BALL::MMFF94AtomTyper Class Reference

#include <BALL/MOLMEC/MMFF94/MMFF94Processors.h>

Inheritance diagram for BALL::MMFF94AtomTyper:

Classes
struct	AromaticType

Public Member Functions
	MMFF94AtomTyper ()
	MMFF94AtomTyper (const MMFF94AtomTyper &t)
virtual	~MMFF94AtomTyper ()
virtual void	assignTo (System &s)
virtual bool	setupHydrogenTypes (Parameters &p, const String &section)
	Read the hydrogen matching from MMFFHDEF.PAR. More...
virtual bool	setupSymbolsToTypes (Parameters &p, const String &section)
	Read the matching from ID to numerical type from MFFSYMB.PAR. More...
virtual bool	setupAromaticTypes (Parameters &p, const String &section)
	Read the matching from general ID to ID in aromatic rings. More...
void	collectHeteroAtomTypes (const MMFF94AtomTypes &atom_types)
Public Member Functions inherited from BALL::AtomTyper
	AtomTyper ()
	AtomTyper (const AtomTyper &t)
virtual	~AtomTyper ()
bool	setup (const String &filename)
	Setup with the given line based file with SMARTS expressions. More...
void	setAromaticRings (const vector< HashSet< Atom * > > &rings)
void	setRings (const vector< HashSet< Atom * > > &rings)

Protected Member Functions
bool	assignAromaticType_5_ (Atom &atom, Position L5, bool anion, bool cation)
Protected Member Functions inherited from BALL::AtomTyper
void	assignTo (Molecule &mol)
virtual void	assignSpecificValues_ (Atom &)
virtual bool	specificSetup_ ()

Protected Attributes
StringHashMap< String >	partner_type_to_htype_
StringHashMap< Position >	id_to_type_
HashMap< String, AromaticType >	aromatic_types_5_map_
HashSet< String >	cation_atoms_
MMFF94AtomTypes *	atom_types_
HashSet< Position >	hetero_atom_types_
Protected Attributes inherited from BALL::AtomTyper
vector< String >	names_
vector< String >	rules_
vector< Index >	types_
vector< vector< String > >	fields_
Size	number_expected_fields_
vector< HashSet< Atom * > >	rings_
vector< HashSet< Atom * > >	aromatic_rings_
StringHashMap< vector< Position > >	element_to_rules_
HashSet< Atom * >	atoms_

Additional Inherited Members
Static Public Attributes inherited from BALL::AtomTyper
static StringHashMap< float >	rule_times

Detailed Description

Definition at line 41 of file MMFF94Processors.h.

Constructor & Destructor Documentation

MMFF94AtomTyper() [1/2]

BALL::MMFF94AtomTyper::MMFF94AtomTyper

(

)

MMFF94AtomTyper() [2/2]

BALL::MMFF94AtomTyper::MMFF94AtomTyper

(

const MMFF94AtomTyper &

t

)

~MMFF94AtomTyper()

virtual BALL::MMFF94AtomTyper::~MMFF94AtomTyper ( )

inlinevirtual

Definition at line 63 of file MMFF94Processors.h.

Member Function Documentation

assignAromaticType_5_()

bool BALL::MMFF94AtomTyper::assignAromaticType_5_ ( Atom &  atom, Position  L5, bool  anion, bool  cation  )

protected

assignTo()

virtual void BALL::MMFF94AtomTyper::assignTo ( System &  s )

virtual

Reimplemented from BALL::AtomTyper.

collectHeteroAtomTypes()

void BALL::MMFF94AtomTyper::collectHeteroAtomTypes

(

const MMFF94AtomTypes &

atom_types

)

setupAromaticTypes()

virtual bool BALL::MMFF94AtomTyper::setupAromaticTypes ( Parameters &  p, const String &  section  )

virtual

Read the matching from general ID to ID in aromatic rings.

setupHydrogenTypes()

virtual bool BALL::MMFF94AtomTyper::setupHydrogenTypes ( Parameters &  p, const String &  section  )

virtual

Read the hydrogen matching from MMFFHDEF.PAR.

setupSymbolsToTypes()

virtual bool BALL::MMFF94AtomTyper::setupSymbolsToTypes ( Parameters &  p, const String &  section  )

virtual

Read the matching from ID to numerical type from MFFSYMB.PAR.

Member Data Documentation

aromatic_types_5_map_

HashMap<String, AromaticType> BALL::MMFF94AtomTyper::aromatic_types_5_map_

protected

Definition at line 86 of file MMFF94Processors.h.

atom_types_

MMFF94AtomTypes* BALL::MMFF94AtomTyper::atom_types_

protected

Definition at line 88 of file MMFF94Processors.h.

cation_atoms_

HashSet<String> BALL::MMFF94AtomTyper::cation_atoms_

protected

Definition at line 87 of file MMFF94Processors.h.

hetero_atom_types_

HashSet<Position> BALL::MMFF94AtomTyper::hetero_atom_types_

protected

Definition at line 89 of file MMFF94Processors.h.

id_to_type_

StringHashMap<Position> BALL::MMFF94AtomTyper::id_to_type_

protected

Definition at line 85 of file MMFF94Processors.h.

partner_type_to_htype_

StringHashMap<String> BALL::MMFF94AtomTyper::partner_type_to_htype_

protected

Definition at line 84 of file MMFF94Processors.h.