BALL::GAFFTypeProcessor Class Reference

#include <BALL/MOLMEC/AMBER/GAFFTypeProcessor.h>

Inheritance diagram for BALL::GAFFTypeProcessor:

Classes
struct	TypeDefinition
	Nested class definitions. More...
struct	Option
struct	Default

Public Member Functions
	GAFFTypeProcessor ()
	GAFFTypeProcessor (const Options &new_options)
virtual	~GAFFTypeProcessor ()
virtual Processor::Result	operator() (Composite &composite)
std::set< String >	getTypeNames () const
Public Member Functions inherited from BALL::UnaryProcessor< Composite >
	UnaryProcessor ()
	UnaryProcessor (const UnaryProcessor &)
virtual	~UnaryProcessor ()
virtual bool	start ()
virtual bool	finish ()

Public Attributes
Options	options

Protected Member Functions
std::vector< TypeDefinition >	getCarbonTypes_ ()
std::vector< TypeDefinition >	getHydrogenTypes_ ()
std::vector< TypeDefinition >	getNitrogenTypes_ ()
std::vector< TypeDefinition >	getOxygenTypes_ ()
std::vector< TypeDefinition >	getSulfurTypes_ ()
void	parseAtomtypeTableFile_ ()
void	precomputeBondProperties_ (Molecule *molecule)
	compute aromaticity, ring memberships, GAFF bond typization, ...
void	precomputeAtomProperties_ (Molecule *molecule)
void	annotateBondTypes_ ()
	Helper for precomputeBondProperties.
void	annotateRingSizes_ ()
	Helper for precomputeAtomProperties.
void	annotateAliphaticAndAromaticRingAtoms_ ()
void	annotatePlanarRingAtoms_ ()
bool	planarAtom_ (const Atom &atom)
bool	assignAtomtype_ (Atom &atom)
void	postProcessAtomTypes_ (Molecule *molecule)

Protected Attributes
StringHashMap< GAFFCESParser * >	ces_parsers_
std::map< Position, std::vector< TypeDefinition > >	atom_types_
std::vector< std::vector< Atom * > >	sssr_
Molecule *	current_molecule_

Additional Inherited Members
Public Types inherited from BALL::UnaryFunctor< ArgumentType, ResultType >
typedef ResultType	result_type
typedef ArgumentType	argument_type
typedef ArgumentType &	argument_reference
typedef const ArgumentType &	const_argument_reference
typedef ArgumentType *	argument_pointer
typedef const ArgumentType *	const_argument_pointer

Detailed Description

Definition at line 37 of file GAFFTypeProcessor.h.

Constructor & Destructor Documentation

GAFFTypeProcessor() [1/2]

BALL::GAFFTypeProcessor::GAFFTypeProcessor

(

)

GAFFTypeProcessor() [2/2]

BALL::GAFFTypeProcessor::GAFFTypeProcessor

(

const Options &

new_options

)

~GAFFTypeProcessor()

virtual BALL::GAFFTypeProcessor::~GAFFTypeProcessor ( )

virtual

Member Function Documentation

annotateAliphaticAndAromaticRingAtoms_()

void BALL::GAFFTypeProcessor::annotateAliphaticAndAromaticRingAtoms_ ( )

protected

annotateBondTypes_()

void BALL::GAFFTypeProcessor::annotateBondTypes_ ( )

protected

Helper for precomputeBondProperties.

annotatePlanarRingAtoms_()

void BALL::GAFFTypeProcessor::annotatePlanarRingAtoms_ ( )

protected

annotateRingSizes_()

void BALL::GAFFTypeProcessor::annotateRingSizes_ ( )

protected

Helper for precomputeAtomProperties.

assignAtomtype_()

bool BALL::GAFFTypeProcessor::assignAtomtype_ ( Atom & atom )

protected

Check the atom against each possible atom type and try to assign one.

getCarbonTypes_()

std::vector< TypeDefinition > BALL::GAFFTypeProcessor::getCarbonTypes_ ( )

inlineprotected

Definition at line 92 of file GAFFTypeProcessor.h.

getHydrogenTypes_()

std::vector< TypeDefinition > BALL::GAFFTypeProcessor::getHydrogenTypes_ ( )

inlineprotected

Definition at line 93 of file GAFFTypeProcessor.h.

getNitrogenTypes_()

std::vector< TypeDefinition > BALL::GAFFTypeProcessor::getNitrogenTypes_ ( )

inlineprotected

Definition at line 94 of file GAFFTypeProcessor.h.

getOxygenTypes_()

std::vector< TypeDefinition > BALL::GAFFTypeProcessor::getOxygenTypes_ ( )

inlineprotected

Definition at line 95 of file GAFFTypeProcessor.h.

getSulfurTypes_()

std::vector< TypeDefinition > BALL::GAFFTypeProcessor::getSulfurTypes_ ( )

inlineprotected

Definition at line 96 of file GAFFTypeProcessor.h.

getTypeNames()

std::set< String > BALL::GAFFTypeProcessor::getTypeNames

(

)

const

operator()()

virtual Processor::Result BALL::GAFFTypeProcessor::operator() ( Composite & )

virtual

operator ()

Reimplemented from BALL::UnaryProcessor< Composite >.

parseAtomtypeTableFile_()

void BALL::GAFFTypeProcessor::parseAtomtypeTableFile_ ( )

protected

Read file with table of atomtypes and push atomtypes and their TypeDefinition in corresponding vector and store a GAFFCESParser for every CESstring. The path to the atom type file is taken from the value of the option ATOMTYPE_FILENAME.

Exceptions

BALL::Exception::FileNotFound

planarAtom_()

bool BALL::GAFFTypeProcessor::planarAtom_ ( const Atom & atom )

protected

postProcessAtomTypes_()

void BALL::GAFFTypeProcessor::postProcessAtomTypes_ ( Molecule * molecule )

protected

Postprocessing and cleanup for GAFF types

precomputeAtomProperties_()

void BALL::GAFFTypeProcessor::precomputeAtomProperties_ ( Molecule * molecule )

protected

Store connectivity, number of attached H-atoms and number of attached N,O,F,Cl and Br-atoms for every atom in molecule

precomputeBondProperties_()

void BALL::GAFFTypeProcessor::precomputeBondProperties_ ( Molecule * molecule )

protected

compute aromaticity, ring memberships, GAFF bond typization, ...

Member Data Documentation

atom_types_

std::map<Position, std::vector<TypeDefinition> > BALL::GAFFTypeProcessor::atom_types_

protected

Definition at line 137 of file GAFFTypeProcessor.h.

ces_parsers_

StringHashMap<GAFFCESParser*> BALL::GAFFTypeProcessor::ces_parsers_

protected

Definition at line 134 of file GAFFTypeProcessor.h.

current_molecule_

Molecule* BALL::GAFFTypeProcessor::current_molecule_

protected

Definition at line 143 of file GAFFTypeProcessor.h.

options

Options BALL::GAFFTypeProcessor::options

Definition at line 88 of file GAFFTypeProcessor.h.

sssr_

std::vector<std::vector<Atom*> > BALL::GAFFTypeProcessor::sssr_

protected

Definition at line 140 of file GAFFTypeProcessor.h.