BALL 1.5.0
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Public Member Functions | Static Public Attributes | Protected Member Functions | Protected Attributes | List of all members
BALL::AtomTyper Class Reference

#include <BALL/STRUCTURE/atomTyper.h>

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

Public Member Functions

 AtomTyper ()
 
 AtomTyper (const AtomTyper &t)
 
virtual ~AtomTyper ()
 
bool setup (const String &filename)
 Setup with the given line based file with SMARTS expressions.
 
virtual void assignTo (System &s)
 
void setAromaticRings (const vector< HashSet< Atom * > > &rings)
 
void setRings (const vector< HashSet< Atom * > > &rings)
 

Static Public Attributes

static StringHashMap< floatrule_times
 

Protected Member Functions

void assignTo (Molecule &mol)
 
virtual void assignSpecificValues_ (Atom &)
 
virtual bool specificSetup_ ()
 

Protected Attributes

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_
 

Detailed Description

Base class for a programable Atom typer. The types are assigned by using a line based file with SMARTS expressions. For usage have a look at the derived class MMFF94AtomTyper.



Usage:
AtomTyper typer;
typer.setRings(...);
typer.setAromaticRings(...);
typer.setup(parameter_file_name);
typer.assignTo(system);
void setRings(const vector< HashSet< Atom * > > &rings)
Definition atomTyper.h:65
bool setup(const String &filename)
Setup with the given line based file with SMARTS expressions.
virtual void assignTo(System &s)
void setAromaticRings(const vector< HashSet< Atom * > > &rings)
Definition atomTyper.h:62

Definition at line 40 of file atomTyper.h.

Constructor & Destructor Documentation

◆ AtomTyper() [1/2]

BALL::AtomTyper::AtomTyper ( )

◆ AtomTyper() [2/2]

BALL::AtomTyper::AtomTyper ( const AtomTyper t)

◆ ~AtomTyper()

virtual BALL::AtomTyper::~AtomTyper ( )
inlinevirtual

Definition at line 53 of file atomTyper.h.

Member Function Documentation

◆ assignSpecificValues_()

virtual void BALL::AtomTyper::assignSpecificValues_ ( Atom )
inlineprotectedvirtual

To be overloaded in derived classes to add support for additional properties e.g. charges

Definition at line 78 of file atomTyper.h.

◆ assignTo() [1/2]

void BALL::AtomTyper::assignTo ( Molecule mol)
protected

◆ assignTo() [2/2]

virtual void BALL::AtomTyper::assignTo ( System s)
virtual

Reimplemented in BALL::MMFF94AtomTyper.

◆ setAromaticRings()

void BALL::AtomTyper::setAromaticRings ( const vector< HashSet< Atom * > > &  rings)
inline

Definition at line 62 of file atomTyper.h.

◆ setRings()

void BALL::AtomTyper::setRings ( const vector< HashSet< Atom * > > &  rings)
inline

Definition at line 65 of file atomTyper.h.

◆ setup()

bool BALL::AtomTyper::setup ( const String filename)

Setup with the given line based file with SMARTS expressions.

◆ specificSetup_()

virtual bool BALL::AtomTyper::specificSetup_ ( )
inlineprotectedvirtual

To be overloaded in derived classes to add support for additional properties e.g. charges

Definition at line 83 of file atomTyper.h.

Member Data Documentation

◆ aromatic_rings_

vector<HashSet<Atom*> > BALL::AtomTyper::aromatic_rings_
protected

Definition at line 93 of file atomTyper.h.

◆ atoms_

HashSet<Atom*> BALL::AtomTyper::atoms_
protected

Definition at line 95 of file atomTyper.h.

◆ element_to_rules_

StringHashMap<vector<Position> > BALL::AtomTyper::element_to_rules_
protected

Definition at line 94 of file atomTyper.h.

◆ fields_

vector<vector<String> > BALL::AtomTyper::fields_
protected

Definition at line 89 of file atomTyper.h.

◆ names_

vector<String> BALL::AtomTyper::names_
protected

Definition at line 85 of file atomTyper.h.

◆ number_expected_fields_

Size BALL::AtomTyper::number_expected_fields_
protected

Definition at line 91 of file atomTyper.h.

◆ rings_

vector<HashSet<Atom*> > BALL::AtomTyper::rings_
protected

Definition at line 92 of file atomTyper.h.

◆ rule_times

StringHashMap<float> BALL::AtomTyper::rule_times
static

Definition at line 68 of file atomTyper.h.

◆ rules_

vector<String> BALL::AtomTyper::rules_
protected

Definition at line 86 of file atomTyper.h.

◆ types_

vector<Index> BALL::AtomTyper::types_
protected

Definition at line 87 of file atomTyper.h.