AtomTyper Class Reference
[Miscellaneous]

Base class for a programable Atom typer. More...

#include <atomTyper.h>

List of all members.

Public Member Functions
	AtomTyper (const AtomTyper &t)
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
StringHashMap< float >	rule_times
Protected Member Functions
void	assignTo (Molecule &mol)
virtual void	assignSpecificValues_ (Atom &)
	To be overloaded in derived classes to add support for additional properties e.g.
virtual bool	specificSetup_ ()
	To be overloaded in derived classes to add support for additional properties e.g.
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_

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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);

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Member Function Documentation

virtual void AtomTyper::assignSpecificValues_ (  Atom &   )  [protected, virtual]

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

virtual bool AtomTyper::specificSetup_ (   )  [protected, virtual]

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