/usr/include/BALL/KERNEL/expression.h is in libball1.4-dev 1.4.3~beta1-4.
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// vi: set ts=2:
//
#ifndef BALL_KERNEL_EXPRESSION_H
#define BALL_KERNEL_EXPRESSION_H
#ifndef BALL_DATATYPE_STRINGHASHMAP_H
# include <BALL/DATATYPE/stringHashMap.h>
#endif
#ifndef BALL_KERNEL_EXPRESSIONPARSER_H
# include <BALL/KERNEL/expressionParser.h>
#endif
namespace BALL
{
class Atom;
class ExpressionTree;
/**
* The class \ref Expression provides a frontend to \ref ExpressionTree.
* \par
* Expressions may be built from the following modules:
* <ul>
* <li><tt>AND</tt> a conjunction
* <li><tt>OR</tt> a disjunction
* <li><tt>!</tt> a negation
* <li><tt>predicate(argument) </tt> a predicate class that is derived from
* \ref ExpressionPredicate and provides <tt>operator()(const \ref Atom& atom) const</tt>.
* </ul>
* 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.
* \par
* <b>Example:</b>
* \code
* !residueID(12) AND (element(N) OR element(C))
* \endcode
* \par
* BALL offers various predefined ExpressionPredicates. These are:
* \par
* <table>
* <tr><th>Syntax</th><th>Description</th></tr>
* <tr><td><b> true() </b></td><td> always true </td></tr>
* <tr><td><b> false() </b></td><td> always false </td></tr>
* <tr><td><b> SMARTS(string) </b></td><td> use a <a href="http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html">SMARTS</a> expression </td></tr>
* <tr><td><b> selected() </b></td><td> true for already selected atoms </td></tr>
* <tr><td><b> name(string) </b></td><td> the name of an atom </td></tr>
* <tr><td><b> type(string) </b></td><td> type name of an atom </td></tr>
* <tr><td><b> element(char) </b></td><td> element (abbreviated by its symbol) </td></tr>
* <tr><td><b> residue(string) </b></td><td> name of a residue </td></tr>
* <tr><td><b> residueID(string) </b></td><td> PDB ID of the residue (usually a number) </td></tr>
* <tr><td><b> protein(string) </b></td><td> name of protein, the atom is contained in </td></tr>
* <tr><td><b> secondaryStruct(string) </b></td><td> name of the secondary structure, the atom is contained in </td></tr>
* <tr><td><b> chain(string) </b></td><td> name of the chain, the atom is contained in </td></tr>
* <tr><td><b> nucleotide(string) </b></td><td> name of the nucleotide the atom is contained in</td></tr>
* <tr><td><b> solvent() </b></td><td> the atom is a solvent atom added by BALL </td></tr>
* <tr><td><b> backbone() </b></td><td> backbone atoms </td></tr>
* <tr><td><b> inRing() </b></td><td> part of a ring</td></tr>
* <tr><td><b> doubleBonds() </b></td><td> atoms with double bonds </td></tr>
* <tr><td><b> tripleBonds() </b></td><td> atoms with triple bonds </td></tr>
* <tr><td><b> numberOfBonds(int) </b></td><td> atoms with a given number of bonds </td></tr>
* <tr><td><b> aromaticBonds() </b></td><td> atoms with aromatic bonds </td></tr>
* <tr><td><b> connectedTo(char) </b></td><td> atoms which are connected to an atom (see \ref ConnectedToPredicate)</td></tr>
* <tr><td><b> charge([op][number]) </b></td><td> select by charge, Possible operators are '<' '<=' '=' '>=' '>' </td></tr>
* <tr><td><b> spHybridized() </b></td><td> </td></tr>
* <tr><td><b> sp2Hybridized() </b></td><td> </td></tr>
* <tr><td><b> sp3Hybridized() </b></td><td> </td></tr>
* <tr><td><b> charge(float) </b></td><td> atoms with given charge </td></tr>
* <tr><td><b> isAxial() </b></td><td> </td></tr>
* <tr><td><b> is4C1() </b></td><td> </td></tr>
* </table>
* \par
* \see ExpressionTree
*
* \ingroup Predicates
*/
class BALL_EXPORT Expression
{
public:
BALL_CREATE(Expression)
/** @name Type Definitions
*/
//@{
/** A creation method for predicates.
*/
typedef void * (*CreationMethod) ();
//@}
/** @name Constructors and Destructor
*/
//@{
/** Default Constructor.
*/
Expression();
/** Copy Constructor.
*/
Expression(const Expression& expression);
/** Construct an Expression with a string
* @throw Exception::ParseError if a syntax error was encountered
*/
Expression(const String& expression_string);
/** Destructor.
*/
virtual ~Expression();
//@}
/** @name Predicates
*/
//@{
/**
*/
bool hasPredicate(const String& name) const;
/** Equality operator
*/
bool operator == (const Expression& expression) const;
//@}
/** @name Accessors
*/
//@{
/** Evaluate the expression of <tt>atom</tt>
@param atom
*/
virtual bool operator () (const Atom& atom) const;
/** Create a new predicate according to the name.
If the predicate is not known, return 0.
@param name the name of the predicate
@param args the optional argument of the predicate
*/
ExpressionPredicate* getPredicate(const String& name,
const String& args = "") const;
/** Register a new predicate class.
*/
void registerPredicate(const String& name, CreationMethod creation_method);
/** Set the expression and build a tree for it.
* @throw Exception::ParseError if a syntax error was encountered
*/
void setExpression(const String& expression);
/** Get the expression string.
*/
const String& getExpressionString() const;
/** Get the expression tree.
*/
const ExpressionTree* getExpressionTree() const;
/** Get the creation methods.
*/
const StringHashMap<CreationMethod>& getCreationMethods() const;
//@}
/** @name Assignment
*/
//@{
/** Assignment operator
*/
Expression& operator = (const Expression& expression);
/** Clear method
*/
virtual void clear();
//@}
protected:
/*_ @name Protected methods
*/
//@{
/*_ Construct the expression tree from the SyntaxTree
* @throw Exception::ParseError if a syntax error was encountered
*/
ExpressionTree* constructExpressionTree_(const ExpressionParser::SyntaxTree& tree);
/*_ Register the predicates defined by default.
See also: BALL/KERNEL/standardPredicates.h
*/
void registerStandardPredicates_();
//@}
/*_ @name Protected attributes
*/
//@{
/*_ The methods to create the ExpressionPredicate instances
*/
StringHashMap<CreationMethod> create_methods_;
/*_ The ExpressionTree constructed from the string.
This tree contains the instances of the predicates.
*/
ExpressionTree* expression_tree_;
/*_ The string describing the expression.
*/
String expression_string_;
//@}
};
}
#endif // BALL_KERNEL_EXPRESSION_H
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