BALL  1.5.0
Classes | Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
BALL::MMFF94AtomTyper Class Reference

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

Inheritance diagram for BALL::MMFF94AtomTyper:
BALL::AtomTyper

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< Stringpartner_type_to_htype_
 
StringHashMap< Positionid_to_type_
 
HashMap< String, AromaticTypearomatic_types_5_map_
 
HashSet< Stringcation_atoms_
 
MMFF94AtomTypesatom_types_
 
HashSet< Positionhetero_atom_types_
 
- Protected Attributes inherited from BALL::AtomTyper
vector< Stringnames_
 
vector< Stringrules_
 
vector< Indextypes_
 
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.