BALL  1.4.1
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Classes | Protected Member Functions | Protected Attributes | List of all members
BALL::HybridisationProcessor Class Reference

#include <BALL/STRUCTURE/hybridisationProcessor.h>

Inheritance diagram for BALL::HybridisationProcessor:
BALL::UnaryProcessor< AtomContainer > BALL::UnaryFunctor< AtomContainer, Processor::Result >

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
 HybridisationProcessor (const HybridisationProcessor &hp)
 copy construcor
 HybridisationProcessor (const String &smarts_file_name, const String &ff_file_name) throw (Exception::FileNotFound)
virtual ~HybridisationProcessor ()
 destructor
Processor-related methods
virtual bool start ()
 processor method which is called before the operator () call
virtual Processor::Result operator() (AtomContainer &ac)
 operator () for the processor
Accessors
Size getNumberOfHybridisationStatesSet ()
 Return the number of hybridisation states set during the last application.
void setAtomTypeSmarts (const String &file_name) throw (Exception::FileNotFound)
 sets the parameters file
vector< std::pair< String, Size > > getHybridisationMap ()
 Return the atom_types–hybridisation Hashmap.
Assignment
HybridisationProcessoroperator= (const HybridisationProcessor &hp)
 assignment operator
- 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
bool readAndInitBondAnglesFromFile_ (const String &file_name="") throw (Exception::FileNotFound)
double AverageBondAngle_ (Atom *a)
 computes the averaged bond angle for the given Atom

Protected Attributes

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

Public Attributes

Options options
 options
void setDefaultOptions ()

Additional Inherited Members

- Public Types inherited from BALL::UnaryFunctor< AtomContainer, Processor::Result >
typedef Processor::Result result_type
typedef AtomContainer argument_type
typedef AtomContainerargument_reference
typedef const AtomContainerconst_argument_reference
typedef AtomContainerargument_pointer
typedef const AtomContainerconst_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.