BALL  1.4.1
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Public Member Functions | Static Public Attributes | Protected Member Functions | Protected Attributes
BALL::AtomTyper Class Reference

#include <BALL/STRUCTURE/atomTyper.h>

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

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< 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);

Definition at line 40 of file atomTyper.h.


Constructor & Destructor Documentation

virtual BALL::AtomTyper::~AtomTyper ( ) [inline, virtual]

Definition at line 53 of file atomTyper.h.


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

Definition at line 78 of file atomTyper.h.

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

Reimplemented in BALL::MMFF94AtomTyper.

void BALL::AtomTyper::assignTo ( Molecule mol) [protected]
void BALL::AtomTyper::setAromaticRings ( const vector< HashSet< Atom * > > &  rings) [inline]

Definition at line 62 of file atomTyper.h.

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

Definition at line 65 of file atomTyper.h.

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

Definition at line 83 of file atomTyper.h.


Member Data Documentation

Definition at line 93 of file atomTyper.h.

Definition at line 95 of file atomTyper.h.

Definition at line 94 of file atomTyper.h.

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

Definition at line 89 of file atomTyper.h.

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

Definition at line 85 of file atomTyper.h.

Definition at line 91 of file atomTyper.h.

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

Definition at line 92 of file atomTyper.h.

Definition at line 68 of file atomTyper.h.

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

Definition at line 86 of file atomTyper.h.

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

Definition at line 87 of file atomTyper.h.

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