BALL::AtomTyper Class Reference
[Miscellaneous]

#include <BALL/STRUCTURE/atomTyper.h>

Inheritance diagram for BALL::AtomTyper:

List of all members.

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< float >	rule_times
Protected Member Functions
void	assignTo (Molecule &mol)
virtual void	assignSpecificValues_ (Atom &)
virtual bool	specificSetup_ ()
Protected Attributes
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_

---

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);

---

Constructor & Destructor Documentation

BALL::AtomTyper::AtomTyper

(

)

BALL::AtomTyper::AtomTyper

(

const AtomTyper &

t

)

virtual BALL::AtomTyper::~AtomTyper

(

)

[inline, virtual]

---

Member Function Documentation

virtual void BALL::AtomTyper::assignSpecificValues_

(

Atom &

)

[inline, protected, virtual]

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

void BALL::AtomTyper::assignTo

(

Molecule &

mol

)

[protected]

virtual void BALL::AtomTyper::assignTo

(

System &

s

)

[virtual]

Reimplemented in BALL::MMFF94AtomTyper.

void BALL::AtomTyper::setAromaticRings

(

const vector< HashSet< Atom * > > &

rings

)

[inline]

void BALL::AtomTyper::setRings

(

const vector< HashSet< Atom * > > &

rings

)

[inline]

bool BALL::AtomTyper::setup

(

const String &

filename

)

Setup with the given line based file with SMARTS expressions.

virtual bool BALL::AtomTyper::specificSetup_

(

)

[inline, protected, virtual]

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

---

Member Data Documentation

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

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

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

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

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

Size BALL::AtomTyper::number_expected_fields_ [protected]

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

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

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

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