BALL::Expression Class Reference

#include <BALL/KERNEL/expression.h>

Public Types
Type Definitions
typedef void *(*	CreationMethod )()

Public Member Functions
Constructors and Destructor
	Expression ()
	Expression (const Expression &expression)
	Expression (const String &expression_string)
virtual	~Expression ()
Predicates
bool	hasPredicate (const String &name) const
bool	operator== (const Expression &expression) const
Accessors
virtual bool	operator() (const Atom &atom) const
ExpressionPredicate *	getPredicate (const String &name, const String &args="") const
void	registerPredicate (const String &name, CreationMethod creation_method)
void	setExpression (const String &expression)
const String &	getExpressionString () const
const ExpressionTree *	getExpressionTree () const
const StringHashMap < CreationMethod > &	getCreationMethods () const
Assignment
Expression &	operator= (const Expression &expression)
virtual void	clear ()

Protected Member Functions
ExpressionTree *	constructExpressionTree_ (const ExpressionParser::SyntaxTree &tree)
void	registerStandardPredicates_ ()

Protected Attributes
StringHashMap< CreationMethod >	create_methods_
ExpressionTree *	expression_tree_
String	expression_string_

Detailed Description

The class Expression provides a frontend to ExpressionTree.

Expressions may be built from the following modules:

• AND a conjunction
• OR a disjunction
• ! a negation
• predicate(argument) a predicate class that is derived from ExpressionPredicate and provides operator()(const Atom& atom) const.

Additionally brackets can be used for grouping. At least one bracket pair must exist which encloses the argument of a predicate. Empty arguments are allowed.

Example:

!residueID(12) AND (element(N) OR element(C))

BALL offers various predefined ExpressionPredicates. These are:

Syntax	Description
true()	always true
false()	always false
SMARTS(string)	use a SMARTS expression
selected()	true for already selected atoms
name(string)	the name of an atom
type(string)	type name of an atom
element(char)	element (abbreviated by its symbol)
residue(string)	name of a residue
residueID(string)	PDB ID of the residue (usually a number)
protein(string)	name of protein, the atom is contained in
secondaryStruct(string)	name of the secondary structure, the atom is contained in
chain(string)	name of the chain, the atom is contained in
nucleotide(string)	name of the nucleotide the atom is contained in
solvent()	the atom is a solvent atom added by BALL
backbone()	backbone atoms
inRing()	part of a ring
doubleBonds()	atoms with double bonds
tripleBonds()	atoms with triple bonds
numberOfBonds(int)	atoms with a given number of bonds
aromaticBonds()	atoms with aromatic bonds
connectedTo(char)	atoms which are connected to an atom (see ConnectedToPredicate)
charge([op][number])	select by charge, Possible operators are '<'  '<='  '='  '>='  '>'
spHybridized()
sp2Hybridized()
sp3Hybridized()
charge(float)	atoms with given charge
isAxial()
is4C1()

See Also

ExpressionTree

Definition at line 79 of file expression.h.

Member Typedef Documentation

typedef void*(* BALL::Expression::CreationMethod)()

A creation method for predicates.

Definition at line 91 of file expression.h.

Constructor & Destructor Documentation

BALL::Expression::Expression

(

)

Default Constructor.

BALL::Expression::Expression

(

const Expression &

expression

)

Copy Constructor.

BALL::Expression::Expression

(

const String &

expression_string

)

Construct an Expression with a string

Exceptions

Exception::ParseError

if a syntax error was encountered

virtual BALL::Expression::~Expression ( )

virtual

Destructor.

Member Function Documentation

virtual void BALL::Expression::clear ( )

virtual

Clear method

ExpressionTree* BALL::Expression::constructExpressionTree_ ( const ExpressionParser::SyntaxTree &  tree )

protected

const StringHashMap<CreationMethod>& BALL::Expression::getCreationMethods

(

)

const

Get the creation methods.

const String& BALL::Expression::getExpressionString

(

)

const

Get the expression string.

const ExpressionTree* BALL::Expression::getExpressionTree

(

)

const

Get the expression tree.

ExpressionPredicate* BALL::Expression::getPredicate	(	const String &	name,
		const String &	args = ""
	)		const

Create a new predicate according to the name. If the predicate is not known, return 0.

Parameters

name	the name of the predicate
args	the optional argument of the predicate

bool BALL::Expression::hasPredicate

(

const String &

name

)

const

virtual bool BALL::Expression::operator() ( const Atom &  atom ) const

virtual

Evaluate the expression of atom

Parameters

atom

Expression& BALL::Expression::operator=

(

const Expression &

expression

)

Assignment operator

bool BALL::Expression::operator==

(

const Expression &

expression

)

const

Equality operator

void BALL::Expression::registerPredicate	(	const String &	name,
		CreationMethod	creation_method
	)

Register a new predicate class.

void BALL::Expression::registerStandardPredicates_ ( )

protected

void BALL::Expression::setExpression

(

const String &

expression

)

Set the expression and build a tree for it.

Exceptions

Exception::ParseError

if a syntax error was encountered

Member Data Documentation

StringHashMap<CreationMethod> BALL::Expression::create_methods_

protected

Definition at line 205 of file expression.h.

String BALL::Expression::expression_string_

protected

Definition at line 214 of file expression.h.

ExpressionTree* BALL::Expression::expression_tree_

protected

Definition at line 210 of file expression.h.