org.openscience.cdk.smarts

Class Smarts

java.lang.Object

org.openscience.cdk.smarts.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 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].

Field Summary

Fields

Modifier and Type	Field and Description
static int	FLAVOR_CACTVS
static int	FLAVOR_CDK
static int	FLAVOR_CDK_LEGACY
static int	FLAVOR_DAYLIGHT
static int	FLAVOR_LOOSE
static int	FLAVOR_MOE
static int	FLAVOR_OECHEM
static ThreadLocal<org.openscience.cdk.smarts.Smarts.SmartsError>	lastError

Constructor Summary

Constructors

Constructor and Description
Smarts()

Method Summary

Modifier and Type	Method and Description
static String	generate(IAtomContainer mol) Generate a SMARTS string from the provided molecule.
static String	generateAtom(Expr expr) Utility to generate an atom expression.
static String	generateBond(Expr expr) Utility to generate a bond expression.
static String	getLastErrorLocation() Access a display of the error position from previously parsed SMARTS (when parse(org.openscience.cdk.interfaces.IAtomContainer, java.lang.String, int)=false)
static String	getLastErrorMesg() Access the error message from previously parsed SMARTS (when parse(org.openscience.cdk.interfaces.IAtomContainer, java.lang.String, int)=false).
static boolean	parse(IAtomContainer mol, String smarts) Parse the provided SMARTS string appending query atom/bonds to the provided molecule.
static boolean	parse(IAtomContainer mol, String smarts, int flavor) Parse the provided SMARTS string appending query atom/bonds to the provided molecule.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

FLAVOR_LOOSE

public static final int FLAVOR_LOOSE

See Also:

Constant Field Values

FLAVOR_DAYLIGHT

public static final int FLAVOR_DAYLIGHT

See Also:

Constant Field Values

FLAVOR_CACTVS

public static final int FLAVOR_CACTVS

See Also:

Constant Field Values

FLAVOR_MOE

public static final int FLAVOR_MOE

See Also:

Constant Field Values

FLAVOR_OECHEM

public static final int FLAVOR_OECHEM

See Also:

Constant Field Values

FLAVOR_CDK

public static final int FLAVOR_CDK

See Also:

Constant Field Values

FLAVOR_CDK_LEGACY

public static final int FLAVOR_CDK_LEGACY

See Also:

Constant Field Values

lastError

public static ThreadLocal<org.openscience.cdk.smarts.Smarts.SmartsError> lastError

Constructor Detail

Smarts

public Smarts()

Method Detail

getLastErrorMesg

public static String getLastErrorMesg()

Access the error message from previously parsed SMARTS (when parse(org.openscience.cdk.interfaces.IAtomContainer, java.lang.String, int)=false).

Returns:

the error message, or null if none

getLastErrorLocation

public static String getLastErrorLocation()

Access a display of the error position from previously parsed SMARTS (when parse(org.openscience.cdk.interfaces.IAtomContainer, java.lang.String, int)=false)

Returns:

the error message, or null if none

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

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

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