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smarts_daylight.tsv
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smarts_daylight.tsv
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name smarts comment
Alkyl Carbon [CX4]
Allenic Carbon [$([CX2](=C)=C)]
Vinylic Carbon [$([CX3]=[CX3])]
Acetylenic Carbon [$([CX2]#C)]
arene c (Ar , aryl-, aromatic hydrocarbons)
carbonyl [CX3]=[OX1] Hits carboxylic acid, ester, ketone, aldehyde, carbonic acid/ester,anhydride, carbamic acid/ester, acyl halide, amide.
Carbonyl group [$([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] -al
Anhydride [CX3](=[OX1])[OX2][CX3](=[OX1])
Amide [NX3][CX3](=[OX1])[#6] -amide
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 Carbonic 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 (carbonic acid diester) C[OX2][CX3](=[OX1])[OX2]C 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]
Ester Also hits anhydrides [#6][CX3](=O)[OX2H0][#6] won't hit formic anhydride.
Ketone [#6][CX3](=O)[#6] -one
Ether [OD2]([#6])[#6]
Hydrogen Atom [H] Hits SMILES that are hydrogen atoms: [H+] [2H] [H][H]
Not a Hydrogen Atom [!#1] Hits SMILES that are not hydrogen atoms.
Proton [H+] Hits positively charged hydrogen atoms: [H+]
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.
Primary or secondary amine, not amide [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 [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)]
Generic amino acid: low specificity [NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N] For use w/ non-standard a.a. search. hits pro but not gly. Hits acids and conjugate bases. Hits single a.a.s and specific residues w/in polypeptides (internal, or terminal).
Dipeptide group. generic amino acid: low specificity [NX3H2,NH3X4+][CX4H]([*])[CX3](=[OX1])[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-] Won't hit pro or gly. Hits acids and conjugate bases.
Amino Acid [$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-,N] Replace * w/ a specific a.a. side chain from the 18_standard_side_chains list to hit a specific standard a.a. Won't work with Proline or Glycine, they have their own SMARTS (see side chain list). Hits acids and conjugate bases. Hits single a.a.s and specific residues w/i n polypeptides (internal, or terminal). {e.g. usage: Alanine side chain is [CH3X4] . Search is [$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([ CH3X4])[CX3](=[OX1])[OX2H,OX1-,N]}
Alanine side chain [CH3X4]
Arginine side chain [CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0])[NH2X3] Hits acid and conjugate base.
Aspargine side chain [CH2X4][CX3](=[OX1])[NX3H2] Also hits Gln side chain when used alone.
Aspartate (or Aspartic acid) side chain [CH2X4][CX3](=[OX1])[OH0-,OH] Hits acid and conjugate base. Also hits Glu side chain when used alone.
Cysteine side chain [CH2X4][SX2H,SX1H0-] Hits acid and conjugate base
Glutamate (or Glutamic acid) side chain [CH2X4][CH2X4][CX3](=[OX1])[OH0-,OH] Hits acid and conjugate base.
Glycine [$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H2][CX3](=[OX1])[OX2H,OX1-,N])]
Histidine side chain [CH2X4][#6X3]1:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]1 Hits acid & conjugate base for either Nitrogen. Note that the Ns can be either ([(Cationic 3-connected with one H) or (Neutral 2-connected without any Hs)] where there is a second-neighbor who is [3-connected with one H]) or (3-connected with one H).
Isoleucine side chain [CHX4]([CH3X4])[CH2X4][CH3X4]
Leucine side chain [CH2X4][CHX4]([CH3X4])[CH3X4]
Lysine side chain [CH2X4][CH2X4][CH2X4][CH2X4][NX4+,NX3+0] Acid and conjugate base
Methionine side chain [CH2X4][CH2X4][SX2][CH3X4]
Phenylalanine side chain [CH2X4][cX3]1[cX3H][cX3H][cX3H][cX3H][cX3H]1
Proline [$([NX3H,NX4H2+]),$([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[OX2H,OX1-,N]
Serine side chain [CH2X4][OX2H]
Thioamide [NX3][CX3]=[SX1]
Threonine side chain [CHX4]([CH3X4])[OX2H]
Tryptophan side chain [CH2X4][cX3]1[cX3H][nX3H][cX3]2[cX3H][cX3H][cX3H][cX3H][cX3]12
Tyrosine side chain [CH2X4][cX3]1[cX3H][cX3H][cX3]([OHX2,OH0X1-])[cX3H][cX3H]1 Acid and conjugate base
Valine side chain [CHX4]([CH3X4])[CH3X4]
Alanine side chain [CH3X4]
Arginine side chain [CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0])[NH2X3] Hits acid and conjugate base.
Aspargine side chain [CH2X4][CX3](=[OX1])[NX3H2] Also hits Gln side chain when used alone.
Aspartate (or Aspartic acid) side chain [CH2X4][CX3](=[OX1])[OH0-,OH] Hits acid and conjugate base. Also hits Glu side chain when used alone.
Cysteine side chain [CH2X4][SX2H,SX1H0-] Hits acid and conjugate base
Glutamate (or Glutamic acid) side chain [CH2X4][CH2X4][CX3](=[OX1])[OH0-,OH] Hits acid and conjugate base.
Glycine N[CX4H2][CX3](=[OX1])[O,N]
Histidine side chain [CH2X4][#6X3]1:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]1 Hits acid & conjugate base for either Nitrogen. Note that the Ns can be either ([(Cationic 3-connected with one H) or (Neutral 2-connected without any Hs)] where there is a second-neighbor who is [3-connected
Isoleucine side chain [CHX4]([CH3X4])[CH2X4][CH3X4]
Leucine side chain [CH2X4][CHX4]([CH3X4])[CH3X4]
Lysine side chain [CH2X4][CH2X4][CH2X4][CH2X4][NX4+,NX3+0] Acid and conjugate base
Methionine side chain [CH2X4][CH2X4][SX2][CH3X4]
Phenylalanine side chain [CH2X4][cX3]1[cX3H][cX3H][cX3H][cX3H][cX3H]1
Proline N1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[O,N]
Serine side chain [CH2X4][OX2H]
Threonine side chain [CHX4]([CH3X4])[OX2H]
Tryptophan side chain [CH2X4][cX3]1[cX3H][nX3H][cX3]2[cX3H][cX3H][cX3H][cX3H][cX3]12
Tyrosine side chain [CH2X4][cX3]1[cX3H][cX3H][cX3]([OHX2,OH0X1-])[cX3H][cX3H]1 Acid and conjugate base
Valine side chain [CHX4]([CH3X4])[CH3X4]
Azide group [$(*-[NX2-]-[NX2+]#[NX1]),$(*-[NX2]=[NX2+]=[NX1-])] Hits any atom with an attached azide.
Azide ion [$([NX1-]=[NX2+]=[NX1-]),$([NX1]#[NX2+]-[NX1-2])] Hits N in azide ion
Nitrogen [#7] "Nitrogen in N-containing compound. aromatic or aliphatic. Most general interpretation of ""azo"""
Azo Nitrogen. Low specificity [NX2]=N Hits diazene, azoxy and some diazo structures
Azo Nitrogen.diazene [NX2]=[NX2] (diaza alkene)
Azoxy Nitrogen [$([NX2]=[NX3+]([O-])[#6]),$([NX2]=[NX3+0](=[O])[#6])]
Diazo Nitrogen [$([#6]=[N+]=[N-]),$([#6-]-[N+]#[N])]
Azole [$([nr5]:[nr5,or5,sr5]),$([nr5]:[cr5]:[nr5,or5,sr5])] 5 member aromatic heterocycle w/ 2double bonds. contains N & another non C (N,O,S) subclasses are furo-, thio-, pyrro- (replace CH o' furfuran, thiophene, pyrrol w/ N)
Hydrazine H2NNH2 [NX3][NX3]
Hydrazone C=NNH2 [NX3][NX2]=[*]
Substituted imine [CX3;$([C]([#6])[#6]),$([CH][#6])]=[NX2][#6] Schiff base
Substituted or un-substituted imine [$([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),$([NX3+](=O)[O-])][!#8] Hits both forms.
Two Nitro groups [$([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]);!$([#7]=[#7])] Hits both forms. Won't hit azoxy, nitro, nitroso,or nitrate.
Hydroxyl [OX2H]
Hydroxyl in Alcohol [#6][OX2H]
Hydroxyl in Carboxylic Acid [OX2H][CX3]=[OX1]
Hydroxyl in H-O-P- [OX2H]P
Enol [OX2H][#6X3]=[#6]
Phenol [OX2H][cX3]:[c]
Enol or Phenol [OX2H][$(C=C),$(cc)]
Hydroxyl_acidic [$([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.
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 at-least one hydrogen [#16!H0]
Thioamide [NX3][CX3]=[SX1]
Sulfide [#16X2H0] -alkylthio Won't hit thiols. Hits disulfides.
Mono-sulfide [#16X2H0][!#16] alkylthio- or alkoxy- Won't hit thiols. Won't hit disulfides.
Di-sulfide [#16X2H0][#16X2H0] Won't hit thiols. Won't hit mono-sulfides.
Two Sulfides [#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 (sulfate ester) Low specificity [$([SX4](=O)(=O)(O)O),$([SX4+2]([O-])([O-])(O)O)] 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]
Any carbon attached to any halogen [#6][F,Cl,Br,I]
Halogen [F,Cl,Br,I]
Three_halides groups [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)