Assignment of bond orders from topology information. More...

#include <BALL/STRUCTURE/assignBondOrderProcessor.h>

Inheritance diagram for BALL::AssignBondOrderProcessor:

Classes
struct	Algorithm

struct	Default
	Default values for options. More...

struct	Option
	Option names. More...

Public Member Functions
Constructors and Destructors
	AssignBondOrderProcessor ()
	Default Constructor. More...

virtual	~AssignBondOrderProcessor ()
	Destructor. More...

Processor-related methods
virtual bool	start ()
	Processor method which is called before the operator()-call. More...

void	clear ()

virtual Processor::Result	operator() (AtomContainer &ac)

virtual bool	finish ()
	Processor method which is called after the operator()-call. More...

Accessors
Size	getNumberOfAddedHydrogens (Position i)

Size	getNumberOfComputedSolutions ()

AtomContainer *	getAtomContainer ()

AtomContainer const *	getAtomContainer () const

const System &	getSolution (Position i) throw (Exception::IndexOverflow)

float	getTotalCharge (Position i)

float	getTotalPenalty (Position i=0)

int	getNumberOfNodeExpansions (Position i)

int	getQueueSize (Position i)

bool	apply (Position i)

void	resetBondOrders ()

bool	computeNextSolution (bool apply_solution=true)

void	setDefaultOptions ()

bool	hasValidOptions ()

float	evaluatePenalty (AtomContainer *ac)

Public Member Functions inherited from BALL::UnaryProcessor< AtomContainer >
	UnaryProcessor ()

	UnaryProcessor (const UnaryProcessor &)

virtual	~UnaryProcessor ()

Public Attributes
Public Attributes
Options	options
	the processor's options More...

Protected Member Functions
bool	readOptions_ ()

bool	readAtomPenalties_ () throw (Exception::FileNotFound())

bool	preassignPenaltyClasses_ ()

int	getPenaltyClass_ (Atom *atom)

bool	precomputeBondLengthPenalties_ ()

float	computeVirtualHydrogens_ (Atom *atom)

bool	apply_ (BondOrderAssignment &solution)

void	storeOriginalConfiguration_ ()

int	getQueueSize_ (const BondOrderAssignment &sol)

float	getTotalCharge_ (const BondOrderAssignment &sol)

float	getTotalPenalty_ (const BondOrderAssignment &sol)

int	getNumberOfNodeExpansions_ (const BondOrderAssignment &sol)

	AssignBondOrderProcessor (const AssignBondOrderProcessor &abop)

AssignBondOrderProcessor &	operator= (const AssignBondOrderProcessor &abop)

Protected Attributes
bool	valid_
	Processor is in a useable valid state. More...

bool	evaluation_mode_
	Processor is in an evaluation mode. Default is false. More...

std::map< Bond *, short >	bond_fixed_

std::vector< Bond * >	free_bonds_

HashMap< Bond *, Index >	bond_to_index_

std::vector< Bond * >	index_to_bond_

HashMap< Atom *, int >	number_of_virtual_hydrogens_

std::vector< int >	virtual_bond_index_to_number_of_virtual_hydrogens_

Size	num_of_virtual_bonds_

vector< Atom * >	virtual_bond_index_to_atom_

HashMap< Atom *, int >	atom_to_virtual_bond_index_

Bond *	virtual_bond_

Position	total_num_of_bonds_

int	num_of_free_bonds_

std::vector< Position >	fixed_val_

vector< BondOrderAssignment >	solutions_

vector< BondOrderAssignment >	starting_configuration_

float	atom_type_normalization_factor_

float	bond_length_normalization_factor_

int	last_applied_solution_

AtomContainer *	ac_

int	max_bond_order_

float	alpha_

int	max_number_of_solutions_

int	max_penalty_

bool	compute_also_non_optimal_solutions_

bool	add_missing_hydrogens_

bool	compute_also_connectivity_

bool	use_fine_penalty_

vector< int >	penalties_

vector< Position >	block_to_start_idx_

vector< Size >	block_to_length_

vector< int >	block_to_start_valence_

vector< std::pair< String, String > >	block_definition_

vector< vector< int > >	atom_to_block_

HashMap< Bond *, vector< float > >	bond_lengths_penalties_

Timer	timer_

StringHashMap < boost::shared_ptr < BondOrderAssignmentStrategy > >	strategies_

Friends
class	PartialBondOrderAssignment

class	BondOrderAssignment

class	PQ_Entry_

class	BondOrderAssignmentStrategy

class	AStarBondOrderStrategy

class	BranchAndBoundBondOrderStrategy

class	FPTBondOrderStrategy

class	ILPBondOrderStrategy

class	KGreedyBondOrderStrategy

Additional Inherited Members
Public Types inherited from BALL::UnaryFunctor< AtomContainer, Processor::Result >
typedef Processor::Result	result_type

typedef AtomContainer	argument_type

typedef AtomContainer &	argument_reference

typedef const AtomContainer &	const_argument_reference

typedef AtomContainer *	argument_pointer

typedef const AtomContainer *	const_argument_pointer

Detailed Description

Assignment of bond orders from topology information.

Called with default options the processor computes up to Default::MAX_NUMBER_OF_SOLUTIONS many possible bond orders with optimal value and applies the first solution found to the given AtomContainer.

All further optimal solutions can be applied by calling the method apply() . Additional solutions can be computed by calling the method computeNextSolution() (except when using the FPT strategy which currently does not support this behaviour).

: Example code:

AssignBondOrderProcessor bop;

bop.options.setBool(AssignBondOrderProcessor::Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS, true);

...

sys.apply(bop);

i = bop.getNumberOfComputedSolutions();

bop.apply(i-1);

...

while (bop.computeNextSolution())

{

i++;

bop.apply(i);

}

Definition at line 88 of file assignBondOrderProcessor.h.

Constructor & Destructor Documentation

BALL::AssignBondOrderProcessor::AssignBondOrderProcessor ( )

Default Constructor.

virtual BALL::AssignBondOrderProcessor::~AssignBondOrderProcessor ( )

virtual

Destructor.

BALL::AssignBondOrderProcessor::AssignBondOrderProcessor ( const AssignBondOrderProcessor & abop )

protected

Member Function Documentation

bool BALL::AssignBondOrderProcessor::apply ( Position i )

Applies the i-th precomputed bond order assignment.

Sets the AtomContainer's bond orders to the ones found in the (already computed!) i-th solution, start counting at 0!

: NOTE: All virtual hydrogens added to the processed AtomContainer by a previous call of apply will be deleted by the current call!

Parameters

i	index of the solution whose bond orders should be assigned.

Returns: bool - true if the i-th solution is valid, false otherwise.

bool BALL::AssignBondOrderProcessor::apply_ ( BondOrderAssignment & solution )

protected

Applies the given solution.

void BALL::AssignBondOrderProcessor::clear ( )

Clears the data structures.

NOTE: The options remain! Use setDefaultOptions() to clear the options.

bool BALL::AssignBondOrderProcessor::computeNextSolution ( bool apply_solution = true )

Computes and applies one of the next best solutions.

Ignores the options MAX_NUMBER_OF_SOLUTIONS and COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS .

Returns: bool - false if no further solution can be found.

float BALL::AssignBondOrderProcessor::computeVirtualHydrogens_ ( Atom * atom )

protected

Adds missing hydrogens as virtual hydrogens to the given atom, determines the possible penalty blocks, and returns the maximal possible atom type penalty.

"virtual" means that NO atoms and bonds are added to the original AtomContainer.

Parameters

atom	the atom, to which the virtual hydrogens should be added.

Returns: float - the max possible penalty the atom can get, if hydrogen(s) are added.

See Also: Option::ADD_HYDROGENS

float BALL::AssignBondOrderProcessor::evaluatePenalty ( AtomContainer * ac )

Evaluates the AtomContainer's bond orders as specified in the Options and returns the computed penalty.

Parameters

ac	AtomContainer, whose bond orders should be evaluated.

Returns: float - computed penalty, -1 if current assignment is not valid or includes aromatic bonds.

virtual bool BALL::AssignBondOrderProcessor::finish ( )

virtual

Processor method which is called after the operator()-call.

Reimplemented from BALL::UnaryProcessor< AtomContainer >.

AtomContainer* BALL::AssignBondOrderProcessor::getAtomContainer ( )

inline

Returns a pointer to the original Molecule as AtomContainer.

Definition at line 391 of file assignBondOrderProcessor.h.

AtomContainer const* BALL::AssignBondOrderProcessor::getAtomContainer ( ) const

inline

Returns a nonmutable pointer to the original Molecule as AtomContainer.

Definition at line 395 of file assignBondOrderProcessor.h.

Size BALL::AssignBondOrderProcessor::getNumberOfAddedHydrogens ( Position i )

inline

Returns the number of added hydrogens in solution i.

NOTE: Hydrogens can only be added using the Option::ADD_HYDROGENS-option.

Returns: Size - number of hydrogens added in assignment solution i.

See Also: Option::ADD_HYDROGENS

Definition at line 362 of file assignBondOrderProcessor.h.

Size BALL::AssignBondOrderProcessor::getNumberOfComputedSolutions ( )

inline

Returns the number of already computed solutions.

NOTE: Having applied the operator with option Option Algorithm::A_STAR this method returns the number of optimal solutions+1!

Returns: Size - number of already computed solutions.

See Also: Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS; Option::MAX_NUMBER_OF_SOLUTIONS

Definition at line 386 of file assignBondOrderProcessor.h.

int BALL::AssignBondOrderProcessor::getNumberOfNodeExpansions ( Position i )

inline

Definition at line 450 of file assignBondOrderProcessor.h.

int BALL::AssignBondOrderProcessor::getNumberOfNodeExpansions_ ( const BondOrderAssignment & sol )

inlineprotected

Definition at line 649 of file assignBondOrderProcessor.h.

int BALL::AssignBondOrderProcessor::getPenaltyClass_ ( Atom * atom )

protected

Finds the first matching SMARTS-expression in the penalty-vector and returns its index.

Return values

int	-1 if there is no matching expression

int BALL::AssignBondOrderProcessor::getQueueSize ( Position i )

inline

Definition at line 467 of file assignBondOrderProcessor.h.

int BALL::AssignBondOrderProcessor::getQueueSize_ ( const BondOrderAssignment & sol )

inlineprotected

Definition at line 613 of file assignBondOrderProcessor.h.

const System& BALL::AssignBondOrderProcessor::getSolution ( Position i ) throw (Exception::IndexOverflow)

Returns a reference to the original system to which solution i was applied.

NOTE: This method has the same effect as calling apply(i)!

Parameters

i	index of the solution, whose bond order assignment should be applied.

Returns: const System& - the original system with bond order assignment of solution i. If i is invalid, an Exception is thrown.

float BALL::AssignBondOrderProcessor::getTotalCharge ( Position i )

inline

Returns the total charge of solution i.

NOTE: This method is still experimental.

Parameters

i	index of the solution, whose charge should be computed.

Returns: float - total charge of solution i.

Definition at line 414 of file assignBondOrderProcessor.h.

float BALL::AssignBondOrderProcessor::getTotalCharge_ ( const BondOrderAssignment & sol )

inlineprotected

Returns the total charge of a solution.

Parameters

sol	solution, whose charge should be computed.

Returns: float - total charge of the given solution.

Definition at line 621 of file assignBondOrderProcessor.h.

float BALL::AssignBondOrderProcessor::getTotalPenalty ( Position i = 0 )

inline

Returns the total penalty of solution i.

Parameters

i	index of the solution, whose penalty should be returned.

Returns: float - total penalty of solution i.

Definition at line 433 of file assignBondOrderProcessor.h.

float BALL::AssignBondOrderProcessor::getTotalPenalty_ ( const BondOrderAssignment & sol )

inlineprotected

Returns the total penalty of the given solution.

Parameters

sol	solution, whose penalty should be returned.

Returns: float - total penalty of solution i.

See Also: Option::BOND_LENGTH_WEIGHTING;

Definition at line 639 of file assignBondOrderProcessor.h.

bool BALL::AssignBondOrderProcessor::hasValidOptions ( )

inline

Checks the options.

Definition at line 515 of file assignBondOrderProcessor.h.

virtual Processor::Result BALL::AssignBondOrderProcessor::operator() ( AtomContainer & ac )

virtual

Operator () for the processor

Called with Default-options the processor computes all possible bond order assignments with optimal atomic penalty value and applies the first solution to the given AtomContainer.

NOTE: Having used the Algorithm::A_STAR-option (default) the method getNumberOfComputedSolutions() will return the number of optimal solutions+1!

Parameters

ac	the AtomContainer to which the processor is applied.

Reimplemented from BALL::UnaryProcessor< AtomContainer >.

AssignBondOrderProcessor& BALL::AssignBondOrderProcessor::operator= ( const AssignBondOrderProcessor & abop )

protected

bool BALL::AssignBondOrderProcessor::preassignPenaltyClasses_ ( )

protected

Assigns every atom of the AtomContainer to which the processor is applied to a block of possible valences and the corresponding penalties.

Return values

bool	- false if the AtomContainer to which the processor is applied to has an atom with no matching penalty block.
bool	- true otherwise

bool BALL::AssignBondOrderProcessor::precomputeBondLengthPenalties_ ( )

protected

Precomputes for every bond of the AtomContainer, to which the processor is applied to, the possible bond length penalties resulting from deviation of the actual bond length to a standard length for bonds with same atom types and the chosen bond order.

: If there is no information for certain atom pairs, penalty 0 is assumed. In case of incomplete information, we assume the missing bond orders to be really unlikely and we set a penalty to 2* max_deviation_found (for this bond).

Return values