Package org.openscience.cdk.smarts

Class Smarts

  • public final class Smarts
extends Object
    Parse and generate the SMARTS query language. Given an IAtomContainer a SMARTS pattern is parsed and new IQueryAtoms and IQueryBonds are appended to the connection table. Each query atom/bond contains an Expr that describes the predicate to check when matching. This Expr is also used for generating SMARTS. 
     
 IAtomContainer mol = ...;
 if (Smarts.parse(mol, "[aD3]a-a([aD3])[aD3]")) {
     String smarts = Smarts.generate(mol);
 }
    When parsing SMARTS several flavors are available. The flavors affect how queries are interpreted. The following flavors are available:
    • FLAVOR_LOOSE - allows all unambiguous extensions.
    • FLAVOR_DAYLIGHT - no extensions, as documented in Daylight theory manual.
    • FLAVOR_CACTVS - '[#X]' hetero atom, '[#G8]' periodic group 8, '[G]' or '[i]' means insaturation. '[Z2]' means 2 aliphatic hetero neighbors, '[z2]' means 2 aliphatic hetero
    • FLAVOR_MOE - '[#X]' hetero atom, '[#G8]' periodic group 8, '[i]' insaturation.
    • FLAVOR_OECHEM - '[R3]' means ring bond count 3 (e.g. [x3]) instead of in 3 rings (problems with SSSR uniqueness). '[^2]' matches hybridisation (2=Sp2)
    • FLAVOR_CDK - Same as FLAVOR_LOOSE
    • FLAVOR_CDK_LEGACY - '[D3]' means heavy degree 3 instead of explicit degree 3. '[^2]' means hybridisation (2=Sp2). '[G8]' periodic group 8

    In threaded environments error handling can be improved by using the SmartsResult return type. Other wise the error message is set on a shared variable which is access via getLastErrorMesg(). 
     
 IAtomContainer mol = ...;
 SmartsResult res = Smarts.parseToResult(mol, "[aD3]a-a([aD3])[aD3]");
 if (res.ok()) {
     String smarts = Smarts.generate(mol);
 } else {
     System.err.println(res.getMessage());
 }

    In addition to the flavors above CACTVS toolkit style ranges are supported. For example [D{2-4}] means degree 2, 3, or 4. On writing such ranges are converted to [D2,D3,D4].

    • Constructor Detail

      • Smarts

        public Smarts()

    • Method Detail

      • parseToResult

        public static SmartsResult parseToResult​(IAtomContainer mol,
                                         String smarts,
                                         int flavor)
        Parse the provided SMARTS string appending query atom/bonds to the provided molecule. This method allows the flavor of SMARTS to specified that changes the meaning of queries.
        Parameters:
        mol - the molecule to store the query in
        smarts - the SMARTS string
        flavor - (optional) the SMARTS flavor, default is FLAVOR_LOOSE.
        Returns:
        the result of the SMARTS
        See Also:
        Expr, IQueryAtom, IQueryBond

      • parseToResult

        public static SmartsResult parseToResult​(IAtomContainer mol,
                                         String smarts)
        Parse the provided SMARTS string appending query atom/bonds to the provided molecule. This method allows the flavor of SMARTS to specified that changes the meaning of queries.
        Parameters:
        mol - the molecule to store the query in
        smarts - the SMARTS string
        Returns:
        the result of the SMARTS
        See Also:
        Expr, IQueryAtom, IQueryBond

      • parse

        public static boolean parse​(IAtomContainer mol,
                            String smarts,
                            int flavor)
        Parse the provided SMARTS string appending query atom/bonds to the provided molecule. This method allows the flavor of SMARTS to specified that changes the meaning of queries.
        Parameters:
        mol - the molecule to store the query in
        smarts - the SMARTS string
        flavor - the SMARTS flavor (e.g. FLAVOR_LOOSE.
        Returns:
        whether the SMARTS was valid, if invalid the getLastErrorMesg() is set.
        See Also:
        Expr, IQueryAtom, IQueryBond

      • parse

        public static boolean parse​(IAtomContainer mol,
                            String smarts)
        Parse the provided SMARTS string appending query atom/bonds to the provided molecule. This method uses FLAVOR_LOOSE.
        Parameters:
        mol - the molecule to store the query in
        smarts - the SMARTS string
        Returns:
        whether the SMARTS was valid, if invalid the getLastErrorMesg() is set.
        See Also:
        Expr, IQueryAtom, IQueryBond

      • generateAtom

        public static String generateAtom​(Expr expr)
        Utility to generate an atom expression. 
        
 Expr   expr  = new Expr(Expr.Type.DEGREE, 4).and(
                  new Expr(Expr.Type.IS_AROMATIC));
 String aExpr = Smarts.generateAtom(expr);
 // aExpr='[D4a]'
        Parameters:
        expr - the expression
        Returns:
        the SMARTS atom expression
        See Also:
        Expr

      • generateBond

        public static String generateBond​(Expr expr)
        Utility to generate a bond expression. 
        
 Expr   expr  = new Expr(Expr.Type.TRUE);
 String bExpr = Smarts.generateBond(expr);
 // bExpr='~'
        Parameters:
        expr - the expression
        Returns:
        the SMARTS atom expression
        See Also:
        Expr

      • generate

        public static String generate​(IAtomContainer mol)
        Generate a SMARTS string from the provided molecule. The generator uses Exprs stored on the QueryAtom and QueryBond instances. 
         
 IAtomContainer mol = ...;
 QueryAtom qatom1 = new QueryAtom(mol.getBuilder());
 QueryAtom qatom2 = new QueryAtom(mol.getBuilder());
 QueryBond qbond  = new QueryBond(mol.getBuilder());
 qatom1.setExpression(new Expr(Expr.Type.IS_AROMATIC));
 qatom2.setExpression(new Expr(Expr.Type.IS_AROMATIC));
 qbond.setExpression(new Expr(Expr.Type.IS_ALIPHATIC));
 qbond.setAtoms(new IAtom[]{qatom1, qatom2});
 mol.addAtom(qatom1);
 mol.addAtom(qatom2);
 mol.addBond(qbond);
 String smartsStr = Smarts.generate(mol);
 // smartsStr = 'a!:a'
        Parameters:
        mol - the query molecule
        Returns:
        the SMARTS
        See Also:
        Expr, IQueryAtom, IQueryBond