BALL::HybridisationProcessor Class Reference

#include <BALL/STRUCTURE/hybridisationProcessor.h>

Inheritance diagram for BALL::HybridisationProcessor:

Classes
struct	AtomNames_
struct	Default
	Default values for options. More...
struct	Elements_
struct	Method
struct	Option
	Option names. More...

Public Member Functions
Constructors and Destructors
	BALL_CREATE (HybridisationProcessor)
	HybridisationProcessor ()
	default constructor More...
	HybridisationProcessor (const HybridisationProcessor &hp)
	copy construcor More...
	HybridisationProcessor (const String &smarts_file_name, const String &ff_file_name) throw (Exception::FileNotFound)
virtual	~HybridisationProcessor ()
	destructor More...
Processor-related methods
virtual bool	start ()
	processor method which is called before the operator () call More...
virtual Processor::Result	operator() (AtomContainer &ac)
	operator () for the processor More...
Accessors
Size	getNumberOfHybridisationStatesSet ()
	Return the number of hybridisation states set during the last application. More...
void	setAtomTypeSmarts (const String &file_name) throw (Exception::FileNotFound)
	sets the parameters file More...
vector< std::pair< String, Size > >	getHybridisationMap ()
	Return the atom_types–hybridisation Hashmap. More...
Assignment
HybridisationProcessor &	operator= (const HybridisationProcessor &hp)
	assignment operator More...
Public Member Functions inherited from BALL::UnaryProcessor< AtomContainer >
	UnaryProcessor ()
	UnaryProcessor (const UnaryProcessor &)
virtual	~UnaryProcessor ()
virtual bool	finish ()

Protected Member Functions
bool	readAtomTypeSmartsFromFile_ (const String &file_name="") throw (Exception::FileNotFound)
	method to read the paramter file More...
bool	readAndInitBondAnglesFromFile_ (const String &file_name="") throw (Exception::FileNotFound)
double	AverageBondAngle_ (Atom *a)
	computes the averaged bond angle for the given Atom More...

Protected Attributes
Size	num_hybridisation_states_
	number of bonds, which are created during the processor call More...
vector< std::pair< String, Size > >	atom_type_smarts_
	structure where atom type smarts and the corresponding hybridisation states are stored in More...
StringHashMap< StringHashMap < StringHashMap< std::multimap < float, AtomNames_ > > > >	bond_angles_
StringHashMap< Elements_ >	elements_
bool	valid_
	the Processors state More...

Public Attributes
Options	options
	options More...
void	setDefaultOptions ()

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

Hybridisation processor

Definition at line 42 of file hybridisationProcessor.h.

Constructor & Destructor Documentation

BALL::HybridisationProcessor::HybridisationProcessor

(

)

default constructor

BALL::HybridisationProcessor::HybridisationProcessor

(

const HybridisationProcessor &

hp

)

copy construcor

BALL::HybridisationProcessor::HybridisationProcessor	(	const String &	smarts_file_name,
		const String &	ff_file_name
	)		throw (Exception::FileNotFound)

Constructor with parameter filename for the smarts based algorithm and parameter filename for the force field based method

virtual BALL::HybridisationProcessor::~HybridisationProcessor ( )

virtual

destructor

Member Function Documentation

double BALL::HybridisationProcessor::AverageBondAngle_ ( Atom *  a )

protected

computes the averaged bond angle for the given Atom

BALL::HybridisationProcessor::BALL_CREATE

(

HybridisationProcessor

)

vector< std::pair<String, Size> > BALL::HybridisationProcessor::getHybridisationMap ( )

inline

Return the atom_types–hybridisation Hashmap.

Definition at line 146 of file hybridisationProcessor.h.

Size BALL::HybridisationProcessor::getNumberOfHybridisationStatesSet

(

)

Return the number of hybridisation states set during the last application.

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

virtual

operator () for the processor

Reimplemented from BALL::UnaryProcessor< AtomContainer >.

HybridisationProcessor& BALL::HybridisationProcessor::operator=

(

const HybridisationProcessor &

hp

)

assignment operator

bool BALL::HybridisationProcessor::readAndInitBondAnglesFromFile_ ( const String &  file_name = "" ) throw (Exception::FileNotFound)

protected

bool BALL::HybridisationProcessor::readAtomTypeSmartsFromFile_ ( const String &  file_name = "" ) throw (Exception::FileNotFound)

protected

method to read the paramter file

void BALL::HybridisationProcessor::setAtomTypeSmarts

(

const String &

file_name

)

throw (Exception::FileNotFound)

sets the parameters file

void BALL::HybridisationProcessor::setDefaultOptions

(

)

reset the options to default values

virtual bool BALL::HybridisationProcessor::start ( )

virtual

processor method which is called before the operator () call

Reimplemented from BALL::UnaryProcessor< AtomContainer >.

Member Data Documentation

vector< std::pair<String, Size> > BALL::HybridisationProcessor::atom_type_smarts_

protected

structure where atom type smarts and the corresponding hybridisation states are stored in

Definition at line 198 of file hybridisationProcessor.h.

StringHashMap<StringHashMap<StringHashMap<std::multimap<float, AtomNames_> > > > BALL::HybridisationProcessor::bond_angles_

protected

Contains the bond angles and their atom types. The bond angles are stored in 'rad'.

Definition at line 203 of file hybridisationProcessor.h.

StringHashMap<Elements_> BALL::HybridisationProcessor::elements_

protected

Maps the atom types onto their elements

Definition at line 209 of file hybridisationProcessor.h.

Size BALL::HybridisationProcessor::num_hybridisation_states_

protected

number of bonds, which are created during the processor call

Definition at line 195 of file hybridisationProcessor.h.

Options BALL::HybridisationProcessor::options

options

Definition at line 160 of file hybridisationProcessor.h.

bool BALL::HybridisationProcessor::valid_

protected

the Processors state

Definition at line 213 of file hybridisationProcessor.h.