BALL::GAFFTypeProcessor Class Reference

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

Inheritance diagram for BALL::GAFFTypeProcessor:

List of all members.

Classes
struct	Default
struct	Option
struct	TypeDefinition
	Nested class definitions. More...
Public Types
enum	BOND_TYPES {   sb, SB, db, DB,   TB, DL, AB }
Public Member Functions
	GAFFTypeProcessor ()
	GAFFTypeProcessor (const Options &new_options)
virtual	~GAFFTypeProcessor ()
virtual Processor::Result	operator() (Composite &composite)
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_ () throw (Exception::FileNotFound)
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_

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Member Enumeration Documentation

enum BALL::GAFFTypeProcessor::BOND_TYPES

Enumerator:

sb
SB
db
DB
TB
DL
AB

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Constructor & Destructor Documentation

BALL::GAFFTypeProcessor::GAFFTypeProcessor

(

)

BALL::GAFFTypeProcessor::GAFFTypeProcessor

(

const Options &

new_options

)

virtual BALL::GAFFTypeProcessor::~GAFFTypeProcessor

(

)

[virtual]

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Member Function Documentation

void BALL::GAFFTypeProcessor::annotateAliphaticAndAromaticRingAtoms_

(

)

[protected]

void BALL::GAFFTypeProcessor::annotateBondTypes_

(

)

[protected]

Helper for precomputeBondProperties.

void BALL::GAFFTypeProcessor::annotatePlanarRingAtoms_

(

)

[protected]

void BALL::GAFFTypeProcessor::annotateRingSizes_

(

)

[protected]

Helper for precomputeAtomProperties.

bool BALL::GAFFTypeProcessor::assignAtomtype_

(

Atom &

atom

)

[protected]

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

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

(

)

[inline, protected]

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

(

)

[inline, protected]

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

(

)

[inline, protected]

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

(

)

[inline, protected]

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

(

)

[inline, protected]

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

(

Composite &

)

[virtual]

operator ()

Reimplemented from BALL::UnaryProcessor< Composite >.

void BALL::GAFFTypeProcessor::parseAtomtypeTableFile_

(

)

throw (Exception::FileNotFound) [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.

bool BALL::GAFFTypeProcessor::planarAtom_

(

const Atom &

atom

)

[protected]

void BALL::GAFFTypeProcessor::postProcessAtomTypes_

(

Molecule *

molecule

)

[protected]

Postprocessing and cleanup for GAFF types

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

void BALL::GAFFTypeProcessor::precomputeBondProperties_

(

Molecule *

molecule

)

[protected]

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

---

Member Data Documentation

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

StringHashMap<GAFFCESParser*> BALL::GAFFTypeProcessor::ces_parsers_ [protected]

Molecule* BALL::GAFFTypeProcessor::current_molecule_ [protected]

Options BALL::GAFFTypeProcessor::options

std::vector<std::vector<Atom*> > BALL::GAFFTypeProcessor::sssr_ [protected]