OX2][#6])]" #Only hits when oxygen is carbon-substituted. Hits Both Depiction Forms.
:sulfamic_acid:
- "[$([#16X4]([NX3])(=[OX1])(=[OX1])[OX2H,OX1H0-]),$([#16X4+2]([NX3])([OX1-])([OX1-])[OX2H,OX1H0-])]" #Hits acid and conjugate base. Hits Both Depiction Forms.
:sulfenic_acid:
- "[#16X2][OX2H,OX1H0-]" #Hits acid and conjugate base.
:sulfenate:
- "[#16X2][OX2H0]"
:carbon_to_any_halogen:
- "[#6][F,Cl,Br,I]"
:halogen:
- "[F,Cl,Br,I]"
#:three_halides_groups: ## NOTE
# - "[F,Cl,Br,I].[F,Cl,Br,I].[F,Cl,Br,I]" #Hits SMILES that have three halides.
:acyl_halide:
- "[CX3](=[OX1])[F,Cl,Br,I]" #(acid halide, -oyl halide)
#experimental SMARTS
:phosphate1:
- "[PX4](=[OX1])([OX2])([OX2])[OX2]"
:phosphate2:
- "[PX4](=[OX1])([#8])([#8])([#8])"
:phosphate_nonspecific:
- "[PX4](=[OX2])" #not specific
:glycerol:
- "[CX4](-[OX2])[CX4](-[OX2])[CX4](-[OX2])"
#:glucose_cyclic:
# - "C1(-[OX2])C(-[CX4OX2)]OC(-[OX2])C(-[OX2])C1(-[OX2])" #do the carbons need the implicit H's?
:aldose:
- "[CX3H1](=[0X1])[CX4]" #aldopentose, aldohexose --> maybe just the aldehyde is sufficient?
:aldopentose:
- "[CX3H1](=[0X1])[CX4](-[0X2])[CX4](-[0X2])[CX4](-[0X2])[CX4](-[0X2])" #open form of arabinose, lyxose, ribose
:ketopentose:
- "[CX4](-[OX2])[CX3](=[OX1])[CX4](-[0X2])[CX4](-[0X2])[CX4](-[0X2])" #open form of ribulose and xylulose
:aldohexose:
- "[CX3H1](=[0X1])[CX4](-[0X2])[CX4](-[0X2])[CX4](-[0X2])[CX4](-[0X2])[CX4](-[0X2])" #hits open forms of glucose, allose, altrose, mannose, gulose, idose, galactose, talose
:ketohexose:
- "[CX4](-[OX2])[CX3](=[OX1])[CX4](-[0X2])[CX4](-[0X2])[CX4](-[0X2])[CX4](-[0X2])" #fructose, psicose, sorbose, tagatose
:choline:
# - "[CX4](-[OX2])[CX4][NX4](-[CX4])(-[CX4])(-[CX4])" #should we represent the positive N like this?
- "[NX4](-[CX4])(-[CX4])(-[CX4])[CX4][CX4][OX2]"
:phosphatidate:
- "[PX4](=[OX1])([#8])([#8])[#8][CX4][CX4](-[OX2][CX3](=O))[CX4][OX2][CX3](=O)"
:phosphocholine:
# - "[NX4](-[CX4])(-[CX4])(-[CX4])[CX4][CX4][OX2][PX4](=[OX1])([OX2H1])([OX2H1])" #hits just phosphocholine as independent lipid
- "[NX4](-[CX4])(-[CX4])(-[CX4])[CX4][CX4][OX2][PX4](=O)(-[#8])(-[#8])" #phosphocholine AND phosphatidylcholine...
:phosphatidylcholine:
- "[CX3](=[OX1])[OX2][CX4][CX4](-[OX2][CX3](=[OX1]))[CX4][OX2][PX4](=[OX1])(-[#8])[OX2][CX4][CX4][NX4](-[CX4])(-[CX4])(-[CX4])" #doesn't include the two 15C side chains; the SMILE --> CCCCCCCCCCCCCCCC(=O)OC[C@H](COP([O-])(=O)OCC[N+](C)(C)C)OC(=O)CCCCCCCCCCCCCCC"
:inositol:
- "C1(-[OX2])C(-[OX2])C(-[OX2])C(-[OX2])C(-[OX2])C1(-[OX2])" #a little fuzzy on cyclic SMARTS
:sphingosine:
# - "[CX4](-[OX2])[CX4](-[NX3])[CX4](-[OX2])[CX3]=[CX3]" #doesn't include last 13 carbons
- "[#8][CX4][CX4](-[#7])[CX4](-[#8])[CX3]=[CX3][CX4]"
:epoxide_ring:
- "c1Oc1" #???
# Ryan's additions
:tertiary_amine:
- "[NX3]"
:quaternary_amine:
- "[NX4+]"
:sulfonyl:
- "[SX4](=O)(=O)"
:phenyl:
- "cccccc"
:para_phenyl:
- "[cX3]cc[cX3]cc"
:ortho_phenyl:
- "[cX3][cX3]cccc"
:meta_phenyl:
- "[cX3]c[cX3]ccc"
#:isoprenoid:
# - "[CX3](CH3)=[CX3][CX4]"
#:turpenoid:
# - "[CX3](CH3)=[CX3][CX4]"
:isoprene:
- "CC(=C)C=C"
:cyclohexane:
- "C1CCCCCC1"
:chlorine:
- "Cl"
:hexanone:
- "cccccc(=O)"
:primary_alcohol:
- "[CX4]([OX2H])"
:pyrrole:
- "n1ccc1"
:saturated_fatty_acid_unit:
- "[CX4H2]"
:unsaturated_fatty_acid_unit:
- "[CX3H1]"
- "[CX3H1]=[CX3H1]"
:four_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H3]"
:six_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H2][CX4H2][CX4H3]"
:eight_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H3]"
:ten_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H3]"
:twelve_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H3]"
:fourteen_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H3]"
:sixteen_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H3]"
:eighteen_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H3]"
:twenty_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H3]"
:twenty_two_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H3]"
:twenty_four_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H3]"
:five_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H2][CX4H3]"
:seven_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H3]"
:nine_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H3]"
:eleven_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H3]"
:thirteen_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H3]"
:fifteen_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H3]"
:seventeen_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H3]"
:nineteen_carbon_terminal_ended_saturated_FA:
- "O[CX3](=O)[CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H2][CX4H3]"
:three_member_heterocyclic_ring:
- "[!#6;r3][r3][r3]"
:four_member_heterocyclic_ring:
- "[!#6;r4][r4][r4][r4]"
:five_member_heterocyclic_ring:
- "[!#6;r5][r5][r5][r5][r5]"
:six_member_heterocyclic_ring:
- "[!#6;r6][r6][r6][r6][r6][r6]"
:seven_member_heterocyclic_ring:
- "[!#6;r7][r7][r7][r7][r7][r7][r7]"
:eight_member_heterocyclic_ring:
- "[!#6;r8][r8][r8][r8][r8][r8][r8][r8]"
:nine_member_heterocyclic_ring:
- "[!#6;r9][r9][r9][r9][r9][r9][r9][r9][r9]"
:ten_member_heterocyclic_ring:
- "[!#6;r10][r10][r10][r10][r10][r10][r10][r10][r10][r10]"
:eleven_member_heterocyclic_ring:
- "[!#6;r11][r11][r11][r11][r11][r11][r11][r11][r11][r11][r11]"
:twelve_member_heterocyclic_ring:
- "[!#6;r12][r12][r12][r12][r12][r12][r12][r12][r12][r12][r12][r12]"
:three_member_aliphatic_carbon_ring:
- "[C;r3][C;r3][C;r3]"
:four_member_aliphatic_carbon_ring:
- "[C;r4][C;r4][C;r4][C;r4]"
:five_member_aliphatic_carbon_ring:
- "[C;r5][C;r5][C;r5][C;r5][C;r5]"
:six_member_aliphatic_carbon_ring:
- "[C;r6][C;r6][C;r6][C;r6][C;r6][C;r6]"
:seven_member_aliphatic_carbon_ring:
- "[C;r7][C;r7][C;r7][C;r7][C;r7][C;r7][C;r7]"
:eight_member_aliphatic_carbon_ring:
- "[C;r8][C;r8][C;r8][C;r8][C;r8][C;r8][C;r8][C;r8]"
:nine_member_aliphatic_carbon_ring:
- "[C;r9][C;r9][C;r9][C;r9][C;r9][C;r9][C;r9][C;r9][C;r9]"
:ten_member_aliphatic_carbon_ring:
- "[C;r10][C;r10][C;r10][C;r10][C;r10][C;r10][C;r10][C;r10][C;r10][C;r10]"
:eleven_member_aliphatic_carbon_ring:
- "[C;r11][C;r11][C;r11][C;r11][C;r11][C;r11][C;r11][C;r11][C;r11][C;r11][C;r11]"
:twelve_member_aliphatic_carbon_ring:
- "[C;r12][C;r12][C;r12][C;r12][C;r12][C;r12][C;r12][C;r12][C;r12][C;r12][C;r12][C;r12]"
:bicyclic_aliphatic_carbon:
- "[C;R2]"
:tricyclic_aliphatic_carbon:
- "[C;R3]"
:polycyclic_aliphatic_carbon:
- "[C;R4]"
:three_member_aromatic_ring:
- "[a;r3][a;r3][a;r3]"
:four_member_aromatic_ring:
- "[a;r4][a;r4][a;r4][a;r4]"
:five_member_aromatic_ring:
- "[a;r5][a;r5][a;r5][a;r5][a;r5]"
:six_member_aromatic_ring:
- "[a;r6][a;r6][a;r6][a;r6][a;r6][a;r6]"
:seven_member_aromatic_ring:
- "[a;r7][a;r7][a;r7][a;r7][a;r7][a;r7][a;r7]"
:eight_member_aromatic_ring:
- "[a;r8][a;r8][a;r8][a;r8][a;r8][a;r8][a;r8][a;r8]"
:nine_member_aromatic_ring:
- "[a;r9][a;r9][a;r9][a;r9][a;r9][a;r9][a;r9][a;r9][a;r9]"
:ten_member_aromatic_ring:
- "[a;r10][a;r10][a;r10][a;r10][a;r10][a;r10][a;r10][a;r10][a;r10][a;r10]"
:eleven_member_aromatic_ring:
- "[a;r11][a;r11][a;r11][a;r11][a;r11][a;r11][a;r11][a;r11][a;r11][a;r11][a;r11]"
:twelve_member_aromatic_ring:
- "[a;r12][a;r12][a;r12][a;r12][a;r12][a;r12][a;r12][a;r12][a;r12][a;r12][a;r12][a;r12]"
:benzene:
- "c1ccccc1"
:acid_anhydride:
- "[#6][CX3](=O)[OX2][CX3](=O)[#6]" #should we take off the flanking C's?
:triglyceride: #not sure if will work
# - "[CX4][CX3](=O)[OX2][CX4][CX4]([OX2][CX3](=O)[CX4])[CX4][OX2][CX3](=O)[CX4]"
- "[CX4](-[OX2][CX3](=O)[CX4])[CX4](-[OX2][CX3](=O)[CX4])[CX4](-[OX2][CX3](=O)[CX4])"
:glycerophosphate: #2,3-dihydroxypropyl phosphate
- "[PX4](-[OX2])(=O)(-[OX2])[OX2][CX4][CX4](-[OX2H1])[CX4][OX2H1]"
#:terpene:
#- ""
:carbon:
- "[#6]"
:not_carbon_or_hydrogen_or_oxygen:
- "[!#6,!#1,!#8]"
:branched_carbon:
- "[$([CD3]);!$(C([!C]))]"
:tert_carbon:
- "[$([CD4]);!$(C([!C]))]"
:methoxy:
- "[#6](-[OX2][CD1])"
:prostaglandin:
- "[$([r5]);!$(CO);$([C@@C])]"
:mycolic_acid:
- "OC(=O)[CX4](C)[CX4](O)(C)"
:ethanolamine:
- "[#7][CX4][CX4][OX2][HX1]"
:Z_config_nonspecif_1:
- "[#6]/[#6]=[#6]\\[#6]"
:Z_config_nonspecif_2:
- "[#6]\\[#6]=[#6]/[#6]"
:Z_config_specif_1:
- "[CX4]/[CX3]=[CX3]\\[CX4]"
:Z_config_specif_2:
- "[CX4]\\[CX3]=[CX3]/[CX4]"
:Z_config_on_oxy_nonspecif_1:
- "[#6]/[#6]=[#6]\\[#8]"
:Z_config_on_oxy_nonspecif_2:
- "[#6]\\[#6]=[#6]/[#8]"
:Z_config_on_oxy_specif_1:
- "[CX4]/[CX3]=[CX3]\\[OX2]"
:Z_config_on_oxy_specif_2:
- "[CX4]\\[CX3]=[CX3]/[OX2]"
:N_acyl4hydroxysphinganine: # phytoceramides
- "[NX3][CX4][CX4]([OX2])[CX4]([OX2])"
#SMARTS ADDED FROM http://tech.knime.org/forum/indigo/molecule-functionality-node-request
:Alkane:
- "[CX4;$([H3][#6]),$([H2]([#6])[#6]),$([H1]([#6])([#6])[#6]),$([#6]([#6])([#6])([#6])[#6])]"
:Alkane_Primary:
- "[CX4H3][#6]"
:Alkane_Secondary:
- "[CX4H2]([#6])[#6]"
:Alkane_Tertiary:
- "[CX4H1]([#6])([#6])[#6]"
:Alkane_Quaternary:
- "[CX4]([#6])([#6])([#6])[#6]"
:Alkene:
- "[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]=[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]"
:Alkyne:
- "[CX2]#[CX2]"
:Allene:
- "[CX3]=[CX2]=[CX3]"
:Aniline:
- "[c][NX3H2]"
:Benzenering:
- "c1ccccc1"
:Carbazole:
- "c1c3c(ccc1)c2ccccc2n3-[$([#1]),$([#6])]"
:Iminoarene:
- "[*;r6]=[NX2]"
:Oxoarene:
- "[*;r6]=[O]"
:Phenol:
- "[c][OX2H]"
:Thioarene:
- "[*;r6]=[S]"
:Amidine:
- "[NX3][C]=[NX2]"
:Amine:
- "[NX3,NX3+0,NX4+;!$([N]~[#7,#8,#15,#16])]"
:Amine_Primary:
- "[NX3H2,NX3H2+0,NX4H3+;!$([N]~[#7,#8,#15,#16])]"
:Amine_Secondary:
- "[NX3H1,NX3H1+0,NX4H2+;!$([N]~[#7,#8,#15,#16])]"
:Amine_Tertiary:
- "[NX3H0,NX3H0+0,NX4H1+;!$([N]~[#7,#8,#15,#16])]"
:Ammonium:
- "[NH4+]"
:Ammonia:
- "[NH3]"
:Aminal:
- "[NX3v3;!$(NC=[#7,#8,#15,#16])]~[CX4;!$(C(N)(N)[!#6])]~[NX3v3;!$(NC=[#7,#8,#15,#16])]"
:Aziridine:
- "C1CN1"
:Azide:
- "[NX1]~[NX2]~[NX2,NX1]"
:Acylazide:
- "[CX3](=[OX1])[NX2]~[NX2]~[NX1]"
:Azo:
- "[#6]-[#7]=[#7]-[#6]"
:Diazo:
- "[$([#6]=[N+]=[N-]),$([#6-]-[N+]#[N])]"
:Diazonium:
- "[#6][NX2+]#[NX1]"
:Carbodiimide:
- "[NX2]=[CX2]=[NX2]"
:Enamine:
- "[NX3;!$(NC~[!#1!#6])][CX3]=[CX3]"
:Guanidine:
- "[N;v3X3,v4X4+][CX3](=[N;v3X2,v4X3+])[N;v3X3,v4X4+]"
:Hydrazine:
- "[NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])]"
:Hydrazone:
- "[NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX2]=[#6]"
:Iminyl:
- "[NX2;$([N][#6]),$([NH]);!$([N][CX3]=[#7,#8,#15,#16])]=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])]"
:Aldimine:
- "[NX2;$([H1]),$([H0][#6])]=[CX3;$([H2]),$([H1])]"
:Aldimine_Primary:
- "[NX2;$([H1])]=[CX3;$([H2]),$([H1])]"
:Aldimine_Secondary:
- "[NX2;$([H0][#6])]=[CX3;$([H2]),$([H1])]"
:ketimine:
- "[NX2;$([H1]),$([H0][#6])]=[CX3;$([H0][#6])]"
:Primary:
- "[NX2;$([H1])]=[CX3;$([H0][#6])]"
:Secondary:
- "[NX2;$([H0][#6])]=[CX3;$([H0][#6])]"
:Isocyanide:
- "[N+]#[C-]"
:Nitrile:
- "[NX1]#[CX2]"
:Thiosemicarbazone:
- "[#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]"
:AcylNitrile:
- "[NX1]#[CX2][CX3]=[OX1]"
:Amide:
- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H2,#7X3H1,#7X3H0]"
:Amide_Primary:
- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[NX3H2]"
:Amide_Secondary:
- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])]"
:Amide_Tertiary:
- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])]"
:Azoxy:
- "[#6][$([NX2]=[NX3+]([O-])[#6]),$([NX2]=[NX3+0](=[O])[#6])]"
:Carbamate:
- "[NX3,NX4+][CX3](=[OX1])[OX2,OX1-]"
:Cyanate:
- "[OX2][CX2]#[NX1]"
:Enamide:
- "[CX3]=[CX3]~[CX3;$([R0][#6]),$([H1R0])](=[OX1])[NX3]"
:Hydroxamicacid:
- "[OX1]=[CX3][NX3;$([H1][OH])]"
:Hydroxylamine:
- "[NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][OX2H1,OX2H0]"
:Hemiaminal:
- "[NX3,NX3+0,NX4+;!$([N]~[#7,#8,#15,#16])]~[CX4]~[OX2H]"
:Imidate:
- "[NX2;$([H1]),$([H0][#6])]=[CX3;$([H0][#8])]"
:Imide:
- "[CX3](=[OX1])[NX3][CX3](=[OX1])"
:Isocyanate:
- "[NX2]=[CX2]=[OX1]"
:Lactam:
- "[#6R][#6X3R](=[OX1])[#7X3H2,#7X3H1,#7X3H0]"
:Nitrate:
- "[NX3+]([OX1-])(=[OX1])([OX1-])"
:Nitrite:
- "[NX2](=[OX1])[O;$([X2]),$([X1-])]"
:Nitro:
- "[$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]"
:Nitrone:
- "[NX3+;$([H1][OX1-]),$([H0][OX1-])]=[C]"
:Nitroso:
- "[NX2](=[OX1])[!#7;!#8]"
:Nitrosamine:
- "[NX3;!$(N=O)][NX2]=[OX1]"
:Oxime:
- "[NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2H]"
:Semicarbazone:
- "[#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]"
:Semicarbazide:
- "[#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]"
:Thionitrite:
- "[SX2][NX2]=[OX1]"
:OximEther:
- "[NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2][#6;!$(C=[#7,#8])]"
:Urea:
- "[NX3][CX3](=[OX1])[NX3]"
:Urethane:
- "[NX3,NX4+][CX3](=[OX1])[OX2,OX1-]"
:Acetal:
- "[CX4][OX2][CX4H1]([#6])[OX2][CX4]"
:Anhydride:
- "[CX3;$([H0][#6]),$([H1])](=[OX1])[#8X2][CX3;$([H0][#6]),$([H1])](=[OX1])"
:Alcohol:
- "[OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])]"
:Alcohol_Primary:
- "[OX2H][CX4H2;!$(C([OX2H])[O,S,#7,#15])]"
:Alcohol_Secondary:
- "[OX2H][CX4H;!$(C([OX2H])[O,S,#7,#15])]"
:Alcohol_Tertiary:
- "[OX2H][CX4;$([H0])]"
:AminoAlcohol_1_2:
- "[OX2H][CX4;!$(C([OX2H])[O,S,#7,#15,F,Cl,Br,I])][CX4;!$(C([N])[O,S,#7,#15])][NX3,NX4+;!$(NC=[O,S,N])]"
:Carbonate:
- "[CX3](=[OX1])([OX2][CX4])[OX2][CX4]"
:Diol_1_2:
- "[OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])][CX4;!$(C([OX2H])[O,S,#7,#15])][OX2H]"
:Diol_1_1:
- "[OX2H][CX4;!$(C([OX2H])([OX2H])[O,S,#7,#15])][OX2H]"
:Carbonyl:
- "[CX3]=[OX1]"
:Aldehyde:
- "[$([CX3H][#6]),$([CX3H2])]=[OX1]"
:Ketone:
- "[#6][CX3](=[OX1])[#6]"
:Enone:
- "[CX3]=[CX3]~[CX3;$([R0][#6]),$([H1R0])](=[OX1])[CX4]"
:CarboxylicAcidDerivative:
- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[$([OX2H]),$([OX1-]),$([OX2][#6;!$(C=[O,N,S])])]"
:CarboxylicAcid:
- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[$([OX2H]),$([OX1-])]"
:CarboxylicEster:
- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[OX2][#6;!$(C=[O,N,S])]"
:Enol:
- "[OX2H][CX3]=[CX3]"
:EnolEster:
- "[OX2][CX3](=[CX3])[CX3]=[O]"
:EnolEther:
- "[OX2]([#6;!$(C=[N,O,S])])[CX3;$([H0][#6]),$([H1])]=[CX3]"
:Epoxide:
- "[OX2r3]1[#6r3][#6r3]1"
:Ether:
- "[OD2;!$(OC~[!#1!#6])]([#6])[#6]"
:Ketene:
- "[CX3]=[CX2]=[OX1]"
:Hemiacetal:
- "[OX2H][CX4H1,!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]"
:Hydrate:
- "[OX2;$([H2])]"
:Lactone:
- "[#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])]"
:Peroxide:
- "[OX2,OX1-][OX2,OX1-]"
:Hydroperoxide:
- "[OX2H][OX2]"
#Halogens
:Acidhalide:
- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1,ClX1,BrX1,IX1]"
:AcidBromide:
- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[BrX1]"
:AcidChloride:
- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[ClX1]"
:AcidFluoride:
- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1]"
:AcidIodide:
- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[IX1]"
:AlkenylHalide:
- "[C]=[C][FX1,ClX1,BrX1,IX1]"
:AlkenylBromide:
- "[C]=[C][BrX1]"
:AlkenylChloride:
- "[C]=[C][ClX1]"
:AlkenylFluoride:
- "[C]=[C][FX1]"
:AlkenylIodide:
- "[C]=[C][IX1]"
:AlkyneHalide:
- "[C]#[C][FX1,ClX1,BrX1,IX1]"
:AlkyneBromide:
- "[C]#[C][BrX1]"
:AlkyneChloride:
- "[C]#[C][ClX1]"
:AlkyneFluoride:
- "[C]#[C][FX1]"
:AlkyneIodide:
- "[C]#[C][IX1]"
:AlkylHalide:
- "[CX4][FX1,ClX1,BrX1,IX1]"
:AlkylBromide:
- "[BrX1][CX4]"
:AlkylChloride:
- "[ClX1][CX4]"
:AlkylFluoride:
- "[FX1][CX4]"
:AlkylIodide:
- "[IX1][CX4]"
:ArylHalide:
- "c1ccccc1[FX1,ClX1,BrX1,IX1]"
:ArylBromide:
- "c1ccccc1[BrX1]"
:ArylChloride:
- "c1ccccc1[ClX1]"
:ArylFluoride:
- "c1ccccc1[FX1]"
:ArylIodide:
- "c1ccccc1[IX1]"
#:Organometallic
:MetallicCompounds:
- "[Li,Na,K,Rb,Cs,Be,Ca,Sr,Mg,Ba,Sc,Ti,V,Cr,Mn,Fe,Co,Ni,Cu,Zn,Al,Ga,Y,Zr,Nb,Mo,Tc,Ru,Rh,Pd,Ag,Cd,In,Sn,Lu,Hf,Ta,W,Re,Os,Ir,Pt,Au,Hg,Tl,Pb,Bi]"
:LithiumIon:
- "[Li+]"
:Lithium:
- "[LiX1]"
:SodiumIon:
- "[Na+]"
:Sodium:
- "[NaX1]"
:PotassiumIon:
- "[K+]"
:Potassium:
- "[KX1]"
:RubidiumIon:
- "[Rb+]"
:Rubidium:
- "[RbX1]"
:CaesiumIon:
- "[Cs+]"
:Caesium:
- "[CsX1]"
:BerylliumIon:
- "[Be++]"
:Beryllium:
- "[BeX2]"
:CalciumIon:
- "[Ca++]"
:Calcium:
- "[CaX2]"
:StrontiumIon:
- "[Sr++]"
:Strontium:
- "[SrX2]"
:MagnesiumIon:
- "[Mg++]"
:Magnesium:
- "[MgX2]"
:BariumIon:
- "[Ba++]"
:Barium:
- "[BaX2]"
:ScandiumIon:
- "[Sc++]"
:Scandium:
- "[ScX3]"
:TitaniumIon:
- "[Ti++++,Ti++++,Ti++]"
:Titanium4Ion:
- "[Ti++++]"
:Titanium3Ion:
- "[Ti+++]"
:Titanium2Ion:
- "[Ti++]"
:Titanium_smarts:
- "[TiX4,TiX3]"
:VanadiumIon:
- "[V+++++,V++++,V+++,V++]"
:Vanadium5Ion:
- "[V+++++]"
:Vanadium4Ion:
- "[V++++]"
:Vanadium3Ion:
- "[V+++]"
:Vanadium2Ion:
- "[V++]"
:Vanadium:
- "[VX5,VX4,VX3,VX2]"
:ChromiumIon:
- "[Cr+++,Cr++]"
:Chromium3Ion:
- "[Cr+++]"
:Chromium2Ion:
- "[Cr++]"
:Chromium:
- "[CrX6,CrX3,CrX2]"
:ManganeseIon:
- "[Mn+++++++,Mn++++++,Mn++++,Mn+++,Mn++]"
:Manganese7Ion:
- "[Mn+++++++]"
:Manganese6Ion:
- "[Mn++++++]"
:Manganese4Ion:
- "[Mn++++]"
:Manganese3Ion:
- "[Mn+++]"
:Manganese2Ion:
- "[Mn++]"
:Manganese:
- "[MnX7,MnX6,MnX5,MnX4,MnX3,MnX2]"
:IronIon:
- "[Fe+++,Fe++]"
:Iron3Ion:
- "[Fe+++]"
:Iron2Ion:
- "[Fe++]"
:Iron:
- "[FeX3,FeX2]"
:CobaltIon:
- "[Co+++,Co++]"
:Cobalt3Ion:
- "[Co+++]"
:Cobalt2Ion:
- "[Co++]"
:Cobalt:
- "[CoX3,CoX2]"
:NickelIon:
- "[Ni+++,Ni++]"
:Nickel3Ion:
- "[Ni+++]"
:Nickel2Ion:
- "[Ni++]"
:Nickel:
- "[NiX3,NiX2]"
:CopperIon:
- "[Cu++,Cu+]"
:Copper2Ion:
- "[Cu++]"
:Copper1Ion:
- "[Cu+]"
:Copper:
- "[CuX2]"
:zincIon:
- "[Zn++]"
:zinc:
- "[ZnX2]"
:AluminiumIon:
- "[Al+++]"
:Aluminium:
- "[AlX3]"
:GalliumIon:
- "[Ga+++]"
:Gallium:
- "[GaX3,GaX2]"
:YttriumIon:
- "[Y+++]"
:Yttrium:
- "[YX3]"
:ZirconiumIon:
- "[Zr++++]"
:Zirconium:
- "[ZrX4,ZrX3,ZrX2]"
:NiobiumIon:
- "[Nb+++++,Nb++++,Nb+++,Nb++]"
:Niobium5Ion:
- "[Nb+++++]"
:Niobium4Ion:
- "[Nb++++]"
:Niobium3Ion:
- "[Nb+++]"
:Niobium2Ion:
- "[Nb++]"
:Niobium:
- "[NbX5,NbX4,NbX3,NbX2]"
:MolybdenumIon:
- "[Mo++++++,Mo+++++,Mo++++,Mo+++,Mo++]"
:Molybdenum6Ion:
- "[Mo++++++]"
:Molybdenum5Ion:
- "[Mo+++++]"
:Molybdenum4Ion:
- "[Mo++++]"
:Molybdenum3Ion:
- "[Mo+++]"
:Molybdenum2Ion:
- "[Mo++]"
:Molybdenum:
- "[MoX6,MoX5,MoX4,MoX3,MoX2]"
:Technetium:
- "[TcX7,TcX6,TcX5,TcX4,TcX2]"
:RutheniumIon:
- "[Ru++++,Ru+++,Ru++]"
:Ruthenium4Ion:
- "[Ru++++]"
:Ruthenium3Ion:
- "[Ru+++]"
:Ruthenium2Ion:
- "[Ru++]"
:Ruthenium:
- "[RuX4,RuX3,RuX2]"
:RhodiumIon:
- "[Rh+++,Rh++]"
:Rhodium3Ion:
- "[Rh+++]"
:Rhodium2Ion:
- "[Rh++]"
:Rhodium:
- "[RhX6,RhX5,RhX4,RhX3,RhX2]"
:PalladiumIon:
- "[Pd++++,Pd++]"
:Palladium3Ion:
- "[Pd++++]"
:Palladium2Ion:
- "[Pd++]"
:Palladium:
- "[PdX4,PdX2]"
:SilverIon:
- "[Ag+++,Ag++,Ag+]"
:Silver3Ion:
- "[Ag+++]"
:Silver2Ion:
- "[Ag++]"
:Silver1Ion:
- "[Ag+]"
:Silver:
- "[AgX3,AgX2,AgX2]"
:CadmiumIon:
- "[Cd++]"
:Cadmium:
- "[CdX2]"
:Indium:
- "[InX3]"
:TinIon:
- "[Sn++++,Sn++]"
:TinIon:
- "[Sn++++]"
:TinIon:
- "[Sn++]"
:Tin:
- "[SnX4,SnX2]"
:Lutetium:
- "[LuX3]"
:Hafnium:
- "[HfX4]"
:Tantalum:
- "[TaX5,TaX4,TaX3]"
:Tungsten:
- "[WX6,WX5,WX4,WX3,WX2,WX2]"
:Rhenium:
- "[ReX7,ReX6,ReX4,ReX2]"
:Osmium:
- "[OsX4,OsX3]"
:Iridium:
- "[IrX6,IrX4,IrX3,IrX2]"
:Platinum:
- "[PtX4,PtX3,PtX2]"
:Gold:
- "[AuX3,AuX1]"
:Mercury:
- "[HgX2,HgX1]"
:Thallium:
- "[TlX3,TlX1]"
:Lead:
- "[PbX4,PbX2]"
:Bismuth:
- "[BiX5,BiX3]"
:Metalloid:
- "[B,Si,Ge,As,Sb,Te,At]"
:Boron:
- "[BX3,BX4-]"
:Silicon:
- "[SiX4,SiX3,SiX2,SiX1,SiX4-,SiX3-,SiX2-,SiX1-]"
:Germanium:
- "[GeX4,GeX3,GeX2,GeX1,GeX4-,GeX3-,GeX2-,GeX1-]"
:Arsenic:
- "[AsX5,AsX3,AsX2,AsX1,AsX3-]"
:Antimony:
- "[SbX5,SbX4+,SbX3,SbX3-]"
:Tellurium:
- "[TeX6,TeX5,TeX4,TeX2,TeX2-]"
:PhosphoricAcidDerivative:
- "[PX4D4](=[!#6])([!#6])([!#6])[!#6]"
:PhosphoricAcid:
- "[PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]"
:PhosphoricMonoester:
- "[PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]"
:PhosphoricDiester:
- "[PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]"
:PhosphoricTriester: