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| <center><h1>SMARTS Examples |
| </h1></center> |
| <a name="TOP"></a><h2>Table of Contents</h2> |
|
|
| <a href="#INTRO">1. Introduction</a><br> |
| <a href="#GROUP">2. Functional Groups by Element</a><br> |
| <a href="#STRUCTUAL">2. Gross Structual Features</a><br> |
| <a href="#META">4. Meta-SMARTS</a><br> |
| <a href="#E-">5. Electron & Proton Features</a><br> |
| <a href="#BREAK">6. Breakdown of Complex SMARTS</a><br> |
| <a href="#EXMPL">7. Interesting Example SMARTS</a><br> |
| <br> |
| <a NAME="INTRO"></a> |
| <H2> |
| 1. Introduction |
| </H2> |
| When using SMARTS to do searches, it is often helpful to have |
| example queries from which to start. This document contains |
| many potentially useful example SMARTS which may be used to |
| perform searches. templates, examples and ideas. |
| <br><br> |
| These SMARTS have been tested, but they may still contain errors. |
| Please send corrections, improvements, additions, and questions to |
| <A HREF="mailto:support@daylight.com">support@daylight.com.</A> |
|
|
| <br><br> |
| <a NAME="GROUP"></a> |
| <H2> |
| 2. Functional Groups by Element |
| </H2> |
|
|
| <table border=1 COLS=8 WIDTH="750"><tr> |
| <td align=center><a href="#C">C</a></td> |
| <td align=center><a href="#CO">C&O</a></td> |
| <td align=center><a href="#H">H</a></td> |
| <td align=center><a href="#N">N</a></td> |
| <td align=center><a href="#O">O</a></td> |
| <td align=center><a href="#P">P</a></td> |
| <td align=center><a href="#S">S</a></td> |
| <td align=center><a href="#X">X</a></td></tr> |
| </table><br> |
| <a NAME="C"></a><h2></a>C</h2> |
| <h3> alkane </h3><dl> |
| <p><dt> Alkyl Carbon |
| <dd> [CX4]</p></dl><br> |
| <h3> alkene (-ene) </h3><dl> |
| <p><dt> Allenic Carbon |
| <dd> [$([CX2](=C)=C)] |
| <p><dt> Vinylic Carbon |
| <dd> [$([CX3]=[CX3])] |
| <dd> Ethenyl carbon </p></dl><br> |
| <h3> alkyne (-yne) </h3><dl> |
| <p><dt> Acetylenic Carbon |
| <dd> [$([CX2]#C)]</p></dl><br> |
| <h3> arene (Ar , aryl-, aromatic hydrocarbons) </h3><dl> |
| <p><dt> Arene |
| <dd> c </p></dl><br> |
| <a NAME="CO"></a><h2>C & O</h2> |
| <h3>carbonyl</h3><dl> |
| <p><dt> Carbonyl group. Low specificity |
| <dd> [CX3]=[OX1] |
| <dd> Hits carboxylic acid, ester, ketone, aldehyde, carbonic |
| acid/ester,anhydride, carbamic acid/ester, acyl halide, amide. |
| <p><dt> Carbonyl group |
| <dd> [$([CX3]=[OX1]),$([CX3+]-[OX1-])] |
| <dd> Hits either resonance structure |
| <p><dt> Carbonyl with Carbon |
| <dd> [CX3](=[OX1])C |
| <dd> Hits aldehyde, ketone, carboxylic acid (except formic), anhydride |
| (except formic), acyl halides (acid halides). Won't hit carbamic |
| acid/ester, carbonic acid/ester. |
| <p><dt> Carbonyl with Nitrogen. |
| <dd> [OX1]=CN |
| <dd> Hits amide, carbamic acid/ester, poly peptide |
| <p><dt> Carbonyl with Oxygen. |
| <dd> [CX3](=[OX1])O |
| <dd> Hits ester, carboxylic acid, carbonic acid or ester, carbamic acid |
| or ester, anhydride Won't hit aldehyde or ketone. |
| <p><dt> Acyl Halide |
| <dd> [CX3](=[OX1])[F,Cl,Br,I] |
| <dd> acid halide, -oyl halide |
| <p><dt> Aldehyde |
| <dd> [CX3H1](=O)[#6] |
| <dd> -al |
| <p><dt> Anhydride |
| <dd> [CX3](=[OX1])[OX2][CX3](=[OX1]) |
| <p><dt> Amide |
| <dd> [NX3][CX3](=[OX1])[#6] |
| <dd> -amide |
| <p><dt> Amidinium |
| <dd> [NX3][CX3]=[NX3+] |
| <p><dt> Carbamate. |
| <dd> [NX3,NX4+][CX3](=[OX1])[OX2,OX1-] |
| <dd> Hits carbamic esters, acids, and zwitterions |
| <p><dt> Carbamic ester |
| <dd> [NX3][CX3](=[OX1])[OX2H0] |
| <p><dt> Carbamic acid. |
| <dd> [NX3,NX4+][CX3](=[OX1])[OX2H,OX1-] |
| <dd> Hits carbamic acids and zwitterions. |
| <p><dt> Carboxylate Ion. |
| <dd> [CX3](=O)[O-] |
| <dd> Hits conjugate bases of carboxylic, carbamic, and carbonic acids. |
| <p><dt> Carbonic Acid or Carbonic Ester |
| <dd> [CX3](=[OX1])(O)O |
| <dd> Carbonic Acid, Carbonic Ester, or combination |
| <p><dt> Carbonic Acid or Carbonic Acid-Ester |
| <dd> [CX3](=[OX1])([OX2])[OX2H,OX1H0-1] |
| <dd> Hits acid and conjugate base. Won't hit carbonic acid diester |
| <p><dt> Carbonic Ester (carbonic acid diester) |
| <dd> C[OX2][CX3](=[OX1])[OX2]C |
| <dd> Won't hit carbonic acid or combination carbonic acid/ester |
| <p><dt> Carboxylic acid |
| <dd> [CX3](=O)[OX2H1] |
| <dd> -oic acid, COOH |
| <p><dt> Carboxylic acid or conjugate base. |
| <dd> [CX3](=O)[OX1H0-,OX2H1] |
| <p><dt> Cyanamide |
| <dd> [NX3][CX2]#[NX1] |
| <p><dt> Ester Also hits anhydrides |
| <dd> [#6][CX3](=O)[OX2H0][#6] |
| <dd> won't hit formic anhydride. |
| <p><dt> Ketone |
| <dd> [#6][CX3](=O)[#6] |
| <dd> -one </p></dl><br> |
| <h3> ether</h3><dl> |
| <p><dt> Ether |
| <dd> [OD2]([#6])[#6]</p></dl><br> |
| <a NAME="H"></a><h2></a>H</h2> |
| <h3> hydrogen atoms</h3><dl> |
| <p><dt> Hydrogen Atom |
| <dd> [H] |
| <dd> Hits SMILES that are hydrogen atoms: [H+] [2H] [H][H] |
| <p><dt> Not a Hydrogen Atom |
| <dd> [!#1] |
| <dd> Hits SMILES that are not hydrogen atoms. |
| <p><dt> Proton |
| <dd> [H+] |
| <dd> Hits positively charged hydrogen atoms: [H+]</p></dl><br> |
| <h3> hydrogen count</h3><dl> |
| <p><dt> Mono-Hydrogenated Cation |
| <dd> [+H] |
| <dd> Hits atoms that have a positive charge and exactly one attached hydrogen: F[C+](F)[H] |
| <p><dt> Not Mono-Hydrogenated |
| <dd> [!H] or [!H1] |
| <dd> Hits atoms that don't have exactly one attached hydrogen.</p></dl><br> |
| <a NAME="N"></a><h2>N</h2> |
| <h3> amide </b> see carbonyl</p><br> |
| mine (-amino) </h3><dl> |
| <p><dt> Primary or secondary amine, not amide. |
| <dd> [NX3;H2,H1;!$(NC=O)] |
| <dd> 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 |
| <p><dt> Enamine |
| <dd> [NX3][CX3]=[CX3] |
| <p><dt> Primary amine, not amide. |
| <dd> [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) |
| <p><dt> Two primary or secondary amines |
| <dd> [NX3;H2,H1;!$(NC=O)].[NX3;H2,H1;!$(NC=O)] |
| <dd> Here we use the disconnection symbol (".") to match two separate unbonded identical patterns. |
| <p><dt> Enamine or Aniline Nitrogen |
| <dd> [NX3][$(C=C),$(cc)]</p></dl><br> |
| <h3> amino acids</h3><dl> |
| <p><dt> Generic amino acid: low specificity. |
| <dd> [NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N] |
| <dd> 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). |
| <p><dt> Dipeptide group. generic amino acid: low specificity. |
| <dd> [NX3H2,NH3X4+][CX4H]([*])[CX3](=[OX1])[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-] |
| <dd> Won't hit pro or gly. Hits acids and conjugate bases. |
| <p><dt> Amino Acid |
| <dd> [$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-,N] |
| <dd> 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]}</p></dl><br> |
| <h3> amino acid side chains</h3><dl> |
| <p><dt> Alanine side chain |
| <dd> [CH3X4] |
|
|
| <p><dt> Arginine side chain. |
| <dd> [CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0])[NH2X3] |
| <dd> Hits acid and conjugate base. |
|
|
| <p><dt> Aspargine side chain. |
| <dd> [CH2X4][CX3](=[OX1])[NX3H2] |
| <dd> Also hits Gln side chain when used alone. |
|
|
| <p><dt> Aspartate (or Aspartic acid) side chain. |
| <dd> [CH2X4][CX3](=[OX1])[OH0-,OH] |
| <dd> Hits acid and conjugate base. Also hits Glu side chain when used alone. |
|
|
| <p><dt> Cysteine side chain. |
| <dd> [CH2X4][SX2H,SX1H0-] |
| <dd> Hits acid and conjugate base |
|
|
| <p><dt> Glutamate (or Glutamic acid) side chain. |
| <dd> [CH2X4][CH2X4][CX3](=[OX1])[OH0-,OH] |
| <dd> Hits acid and conjugate base. |
|
|
| <p><dt> Glycine |
| <dd> [$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H2][CX3](=[OX1])[OX2H,OX1-,N])] |
| <p><dt> Histidine side chain. |
| <dd> [CH2X4][#6X3]1:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]:<br>[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]1 |
| <dd> Hits acid & conjugate base for either Nitrogen. Note that the Ns can be either ([(Cationic 3-connected with one H) or (Neutral |
| 2-connected without any Hs)] where there is a second-neighbor who is [3-connected with one H]) or (3-connected with one H). |
|
|
| <p><dt> Isoleucine side chain |
| <dd> [CHX4]([CH3X4])[CH2X4][CH3X4] |
|
|
| <p><dt> Leucine side chain |
| <dd> [CH2X4][CHX4]([CH3X4])[CH3X4] |
|
|
| <p><dt> Lysine side chain. |
| <dd> [CH2X4][CH2X4][CH2X4][CH2X4][NX4+,NX3+0] |
| <dd> Acid and conjugate base |
|
|
| <p><dt> Methionine side chain |
| <dd> [CH2X4][CH2X4][SX2][CH3X4] |
|
|
| <p><dt> Phenylalanine side chain |
| <dd> [CH2X4][cX3]1[cX3H][cX3H][cX3H][cX3H][cX3H]1 |
|
|
| <p><dt> Proline |
| <dd> [$([NX3H,NX4H2+]),$([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[OX2H,OX1-,N] |
|
|
| <p><dt> Serine side chain |
| <dd> [CH2X4][OX2H] |
|
|
| <p><dt> Thioamide |
| <dd> [NX3][CX3]=[SX1] |
|
|
| <p><dt> Threonine side chain |
| <dd> [CHX4]([CH3X4])[OX2H] |
|
|
| <p><dt> Tryptophan side chain |
| <dd> [CH2X4][cX3]1[cX3H][nX3H][cX3]2[cX3H][cX3H][cX3H][cX3H][cX3]12 |
|
|
| <p><dt> Tyrosine side chain. |
| <dd> [CH2X4][cX3]1[cX3H][cX3H][cX3]([OHX2,OH0X1-])[cX3H][cX3H]1 |
| <dd> Acid and conjugate base |
|
|
| <p><dt> Valine side chain |
| <dd> [CHX4]([CH3X4])[CH3X4] |
|
|
| <p><dt> Alanine side chain |
| <dd> [CH3X4] |
|
|
| <p><dt> Arginine side chain. |
| <dd> [CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0])[NH2X3] |
| <dd> Hits acid and conjugate base. |
|
|
| <p><dt> Aspargine side chain. |
| <dd> [CH2X4][CX3](=[OX1])[NX3H2] |
| <dd> Also hits Gln side chain when used alone. |
|
|
| <p><dt> Aspartate (or Aspartic acid) side chain. |
| <dd> [CH2X4][CX3](=[OX1])[OH0-,OH] |
| <dd> Hits acid and conjugate base. Also hits Glu side chain when used alone. |
|
|
| <p><dt> Cysteine side chain. |
| <dd> [CH2X4][SX2H,SX1H0-] |
| <dd> Hits acid and conjugate base |
|
|
| <p><dt> Glutamate (or Glutamic acid) side chain. |
| <dd> [CH2X4][CH2X4][CX3](=[OX1])[OH0-,OH] |
| <dd> Hits acid and conjugate base. |
|
|
| <p><dt> Glycine |
| <dd> N[CX4H2][CX3](=[OX1])[O,N] |
|
|
| <p><dt> Histidine side chain. |
| <dd> [CH2X4][#6X3]1:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]:<br>[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]1 |
| <dd> Hits acid & conjugate base for either Nitrogen. Note that the Ns can be either ([(Cationic 3-connected with one H) or (Neutral |
| 2-connected without any Hs)] where there is a second-neighbor who is [3-connected |
|
|
| <p><dt> Isoleucine side chain |
| <dd> [CHX4]([CH3X4])[CH2X4][CH3X4] |
|
|
| <p><dt> Leucine side chain |
| <dd> [CH2X4][CHX4]([CH3X4])[CH3X4] |
|
|
| <p><dt> Lysine side chain. |
| <dd> [CH2X4][CH2X4][CH2X4][CH2X4][NX4+,NX3+0] |
| <dd> Acid and conjugate base |
|
|
| <p><dt> Methionine side chain |
| <dd> [CH2X4][CH2X4][SX2][CH3X4] |
|
|
| <p><dt> Phenylalanine side chain |
| <dd> [CH2X4][cX3]1[cX3H][cX3H][cX3H][cX3H][cX3H]1 |
|
|
| <p><dt> Proline |
| <dd> N1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[O,N] |
|
|
| <p><dt> Serine side chain |
| <dd> [CH2X4][OX2H] |
|
|
| <p><dt> Threonine side chain |
| <dd> [CHX4]([CH3X4])[OX2H] |
|
|
| <p><dt> Tryptophan side chain |
| <dd> [CH2X4][cX3]1[cX3H][nX3H][cX3]2[cX3H][cX3H][cX3H][cX3H][cX3]12 |
|
|
| <p><dt> Tyrosine side chain. |
| <dd> [CH2X4][cX3]1[cX3H][cX3H][cX3]([OHX2,OH0X1-])[cX3H][cX3H]1 |
| <dd> Acid and conjugate base |
|
|
| <p><dt> Valine side chain |
| <dd> [CHX4]([CH3X4])[CH3X4]</p></dl><br> |
|
|
| <h3> azide (-azido) </h3><dl> |
|
|
| <p><dt> Azide group. |
| <dd> [$(*-[NX2-]-[NX2+]#[NX1]),$(*-[NX2]=[NX2+]=[NX1-])] |
| <dd> Hits any atom with an attached azide. |
|
|
| <p><dt> Azide ion. |
| <dd> [$([NX1-]=[NX2+]=[NX1-]),$([NX1]#[NX2+]-[NX1-2])] |
| <dd> Hits N in azide ion</p></dl><br> |
|
|
| <h3> azo </h3><dl> |
|
|
| <p><dt> Nitrogen. |
| <dd> [#7] |
| <dd> Nitrogen in N-containing compound. aromatic or aliphatic. Most general interpretation of "azo" |
|
|
| <p><dt> Azo Nitrogen. Low specificity. |
| <dd> [NX2]=N |
| <dd> Hits diazene, azoxy and some diazo structures |
|
|
| <p><dt> Azo Nitrogen.diazene |
| <dd> [NX2]=[NX2] |
| <dd> (diaza alkene) |
|
|
| <p><dt> Azoxy Nitrogen. |
| <dd> [$([NX2]=[NX3+]([O-])[#6]),$([NX2]=[NX3+0](=[O])[#6])] |
|
|
| <p><dt> Diazo Nitrogen |
| <dd> [$([#6]=[N+]=[N-]),$([#6-]-[N+]#[N])] |
|
|
| <p><dt> Azole. |
| <dd> [$([nr5]:[nr5,or5,sr5]),$([nr5]:[cr5]:[nr5,or5,sr5])] |
| <dd> 5 member aromatic heterocycle w/ 2double bonds. contains N & another non C (N,O,S) subclasses are furo-, thio-, pyrro- (replace |
| CH o' furfuran, thiophene, pyrrol w/ N)</p></dl><br> |
|
|
| <h3> hydrazine</h3><dl> |
|
|
| <p><dt> Hydrazine H2NNH2 |
| <dd> [NX3][NX3]</p></dl><br> |
|
|
| <h3> hydrazone </h3><dl> |
|
|
| <p><dt> Hydrazone C=NNH2 |
| <dd> [NX3][NX2]=[*]</p></dl><br> |
|
|
| <h3> imine </h3><dl> |
|
|
| <p><dt> Substituted imine |
| <dd> [CX3;$([C]([#6])[#6]),$([CH][#6])]=[NX2][#6] |
| <dd> Schiff base |
|
|
| <p><dt> Substituted or un-substituted imine |
| <dd> [$([CX3]([#6])[#6]),$([CX3H][#6])]=[$([NX2][#6]),$([NX2H])] |
|
|
| <p><dt> Iminium |
| <dd> [NX3+]=[CX3]</p></dl><br> |
|
|
| <h3> imide </h3><dl> |
|
|
| <p><dt> Unsubstituted dicarboximide |
| <dd> [CX3](=[OX1])[NX3H][CX3](=[OX1]) |
|
|
| <p><dt> Substituted dicarboximide |
| <dd> [CX3](=[OX1])[NX3H0]([#6])[CX3](=[OX1]) |
|
|
| <p><dt> Dicarboxdiimide |
| <dd> [CX3](=[OX1])[NX3H0]([NX3H0]([CX3](=[OX1]))[CX3](=[OX1]))[CX3](=[OX1])</p></dl><br> |
|
|
| <h3> nitrate </h3><dl> |
|
|
| <p><dt> Nitrate group |
| <dd> [$([NX3](=[OX1])(=[OX1])O),$([NX3+]([OX1-])(=[OX1])O)] |
| <dd> Also hits nitrate anion |
|
|
| <p><dt> Nitrate Anion |
| <dd> [$([OX1]=[NX3](=[OX1])[OX1-]),$([OX1]=[NX3+]([OX1-])[OX1-])]</p></dl><br> |
|
|
| <h3> nitrile </h3><dl> |
|
|
| <p><dt> Nitrile |
| <dd> [NX1]#[CX2] |
|
|
| <p><dt> Isonitrile |
| <dd> [CX1-]#[NX2+]</p></dl><br> |
|
|
| <h3> nitro </h3><dl> |
|
|
| <p><dt> Nitro group. |
| <dd> [$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8] Hits both forms. |
|
|
| <p><dt> Two Nitro groups |
| <dd> [$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8].[$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]</p></dl><br> |
|
|
| <h3> nitroso </h3><dl> |
|
|
| <p><dt> Nitroso-group |
| <dd> [NX2]=[OX1]</p></dl><br> |
|
|
| <h3> n-oxide </h3><dl> |
|
|
| <p><dt> N-Oxide |
| <dd> [$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])] |
| <dd> Hits both forms. Won't hit azoxy, nitro, nitroso,or nitrate.</p></dl><br> |
|
|
|
|
| <a NAME="O"></a><h2>O</h2> |
|
|
|
|
| <h3> hydroxyl (includes alcohol, phenol) </h3><dl> |
|
|
| <p><dt> Hydroxyl |
| <dd> [OX2H] |
|
|
| <p><dt> Hydroxyl in Alcohol |
| <dd> [#6][OX2H] |
|
|
| <p><dt> Hydroxyl in Carboxylic Acid |
| <dd> [OX2H][CX3]=[OX1] |
|
|
| <p><dt> Hydroxyl in H-O-P- |
| <dd> [OX2H]P |
|
|
| <p><dt> Enol |
| <dd> [OX2H][#6X3]=[#6] |
|
|
| <p><dt> Phenol |
| <dd> [OX2H][cX3]:[c] |
|
|
| <p><dt> Enol or Phenol |
| <dd> [OX2H][$(C=C),$(cc)] |
|
|
| <p><dt> Hydroxyl_acidic |
| <dd> [$([OH]-*=[!#6])] |
| <dd> 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.</p></dl><br> |
|
|
| <h3> peroxide </h3><dl> |
|
|
| <p><dt> Peroxide groups. |
| <dd> [OX2,OX1-][OX2,OX1-] |
| <dd> Also hits anions.</p></dl><br> |
|
|
|
|
| <a NAME="P"></a><h2>P</h2> |
|
|
|
|
| <h3> phosphoric compounds </h3><dl> |
|
|
| <p><dt> Phosphoric_acid groups. |
| <dd> [$(P(=[OX1])([$([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)])] |
| <dd> 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). |
|
|
| <p><dt> Phosphoric_ester groups. |
| <dd> [$(P(=[OX1])([OX2][#6])([$([OX2H]),$([OX1-]),$([OX2][#6])])[$([OX2H]),$([OX1-]),$([OX2][#6]),$([OX2]P)]),$([P+]([OX1-])([OX2][#6])([$([OX2H]),$([OX1-]),$([OX2][#6])])[$([OX2H]),$([OX1-]),$([OX2][#6]),$([OX2]P)])] |
| <dd> Hits both depiction forms. Doesn't hit non-ester phosphoric_acid groups.</p></dl><br> |
|
|
| <a NAME="S"></a><h2>S</h2> |
|
|
|
|
| <h3>thio groups ( thio-, thi-, sulpho-, mercapto- )</h3><dl> |
|
|
|
|
| <p><dt> Carbo-Thiocarboxylate |
| <dd> [S-][CX3](=S)[#6] |
|
|
| <p><dt> Carbo-Thioester |
| <dd> S([#6])[CX3](=O)[#6] |
|
|
| <p><dt> Thio analog of carbonyl |
| <dd> [#6X3](=[SX1])([!N])[!N] |
| <dd> Where S replaces O. Not a thioamide. |
|
|
| <p><dt> Thiol, Sulfide or Disulfide Sulfur |
| <dd> [SX2] |
|
|
| <p><dt> Thiol |
| <dd> [#16X2H] |
|
|
| <p><dt> Sulfur with at-least one hydrogen. |
| <dd> [#16!H0] |
|
|
| <p><dt> Thioamide |
| <dd> [NX3][CX3]=[SX1]</p></dl><br> |
|
|
| <h3>sulfide</h3><dl> |
|
|
| <p><dt> Sulfide |
| <dd> [#16X2H0] |
| <dd> -alkylthio Won't hit thiols. Hits disulfides. |
|
|
| <p><dt> Mono-sulfide |
| <dd> [#16X2H0][!#16] |
| <dd> alkylthio- or alkoxy- Won't hit thiols. Won't hit disulfides. |
|
|
| <p><dt> Di-sulfide |
| <dd> [#16X2H0][#16X2H0] |
| <dd> Won't hit thiols. Won't hit mono-sulfides. |
|
|
| <p><dt> Two Sulfides |
| <dd> [#16X2H0][!#16].[#16X2H0][!#16] |
| <dd> Won't hit thiols. Won't hit mono-sulfides. Won't hit disulfides.</p></dl><br> |
|
|
| <h3>sulfinate</h3><dl> |
|
|
| <p><dt> Sulfinate |
| <dd> [$([#16X3](=[OX1])[OX2H0]),$([#16X3+]([OX1-])[OX2H0])] |
| <dd> Won't hit Sulfinic Acid. Hits Both Depiction Forms. |
|
|
| <p><dt> Sulfinic Acid |
| <dd> [$([#16X3](=[OX1])[OX2H,OX1H0-]),$([#16X3+]([OX1-])[OX2H,OX1H0-])] |
| <dd> Won't hit substituted Sulfinates. Hits Both Depiction Forms. |
| Hits acid and conjugate base (sulfinate).</p></dl><br> |
|
|
| <h3>sulfone</h3><dl> |
|
|
| <p><dt> Sulfone. Low specificity. |
| <dd> [$([#16X4](=[OX1])=[OX1]),$([#16X4+2]([OX1-])[OX1-])] |
| <dd> Hits all sulfones, including heteroatom-substituted sulfones: sulfonic acid, sulfonate, sulfuric acid mono- & di- esters, sulfamic |
| acid, sulfamate, sulfonamide... Hits Both Depiction Forms. |
|
|
| <p><dt> Sulfone. High specificity. |
| <dd> [$([#16X4](=[OX1])(=[OX1])([#6])[#6]),$([#16X4+2]([OX1-])([OX1-])([#6])[#6])] |
| <dd> Only hits carbo- sulfones (Won't hit herteroatom-substituted molecules). Hits Both Depiction Forms. |
|
|
| <p><dt> Sulfonic acid. High specificity. |
| <dd> [$([#16X4](=[OX1])(=[OX1])([#6])[OX2H,OX1H0-]),$([#16X4+2]([OX1-])([OX1-])([#6])[OX2H,OX1H0-])] |
| <dd> Only hits carbo- sulfonic acids (Won't hit herteroatom-substituted molecules). |
| Hits acid and conjugate base. Hits Both Depiction Forms. Hits Arene sulfonic acids. |
|
|
| <p><dt> Sulfonate |
| <dd> [$([#16X4](=[OX1])(=[OX1])([#6])[OX2H0]),$([#16X4+2]([OX1-])([OX1-])([#6])[OX2H0])] |
| <dd> (sulfonic ester) Only hits carbon-substituted sulfur |
| (Oxygen may be herteroatom-substituted). Hits Both Depiction Forms. |
|
|
| <p><dt> Sulfonamide. |
| <dd> [$([#16X4]([NX3])(=[OX1])(=[OX1])[#6]),$([#16X4+2]([NX3])([OX1-])([OX1-])[#6])] |
| <dd> Only hits carbo- sulfonamide. Hits Both Depiction Forms. |
|
|
| <p><dt> Carbo-azosulfone |
| <dd> [SX4](C)(C)(=O)=N |
| <dd> Partial N-Analog of Sulfone |
|
|
| <p><dt> Sulfonamide |
| <dd> [$([SX4](=[OX1])(=[OX1])([!O])[NX3]),$([SX4+2]([OX1-])([OX1-])([!O])[NX3])] |
| <dd> (sulf drugs) Won't hit sulfamic acid or sulfamate. Hits Both Depiction Forms.</p></dl><br> |
|
|
| <h3>sulfoxide</h3><dl> |
|
|
| <p><dt> Sulfoxide Low specificity. |
| <dd> [$([#16X3]=[OX1]),$([#16X3+][OX1-])] |
| <dd> ( 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. |
|
|
| <p><dt> Sulfoxide High specificity |
| <dd> [$([#16X3](=[OX1])([#6])[#6]),$([#16X3+]([OX1-])([#6])[#6])] |
| <dd> (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.</p></dl><br> |
|
|
| <h3>sulfate</h3><dl> |
|
|
| <p><dt> Sulfate |
| <dd> [$([#16X4](=[OX1])(=[OX1])([OX2H,OX1H0-])[OX2][#6]),$([#16X4+2]([OX1-])([OX1-])([OX2H,OX1H0-])[OX2][#6])] |
| <dd> (sulfuric acid monoester) Only hits when oxygen is carbon-substituted. |
| Hits acid and conjugate base. Hits Both Depiction Forms. |
|
|
| <p><dt> Sulfuric acid ester (sulfate ester) Low specificity. |
| <dd> [$([SX4](=O)(=O)(O)O),$([SX4+2]([O-])([O-])(O)O)] |
| <dd> Hits sulfuric acid, sulfuric acid monoesters (sulfuric acids) and diesters (sulfates). |
| Hits acid and conjugate base. Hits Both Depiction Forms. |
| <p><dt> Sulfuric Acid Diester. |
| <dd> [$([#16X4](=[OX1])(=[OX1])([OX2][#6])[OX2][#6]),$([#16X4](=[OX1])(=[OX1])([OX2][#6])[OX2][#6])] |
| <dd> Only hits when oxygen is carbon-substituted. Hits Both Depiction Forms.</p></dl><br> |
|
|
| <h3>sulfamate</h3><dl> |
|
|
| <p><dt> Sulfamate. |
| <dd> [$([#16X4]([NX3])(=[OX1])(=[OX1])[OX2][#6]),$([#16X4+2]([NX3])([OX1-])([OX1-])[OX2][#6])] |
| <dd> Only hits when oxygen is carbon-substituted. Hits Both Depiction Forms. |
|
|
| <p><dt> Sulfamic Acid. |
| <dd> [$([#16X4]([NX3])(=[OX1])(=[OX1])[OX2H,OX1H0-]),$([#16X4+2]([NX3])([OX1-])([OX1-])[OX2H,OX1H0-])] |
| <dd> Hits acid and conjugate base. Hits Both Depiction Forms.</p></dl><br> |
|
|
| <h3>sulfene</h3><dl> |
|
|
| <p><dt> Sulfenic acid. |
| <dd> [#16X2][OX2H,OX1H0-] |
| <dd> Hits acid and conjugate base. |
|
|
| <p><dt> Sulfenate. |
| <dd> [#16X2][OX2H0]</p></dl><br> |
|
|
|
|
| <a NAME="X"></a><h2>X</h2> |
|
|
|
|
| <h3> halide (-halo -fluoro -chloro -bromo -iodo) </h3><dl> |
|
|
| <p><dt> Any carbon attached to any halogen |
| <dd> [#6][F,Cl,Br,I] |
|
|
| <p><dt> Halogen |
| <dd> [F,Cl,Br,I] |
|
|
| <p><dt> Three_halides groups |
| <dd> [F,Cl,Br,I].[F,Cl,Br,I].[F,Cl,Br,I] |
| <dd> Hits SMILES that have three halides.</p></dl><br> |
|
|
| <h3> acyl halide </h3><dl> |
|
|
| <p><dt> Acyl Halide |
| <dd> [CX3](=[OX1])[F,Cl,Br,I] |
| <dd> (acid halide, -oyl halide)</p></dl><br> |
|
|
|
|
| <a NAME="STRUCTUAL"></a> |
| <H2> |
| 3. Gross Structual Features |
| </H2><br><br> |
|
|
|
|
| <table BORDER COLS=6 WIDTH="750" NOSAVE ><tr> |
| <td align=center><a href="#CHIRALITY">Chirality</a></td> |
| <td align=center><a href="#ORBITAL">Orbital Configuration</a></td> |
| <td align=center><a href="#CONNECT">Connectivity</a></td> |
| <td align=center><a href="#CHAIN"> Chains & Branching</a></td> |
| <td align=center><a href="#ROTATE">Rotation</a></td> |
| <td align=center><a href="#CYCLE">Cyclic Features</a></td> |
| </table><br><br> |
|
|
|
|
| <a NAME="CHIRALITY"></a><h2>Chirality</h2> |
| <dl> |
| <p><dt> Specified chiral carbon. |
| <dd> [$([#6X4@](*)(*)(*)*),$([#6X4@H](*)(*)*)] |
| <dd> Matches carbons whose chirality is specified (clockwise or anticlockwise) Will not match molecules whose chirality is unspecified b |
| ut that could otherwise be considered chiral. Also,therefore won't match molecules that would be chiral due to an implicit connection (i.e.i |
| mplicit H). |
|
|
| <p><dt> "No-conflict" chiral match |
| <dd> C[C@?](F)(Cl)Br |
| <dd> Will match molecules with chiralities as specified or unspecified. |
|
|
| <p><dt> "No-conflict" chiral match where an H is present |
| <dd> C[C@?H](Cl)Br |
| <dd> Will match molecules with chiralities as specified or unspecified.</p></dl><br> |
|
|
| <a NAME="ORBITAL"></a><h2>Orbital Configuration</h2> |
|
|
| <dl> |
| <p><dt> sp2 cationic carbon |
| <dd> [$([cX2+](:*):*)] |
| <dd> Aromatic cationic sp2 carbon with a free electron in a non-bonding sp2 hybrid orbital |
|
|
| <p><dt> Aromatic sp2 carbon. |
| <dd> [$([cX3](:*):*),$([cX2+](:*):*)] |
| <dd> The first recursive SMARTS matches carbons that are three-connected, the second case matches two-connected carbons (i.e cations with |
| a free electron in a non-bonding sp2 hybrid orbital) |
|
|
| <p><dt> Any sp2 carbon. |
| <dd> [$([cX3](:*):*),$([cX2+](:*):*),$([CX3]=*),$([CX2+]=*)] |
| <dd> The first recursive SMARTS matches carbons that are three-connected and aromatic. The second case matches two-connected aromatic ca |
| rbons (i.e cations with a free electron in a non-bonding sp2 hybrid orbital). The third case matches three-connected non-aromatic carbons ( |
| alkenes). The fourth case matches non-aromatic cationic alkene carbons. |
|
|
| <p><dt> Any sp2 nitrogen. |
| <dd> [$([nX3](:*):*),$([nX2](:*):*),$([#7X2]=*),$([NX3](=*)=*),$([#7X3+](-*)=*),$([#7X3+H]=*)] |
|
|
| <dd> Can be aromatic 3-connected with 2 aromatic bonds (eg pyrrole,Pyridine-N-oxide), aromatic 2-connected with 2 aromatic bonds (and a free |
| pair of electrons in a nonbonding orbital, e.g.Pyridine), either aromatic or non-aromatic 2-connected with a double bond (and a free pair |
| of electrons in a nonbonding orbital, e.g. C=N ), non aromatic 3-connected with 2 double bonds (e.g. a nitro group; this form does not exist |
| in reality, SMILES can represent the charge-separated resonance structures as a single uncharged structure), either aromatic or non-aromatic |
| 3-connected cation w/ 1 single bond and 1 double bond (e.g. a nitro group, here the individual charge-separated resonance structures are |
| specified), either aromatic or non-aromatic 3-connected hydrogenated cation with a double bond (as the previous case but R is hydrogen), |
| rspectively. |
|
|
| <p><dt> Explicit Hydrogen on sp2-Nitrogen |
| <dd> [$([#1X1][$([nX3](:*):*),$([nX2](:*):*),$([#7X2]=*),$([NX3](=*)=*),$([#7X3+](-*)=*),$([#7X3+H]=*)])] |
| <dd> (H must be an isotope or ion) |
|
|
| <p><dt> sp3 nitrogen |
| <dd> [$([NX4+]),$([NX3]);!$(*=*)&!$(*:*)] |
| <dd> One atom that is (a 4-connected N cation or a 3-connected N) and is not double bonded and is not aromatically bonded. |
|
|
| <p><dt> Explicit Hydrogen on an sp3 N. |
| <dd> [$([#1X1][$([NX4+]),$([NX3]);!$(*=*)&!$(*:*)])] |
| <dd> One atom that is a 1-connected H that is bonded to an sp3 N. (H must be an isotope or ion) |
|
|
| <p><dt> sp2 N in N-Oxide |
| <dd> [$([$([NX3]=O),$([NX3+][O-])])] |
|
|
| <p><dt> sp3 N in N-Oxide Exclusive: |
| <dd> [$([$([NX4]=O),$([NX4+][O-])])] |
| <dd> Only hits if O is explicitly present. Won't hit if * is in SMILES in place of O. |
|
|
| <p><dt> sp3 N in N-Oxide Inclusive: |
| <dd> [$([$([NX4]=O),$([NX4+][O-,#0])])] |
| <dd> Hits if O could be present. Hits if * if used in place of O in smiles.</p></dl><br> |
|
|
|
|
| <a NAME="CONNECT"></a><h2>Connectivity</h2> |
|
|
| <dl> |
| <p><dt> Quaternary Nitrogen |
| <dd> [$([NX4+]),$([NX4]=*)] |
| <dd> Hits non-aromatic Ns. |
| <p><dt> Tricoordinate S double bonded to N. |
| <dd> [$([SX3]=N)] |
|
|
| <p><dt> S double-bonded to Carbon |
| <dd> [$([SX1]=[#6])] |
| <dd> Hits terminal (1-connected S) |
|
|
| <p><dt> Triply bonded N |
| <dd> [$([NX1]#*)] |
|
|
| <p><dt> Divalent Oxygen |
| <dd> [$([OX2])]</p></dl><br> |
|
|
|
|
| <a NAME="CHAIN"></a><h2>Chains & Branching </h2> |
|
|
| <dl> |
| <p><dt> Unbranched_alkane groups. |
| <dd> [R0;D2][R0;D2][R0;D2][R0;D2] |
| <dd> Only hits alkanes (single-bond chains). Only hits chains of at-least 4 members. All non-(implicit-hydrogen) atoms count as branches |
| (e.g. halide substituted chains count as branched). |
|
|
| <p><dt> Unbranched_chain groups. |
| <dd> [R0;D2]~[R0;D2]~[R0;D2]~[R0;D2] |
| <dd> Hits any bond (single, double, triple). Only hits chains of at-least 4 members. All non-(implicit-hydrogen) atoms count as branches |
| (e.g. halide substituted chains count as branched). |
|
|
| <p><dt> Long_chain groups. |
| <dd> [AR0]~[AR0]~[AR0]~[AR0]~[AR0]~[AR0]~[AR0]~[AR0] |
| <dd> Aliphatic chains at-least 8 members long. |
|
|
| <p><dt> Atom_fragment |
| <dd> [!$([#6+0]);!$(C(F)(F)F);!$(c(:[!c]):[!c])!$([#6]=,#[!#6])] |
| <dd> (CLOGP definition) A fragment atom is a not an isolating carbon |
|
|
| <p><dt> Carbon_isolating |
| <dd> [$([#6+0]);!$(C(F)(F)F);!$(c(:[!c]):[!c])!$([#6]=,#[!#6])] |
| <dd> This definition is based on that in CLOGP, so it is a charge-neutral carbon, which is not a CF3 or an aromatic C between two aromati |
| c hetero atoms eg in tetrazole, it is not multiply bonded to a hetero atom. |
|
|
| <p><dt> Terminal S bonded to P |
| <dd> [$([SX1]~P)] |
|
|
| <p><dt> Nitrogen on -N-C=N- |
| <dd> [$([NX3]C=N)] |
|
|
| <p><dt> Nitrogen on -N-N=C- |
| <dd> [$([NX3]N=C)] |
|
|
| <p><dt> Nitrogen on -N-N=N- |
| <dd> [$([NX3]N=N)] |
|
|
| <p><dt> Oxygen in -O-C=N- |
| <dd> [$([OX2]C=N)] </p></dl><br> |
|
|
|
|
| <a NAME="ROTATE"></a><h2>Rotation</h2> |
|
|
| <dl> |
| <p><dt> Rotatable bond |
| <dd> [!$(*#*)&!D1]-!@[!$(*#*)&!D1] |
| <dd> An atom which is not triply bonded and not one-connected i.e.terminal connected by a single non-ring bond to and equivalent atom. Note |
| that logical operators can be applied to bonds ("-&!@"). Here, the overall SMARTS consists of two atoms and one bond. The bond is "site |
| and not ring". *#* any atom triple bonded to any atom. By enclosing this SMARTS in parentheses and preceding with $, this enables us to |
| use $(*#*) to write a recursive SMARTS using that string as an atom primitive. The purpose is to avoid bonds such as c1ccccc1-C#C which wo |
| be considered rotatable without this specification.</p></dl><br> |
|
|
|
|
| <a NAME="CYCLE"></a><h2>Cyclic Features</h2> |
|
|
| <dl> |
| <p><dt> Bicyclic |
| <dd> [$([*R2]([*R])([*R])([*R]))].[$([*R2]([*R])([*R])([*R]))] |
| <dd> Bicyclic compounds have 2 bridgehead atoms with 3 arms connecting the bridgehead atoms. |
|
|
| <p><dt> Ortho |
| <dd> *-!:aa-!:* |
| <dd> Ortho-substituted ring |
|
|
| <p><dt> Meta |
| <dd> *-!:aaa-!:* |
| <dd> Meta-substituted ring |
|
|
| <p><dt> Para |
| <dd> *-!:aaaa-!:* |
| <dd> Para-substituted ring |
|
|
| <p><dt> Acylic-bonds |
| <dd> *!@* |
|
|
| <p><dt> Single bond and not in a ring |
| <dd> *-!@* |
|
|
| <p><dt> Non-ring atom |
| <dd> [R0] or [!R] |
|
|
| <p><dt> Macrocycle groups. |
| <dd> [r;!r3;!r4;!r5;!r6;!r7] |
|
|
| <p><dt> S in aromatic 5-ring with lone pair |
| <dd> [sX2r5] |
|
|
| <p><dt> Aromatic 5-Ring O with Lone Pair |
| <dd> [oX2r5] |
|
|
| <p><dt> N in 5-sided aromatic ring |
| <dd> [nX2r5] |
|
|
| <p><dt> Spiro-ring center |
| <dd> [X4;R2;r4,r5,r6](@[r4,r5,r6])(@[r4,r5,r6])(@[r4,r5,r6])@[r4,r5,r6]rings size 4-6 |
|
|
| <p><dt> N in 5-ring arom |
| <dd> [$([nX2r5]:[a-]),$([nX2r5]:[a]:[a-])] anion |
|
|
| <p><dt> CIS or TRANS double bond in a ring |
| <dd> */,\[R]=;@[R]/,\* |
| <dd> An isomeric SMARTS consisting of four atoms and three bonds. |
|
|
| <p><dt> CIS or TRANS double or aromatic bond in a ring |
| <dd> */,\[R]=,:;@[R]/,\* |
|
|
| <p><dt> Unfused benzene ring |
| <dd> [cR1]1[cR1][cR1][cR1][cR1][cR1]1 |
| <dd> To find a benzene ring which is not fused, we write a SMARTS of 6 aromatic carbons in a ring where each atom is only in one ring: |
|
|
| <p><dt> Multiple non-fused benzene rings |
| <dd> [cR1]1[cR1][cR1][cR1][cR1][cR1]1.[cR1]1[cR1][cR1][cR1][cR1][cR1]1 |
|
|
| <p><dt> Fused benzene rings |
| <dd> c12ccccc1cccc2</p></dl><br> |
|
|
|
|
| <a NAME="META"></a> |
| <H2> |
| 4. Meta-SMARTS |
| </H2><br><br> |
|
|
| <table BORDER COLS=3 WIDTH="750" NOSAVE ><tr> |
| <td align=center><a href="#AA">Amino Acids </a></td> |
| <td align=center><a href="#RECUR"> Recursive or Multiple </a></td> |
| <td align=center><a href="#TOOL">Tools &Tricks </a></td> |
| </table><br><br> |
|
|
|
|
| <a NAME="AA"></a><h2>Amino Acids</h2> |
|
|
| <dl> |
| <p><dt> Generic amino acid: low specificity. |
| <dd> [NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N] |
| <dd> 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). |
|
|
| <p><dt> A.A. Template for 20 standard a.a.s |
| <dd> [$([$([NX3H,NX4H2+]),$([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[OX2H,OX1-,N]),<br>$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H2][CX3](=[OX1])[OX2H,OX1-,N]),$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-,N])] |
|
|
| <dd> Pro, Gly, Other. Replace * w/ the entire 18_standard_side_chains list to get "any standard a.a." Hits acids and conjugate bases. |
| Hits single a.a.s and specific residues w/in polypeptides (internal, or terminal). |
|
|
| <p><dt> Proline |
| <dd> [$([NX3H,NX4H2+]),$([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[OX2H,OX1-,N] |
|
|
| <p><dt> Glycine |
| <dd> [$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H2][CX3](=[OX1])[OX2H,OX1-,N])] |
|
|
| <p><dt> Other a.a. |
| <dd> [$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-,N] |
| <dd> 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 |
| polypeptides (internal, or terminal).<br> |
| Example usage:<br> |
| Alanine side chain is [CH3X4] <br> |
| Alanine Search is [$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([CH3X4])[CX3](=[OX1])[OX2H,OX1-,N] |
|
|
| <p><dt> 18_standard_aa_side_chains. |
| <dd> ([$([CH3X4]),$([CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0])[NH2X3]),<br> |
| $([CH2X4][CX3](=[OX1])[NX3H2]),$([CH2X4][CX3](=[OX1])[OH0-,OH]),<br> |
| $([CH2X4][SX2H,SX1H0-]),$([CH2X4][CH2X4][CX3](=[OX1])[OH0-,OH]),<br> |
| $([CH2X4][#6X3]1:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:<br> |
| [#6X3H]:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]1),<br> |
| $([CHX4]([CH3X4])[CH2X4][CH3X4]),$([CH2X4][CHX4]([CH3X4])[CH3X4]),<br> |
| $([CH2X4][CH2X4][CH2X4][CH2X4][NX4+,NX3+0]),$([CH2X4][CH2X4][SX2][CH3X4]),<br> |
| $([CH2X4][cX3]1[cX3H][cX3H][cX3H][cX3H][cX3H]1),$([CH2X4][OX2H]),<br> |
| $([CHX4]([CH3X4])[OX2H]),$([CH2X4][cX3]1[cX3H][nX3H][cX3]2[cX3H][cX3H][cX3H][cX3H][cX3]12),<br> |
| $([CH2X4][cX3]1[cX3H][cX3H][cX3]([OHX2,OH0X1-])[cX3H][cX3H]1),$([CHX4]([CH3X4])[CH3X4])]) |
| <dd>Can be any of the standard 18 (Pro & Gly are treated separately) Hits acids and conjugate bases. |
|
|
| <p><dt> N in Any_standard_amino_acid. |
| <dd> [$([$([NX3H,NX4H2+]),$([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3]<br> |
| (=[OX1])[OX2H,OX1-,N]),$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H2][CX3]<br> |
| (=[OX1])[OX2H,OX1-,N]),$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([$([CH3X4]),<br> |
| $([CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0])[NH2X3]),$<br> |
| ([CH2X4][CX3](=[OX1])[NX3H2]),$([CH2X4][CX3](=[OX1])[OH0-,OH]),<br> |
| $([CH2X4][SX2H,SX1H0-]),$([CH2X4][CH2X4][CX3](=[OX1])[OH0-,OH]),<br> |
| $([CH2X4][#6X3]1:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:<br> |
| [#6X3H]:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]1),<br> |
| $([CHX4]([CH3X4])[CH2X4][CH3X4]),$([CH2X4][CHX4]([CH3X4])[CH3X4]),<br> |
| $([CH2X4][CH2X4][CH2X4][CH2X4][NX4+,NX3+0]),$([CH2X4][CH2X4][SX2][CH3X4]),<br> |
| $([CH2X4][cX3]1[cX3H][cX3H][cX3H][cX3H][cX3H]1),$([CH2X4][OX2H]),<br> |
| $([CHX4]([CH3X4])[OX2H]),$([CH2X4][cX3]1[cX3H][nX3H][cX3]2[cX3H][cX3H][cX3H][cX3H][cX3]12),<br> |
| $([CH2X4][cX3]1[cX3H][cX3H][cX3]([OHX2,OH0X1-])[cX3H][cX3H]1),<br> |
| $([CHX4]([CH3X4])[CH3X4])])[CX3](=[OX1])[OX2H,OX1-,N])] |
| <dd> Format is A.A.Template for 20 standard a.a.s. where * is replaced by the entire 18_standard_side_chains list (or'd together). A gen |
| eric amino acid with any of the 18 side chains or, proline or glycine. Hits "standard" amino acids that have terminally appended groups (i.e |
| . "standard" refers to the side chains). (Pro, Gly, or 18 normal a.a.s.) Hits single a.a.s and specific residues w/in polypeptides (intern |
| al, or terminal). |
|
|
| <p><dt> Non-standard amino acid. |
| <dd> [$([NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]);!$([$([$([NX3H,NX4H2+]),<br> |
| $([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[OX2H,OX1-,N]),<br> |
| $([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H2][CX3](=[OX1])[OX2H,OX1-,N]),<br> |
| $([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([$([CH3X4]),$([CH2X4][CH2X4][CH2X4][NHX3][CH0X3]<br> |
| (=[NH2X3+,NHX2+0])[NH2X3]),$([CH2X4][CX3](=[OX1])[NX3H2]),$([CH2X4][CX3](=[OX1])[OH0-,OH]),<br> |
| $([CH2X4][SX2H,SX1H0-]),$([CH2X4][CH2X4][CX3](=[OX1])[OH0-,OH]),$([CH2X4][#6X3]1:<br> |
| [$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:<br> |
| [#6X3H]:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),<br> |
| $([#7X3H])]:[#6X3H]1),$([CHX4]([CH3X4])[CH2X4][CH3X4]),$([CH2X4][CHX4]([CH3X4])[CH3X4]),<br> |
| $([CH2X4][CH2X4][CH2X4][CH2X4][NX4+,NX3+0]),$([CH2X4][CH2X4][SX2][CH3X4]),<br> |
| $([CH2X4][cX3]1[cX3H][cX3H][cX3H][cX3H][cX3H]1),$([CH2X4][OX2H]),$([CHX4]([CH3X4])[OX2H]),<br> |
| $([CH2X4][cX3]1[cX3H][nX3H][cX3]2[cX3H][cX3H][cX3H][cX3H][cX3]12),<br> |
| $([CH2X4][cX3]1[cX3H][cX3H][cX3]([OHX2,OH0X1-])[cX3H][cX3H]1),<br> |
| $([CHX4]([CH3X4])[CH3X4])])[CX3](=[OX1])[OX2H,OX1-,N])])] |
| <dd> Generic amino acid but not a "standard" amino acid ("standard" refers to the 20 normal side chains). Won't hit amino acids that are |
| non-standard due solely to the fact that groups are terminally-appended to the polypeptide chain (N or C term). format is [$(generic a.a.); |
| !$(not a standard one)] Hits single a.a.s and specific residues w/in polypeptides (internal, or terminal).</p></dl><br> |
|
|
|
|
| <a NAME="RECUR"></a><h2>Recursive or Multiple </h2> |
|
|
| <h3> Recursive SMARTS: Atoms connected to particular SMARTS</h3><dl> |
|
|
| <p><dt> Ortho |
| <dd>[SMARTS_expression]-!:aa-!:[SMARTS_expression] |
|
|
| <p><dt> Meta |
| <dd> [SMARTS_expression]-!:aaa-!:[SMARTS_expression] |
|
|
| <p><dt> Para |
| <dd> [SMARTS_expression]-!:aaaa-!:[SMARTS_expression] |
|
|
| <p><dt> Hydrogen |
| <dd> [$([#1][SMARTS_expression])] |
| <dd> Hydrogen must be explicit i.e. an isotope or charged |
|
|
| <p><dt> Nitrogen |
| <dd> [$([#7][SMARTS_expression])] |
|
|
| <p><dt> Oxygen |
| <dd> [$([#8][SMARTS_expression])] |
|
|
| <p><dt> Fluorine |
| <dd> [$([#9][SMARTS_expression])]</p></dl><br> |
|
|
| <h3> Recursive SMARTS: Multiple groups</h3><dl> |
|
|
| <p><dt> Two possible groups |
| <dd> [$(SMARTS_expression_A),$(SMARTS_expression_B)] |
| <dd> Hits atoms in either environment or group of interest, A or B.<br> |
| Example usages:<br> |
| Azide group is : [$(*-[NX2-]-[NX2+]#[NX1]),$(*-[NX2]=[NX2+]=[NX1-])]<br> |
| Azide ion is: [$([NX1-]=[NX2+]=[NX1-]),$([NX1]#[NX2+]-[NX1-2])]<br> |
| Azide or azide ion is: [$([$(*-[NX2-]-[NX2+]#[NX1]),$(*-[NX2]=[NX2+]=[NX1-])]),$([$([NX1-]=[NX2+]=[NX1-]),$( |
| [NX1]#[NX2+]-[NX1-2])])] |
|
|
| <p><dt> Recursive SMARTS |
| <dd> [$([atom_that_gets_hit][other_atom][other_atom])] |
| <dd> Hits first atom within parenthesis |
| Example usages:<br> |
| [$([CX3]=[OX1])] hits Carbonyl Carbon |
| [$([OX1]=[CX3])] hits Carbonyl Oxygen </p></dl><br> |
|
|
| <h3> Single only, Double only, Single or Double</h3><dl> |
|
|
| <p><dt> Sulfide |
| <dd> [#16X2H0] |
| <dd> (-alkylthio) Won't hit thiols. Hits disulfides too. |
|
|
| <p><dt> Mono-sulfide |
| <dd> [#16X2H0][!#16] |
| <dd> (alkylthio- or alkoxy-) R-S-R Won't hit thiols. Won't hit disulfides. |
|
|
| <p><dt> Di-sulfide |
| <dd> [#16X2H0][#16X2H0] |
| <dd> Won't hit thiols. Won't hit mono-sulfides. |
|
|
| <p><dt> Two sulfides |
| <dd> [#16X2H0][!#16].[#16X2H0][!#16] |
|
|
| <dd> Won't hit thiols. Won't hit mono-sulfides. Won't hit disulfides. |
|
|
| <p><dt> Acid/conj-base |
| <dd> [OX2H,OX1H0-] |
| <dd> Hits acid and conjugate base. acid/base |
|
|
| <p><dt> Non-acid Oxygen |
| <dd> [OX2H0] |
|
|
| <p><dt> Acid/base |
| <dd> [H1,H0-] |
| <dd> Works for any atom if base form has no Hs & acid has only one.</p></dl><br> |
|
|
| <h3> Muntiple Disconnected Groups</h3><dl> |
|
|
| <p><dt> Two disconnected SMARTS fragments |
| <dd> ([Cl!$(Cl~c)].[c!$(c~Cl)]) |
| <dd> A molecule that contains a chlorine and an aromatic carbon but which are not connected to each other. Uses component-level SMARTS. B |
| oth SMARTS fragments must be in the same SMILES target fragment. |
|
|
| <p><dt> Two disconnected SMARTS fragments |
| <dd> ([Cl]).([c]) |
| <dd> Hits SMILES that contain a chlorine and an aromatic carbon but which are in different SMILES fragments. |
|
|
| <p><dt> Two not-necessarily connected SMARTS fragments |
| <dd> ([Cl].[c]) |
| <dd> Uses component-level SMARTS. Both SMARTS fragments must be in the same SMILES target fragment. |
|
|
| <p><dt> Two not-necessarily connected fragments |
| <dd> ([SMARTS_expression]).([SMARTS_expression]) |
| <dd> Uses component-level SMARTS. SMARTS fragments are each in different SMILES target fragments. |
|
|
| <p><dt> Two primary or secondary amines |
| <dd> [NX3;H2,H1;!$(NC=O)].[NX3;H2,H1;!$(NC=O)] |
| <dd> Here we use the "disconnection" symbol (".") to match two separate not-necessarily bonded identical patterns.</p></dl><br> |
|
|
|
|
| <a NAME="TOOL"></a><h2>Tools &Tricks</h2> |
|
|
| <h3> Alternative/Equivalent Representations </h3><dl> |
|
|
| <p><dt> Any carbon aromatic or non-aromatic |
| <dd> [#6] or [c,C] |
|
|
| <p><dt> SMILES wildcard |
| <dd> [#0] |
| <dd> This SMARTS hits the SMILES * |
|
|
| <p><dt> Factoring |
| <dd> [OX2,OX1-][OX2,OX1-] or [O;X2,X1-][O;X2,X1-] |
| <dd> Factor out common atomic expressions in the recursive SMARTS. May improve human readability. |
|
|
| <p><dt> High-precidence "and" |
| <dd> [N&X4&+,N&X3&+0] or [NX4+,NX3+0] |
| <dd> High-precidence "and" (&) is the default logical operator. "Or" (,) is higher precidence than & and low-precidence "and" (;) |
| is lower precidence than &. </p></dl><br> |
|
|
| <h3> Hydrogens </h3><dl> |
|
|
| <p><dt> Any atom w/ at-least 1 H |
| <dd> [*!H0,#1] |
| <dd> In SMILES and SMARTS, Hydrogen is not considered an atom (unless it is specified as an isotope). The hydrogen count is instead consi |
| dered a property of an atom. This SMARTS provides a way to effectively hit Hs themselves. |
|
|
| <p><dt> Hs on Carbons |
| <dd> [#6!H0,#1] |
|
|
| <p><dt> Atoms w/ 1 H |
| <dd> [H,#1] </p></dl><br> |
|
|
|
|
| <a NAME="E-"></a> |
| <H2> |
| 5. Electron & Proton Features |
| </H2><br><br> |
|
|
| <table BORDER COLS=3 WIDTH="750" NOSAVE ><tr> |
| <td align=center><a href="#ACID">Acids & Bases </a></td> |
| <td align=center><a href="#CHARGE">Charge</a></td> |
| <td align=center><a href="#H_BOND"> H-bond Donors & Acceptors</a></td> |
| <td align=center><a href="#RAD"> Radicals </a></td> |
| </table><br><br> |
|
|
|
|
| <a NAME="ACID"></a><h2> Acids & Bases </h2> |
|
|
| <dl> |
| <p><dt> Acid |
| <dd> [!H0;F,Cl,Br,I,N+,$([OH]-*=[!#6]),+] |
| <dd> Proton donor |
|
|
| <p><dt> Carboxylic acid |
| <dd> [CX3](=O)[OX2H1] |
| <dd> (-oic acid, COOH) |
|
|
| <p><dt> Carboxylic acid or conjugate base. |
| <dd> [CX3](=O)[OX1H0-,OX2H1] |
|
|
| <p><dt> Hydroxyl_acidic |
| <dd> [$([OH]-*=[!#6])] |
| <dd> An acidic hydroxyl is a hydroxyl bonded to an atom which is multiply bonded to a hetero atom, this includes carboxylic, sulphur, pho |
| sphorous, halogen and nitrogen oxyacids |
|
|
| <p><dt> Phosphoric_Acid |
| <dd> [$(P(=[OX1])([$([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)])] |
| <dd> Hits both forms. Hits orthophosphoric acid and polyphosphoric acid anhydrides. Doesn't hit monophosphoric acid anhydride esters (in |
| cluding acidic mono- & di- esters) but will hit some polyphosphoric acid anhydride esters (mono- esters on pyrophosphoric acid and longe |
| r, di- esters on linear triphosphoric acid and longer). Hits acid and conjugate base. |
|
|
| <p><dt> Sulfonic Acid. High specificity. |
| <dd> [$([#16X4](=[OX1])(=[OX1])([#6])[OX2H,OX1H0-]),$([#16X4+2]([OX1-])([OX1-])([#6])[OX2H,OX1H0-])] |
| <dd> Only hits carbo- sulfonic acids (Won't hit herteroatom-substituted molecules). Hits acid and conjugate base. Hits Both Depiction Fo |
| rms. Hits Arene sulfonic acids. |
|
|
| <p><dt> Acyl Halide |
| <dd> [CX3](=[OX1])[F,Cl,Br,I] |
| <dd> (acid halide, -oyl halide)</p></dl><br> |
|
|
|
|
| <a NAME="CHARGE"></a><h2>Charge </h2> |
|
|
| <dl> |
| <p><dt> Anionic divalent Nitrogen |
| <dd> [NX2-] |
|
|
| <p><dt> Oxenium Oxygen |
| <dd> [OX2H+]=* |
|
|
| <p><dt> Oxonium Oxygen |
| <dd> [OX3H2+] |
|
|
| <p><dt> Carbocation |
| <dd> [#6+] |
|
|
| <p><dt> sp2 cationic carbon. |
| <dd> [$([cX2+](:*):*)] |
| <dd> Aromatic cationic sp2 carbon with a free electron in a non-bonding sp2 hybrid orbital |
|
|
| <p><dt> Azide ion. |
| <dd> [$([NX1-]=[NX2+]=[NX1-]),$([NX1]#[NX2+]-[NX1-2])] |
| <dd> Hits N in azide ion |
|
|
| <p><dt> Zwitterion High Specificity |
| <dd> [+1]~*~*~[-1] |
| <dd> +1 charged atom separated by any 3 bonds from a -1 charged atom. |
|
|
| <p><dt> Zwitterion Low Specificity, Crude |
| <dd>[$([!-0!-1!-2!-3!-4]~*~[!+0!+1!+2!+3!+4]),$([!-0!-1!-2!-3!-4]~*~*~[!+0!+1!+2!+3!+4]),$([!-0!-1!-2!-3!-4]~*~*~*~[!+0!+1!+2!+3!+4]),$([!-0!-1!-2!-3!-4]~*~*~*~*~[!+0!+1!+2!+3!+4]),$([!-0!-1!-2!-3!-4]~*~*~*~*~*~[!+0!+1!+2!+3!+4]),$([!-0!-1!-2!-3!-4]~*~*~*~*~*~*~[!+0!+1!+2!+3!+4]),$([!-0!-1!-2!-3!-4]~*~*~*~*~*~*~*~[!+0!+1!+2!+3!+4]),$([!-0!-1!-2!-3!-4]~*~*~*~*~*~*~*~*~[!+0!+1!+2!+3!+4]),$([!-0!-1!-2!-3!-4]~*~*~*~*~*~*~*~*~*~[!+0!+1!+2!+3!+4])] |
| <dd> Variously charged moieties separated by up to ten bonds. |
|
|
| <p><dt> Zwitterion Low Specificity |
| <dd> ([!-0!-1!-2!-3!-4].[!+0!+1!+2!+3!+4]) |
| <dd> Variously charged moieties that are within the same molecule but not-necessarily connected. Uses component-level grouping.</p></dl> |
| <br> |
|
|
|
|
| <a NAME="H_BOND"></a><h2> H-bond Donors & Acceptors</h2> |
|
|
| <dl> |
| <p><dt> Hydrogen-bond acceptor |
| <dd> [#6,#7;R0]=[#8] |
| <dd> Only hits carbonyl and nitroso. Matches a 2-atom pattern consisting of a carbon or nitrogen not in a ring, double bonded to an oxyge |
| n. |
|
|
| <p><dt> Hydrogen-bond acceptor |
| <dd> [!$([#6,F,Cl,Br,I,o,s,nX3,#7v5,#15v5,#16v4,#16v6,*+1,*+2,*+3])] |
| <dd> A H-bond acceptor is a heteroatom with no positive charge, note that negatively charged oxygen or sulphur are included. Excluded are |
| halogens, including F, heteroaromatic oxygen, sulphur and pyrrole N. Higher oxidation levels of N,P,S are excluded. Note P(III) is currentl |
| y included. Zeneca's work would imply that (O=S=O) shoud also be excluded. |
|
|
| <p><dt> Hydrogen-bond donor. |
| <dd> [!$([#6,H0,-,-2,-3])] |
| <dd> A H-bond donor is a non-negatively charged heteroatom with at least one H |
|
|
| <p><dt> Hydrogen-bond donor. |
| <dd> [!H0;#7,#8,#9] |
| <dd> Must have an N-H bond, an O-H bond, or a F-H bond |
|
|
| <p><dt> Possible intramolecular H-bond |
| <dd> [O,N;!H0]-*~*-*=[$([C,N;R0]=O)] |
| <dd> Note that the overall SMARTS consists of five atoms. The fifth atom is defined by a "recursive SMARTS", where "$()" encloses a valid |
| nested SMARTS and acts syntactically like an atom-primitive in the overall SMARTS. Multiple nesting is allowed.</p></dl><br> |
|
|
| <a NAME="RAD"></a><h2>Radicals </h2> |
|
|
| <dl> |
| <p><dt> Carbon Free-Radical |
| <dd> [#6;X3v3+0] |
| <dd> Hits a neutral carbon with three single bonds. |
|
|
| <p><dt> Nitrogen Free-Radical |
| <dd> [#7;X2v4+0] |
| <dd> Hits a neutral nitrogen with two single bonds or with a single and a triple bond. </p></dl><br> |
|
|
|
|
| <a NAME="BREAK"></a> |
| <H2> |
| 6. Breakdown of Complex SMARTS |
| </H2></center><br><br> |
|
|
|
|
| <table BORDER COLS=2 WIDTH="750" NOSAVE ><tr> |
| <td align=center><a href="#AM_AC"> Amino Acid </a></td> |
| <td align=center><a href="#ES_AM"> Ester or Amide </a></td> |
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