OBAromaticTyper Class Reference

Assigns aromatic typing to atoms and bonds. More...

#include <openbabel/typer.h>

Inheritance diagram for OBAromaticTyper:

List of all members.

Public Member Functions

OBAromaticTyper ()

~OBAromaticTyper ()

unsigned int GetSize ()

void ParseLine (const char *)

void AssignAromaticFlags (OBMol &)

void PropagatePotentialAromatic (OBAtom *)

void SelectRootAtoms (OBMol &, bool avoidInnerRingAtoms=true)

void ExcludeSmallRing (OBMol &)

void CheckAromaticity (OBAtom *root, int searchDepth)

bool TraverseCycle (OBAtom *root, OBAtom *atom, OBBond *prev, std::pair< int, int > &er, int depth)

void Init ()

void SetReadDirectory (char *dir)

void SetEnvironmentVariable (char *var)

Protected Attributes

bool _init

const char * _dataptr

std::string _filename

std::string _dir

std::string _subdir

std::string _envvar

Detailed Description

Assigns aromatic typing to atoms and bonds.

The OBAromaticTyper class is designed to read in a list of aromatic perception rules and apply them to molecules. The code that performs typing is not usually used directly -- it is usually done automatically when their corresponding values are requested of atoms or bonds.

    atom->IsAromatic();
    bond->IsAromatic();
    bond->IsDouble(); // needs to check aromaticity and define Kekule structures

Constructor & Destructor Documentation

OBAromaticTyper ( )

~OBAromaticTyper ( )

Member Function Documentation

unsigned int GetSize ( ) [inline, virtual]

Returns:: the number of SMARTS patterns

Reimplemented from OBGlobalDataBase.

void ParseLine ( const char * ) [virtual]

Specified by particular table classes (parses an individual data line).

Reimplemented from OBGlobalDataBase.

void AssignAromaticFlags ( OBMol & mol )

Assign aromaticity flag to atoms and bonds.

Referenced by OBAtomTyper::AssignHyb(), OBBond::IsAromatic(), OBAtom::IsAromatic(), OBBond::IsDouble(), OBBond::IsSingle(), and OBBond::IsTriple().

void PropagatePotentialAromatic ( OBAtom * atom )

"Anti-alias" potentially aromatic flags around a molecule (aromatic atoms need to have >= 2 neighboring ring atoms)

Referenced by OBAromaticTyper::AssignAromaticFlags().

void SelectRootAtoms	(	OBMol &	mol,
		bool	avoidInnerRingAtoms = `true`
	)

Select the root atoms for traversing atoms in rings.

Picking only the begin atom of a closure bond can cause difficulties when the selected atom is an inner atom with three neighbour ring atoms. Why ? Because this atom can get trapped by the other atoms when determining aromaticity, because a simple visited flag is used in the OBAromaticTyper::TraverseCycle() method.

Ported from JOELib, copyright Joerg Wegner, 2003 under the GPL version 2

Parameters:

	mol	the molecule
	avoidInnerRingAtoms	inner closure ring atoms with more than 2 neighbours will be avoided

Referenced by OBAromaticTyper::AssignAromaticFlags().

void ExcludeSmallRing ( OBMol & mol )

Remove 3-member rings from consideration.

Referenced by OBAromaticTyper::AssignAromaticFlags().

void CheckAromaticity	(	OBAtom *	root,
		int	searchDepth
	)

Check aromaticity starting from the root atom, up to a specified depth.

Referenced by OBAromaticTyper::AssignAromaticFlags().

bool TraverseCycle	(	OBAtom *	root,
		OBAtom *	atom,
		OBBond *	prev,
		std::pair< int, int > &	er,
		int	depth
	)

Traverse a potentially aromatic cycle starting at root.

Returns:: True if the cycle is likely aromatic

Parameters:

	root	The initial, "root" atom in traversing this ring
	atom	The current atom to visit and check
	prev	The bond traversed in moving to this `atom`
	er	The min and max number of pi electrons for this ring
	depth	The maximum number of atoms to visit in a ring (e.g., 6)

This method traverses a potentially aromatic ring, adding up the possible pi electrons for each atom. At the end (e.g., when atom == root) the Huekel 4n+2 rule is checked to see if there is a possible electronic configuration which corresponds to aromaticity.

Referenced by OBAromaticTyper::CheckAromaticity().

void Init ( ) [inherited]

Read in the data file, falling back as needed.

void SetReadDirectory ( char * dir ) [inline, inherited]

Set the directory before calling Init().

void SetEnvironmentVariable ( char * var ) [inline, inherited]

Set the environment variable to use before calling Init().

Member Data Documentation

bool _init [protected, inherited]

Whether the data been read already.

const char* _dataptr [protected, inherited]

Default data table if file is unreadable.

Referenced by OBGlobalDataBase::Init(), OBAromaticTyper::OBAromaticTyper(), OBAtomTyper::OBAtomTyper(), OBBondTyper::OBBondTyper(), OBElementTable::OBElementTable(), OBIsotopeTable::OBIsotopeTable(), OBPhModel::OBPhModel(), OBResidueData::OBResidueData(), OBRotorRules::OBRotorRules(), and OBTypeTable::OBTypeTable().

std::string _filename [protected, inherited]

File to search for.

Referenced by OBGlobalDataBase::Init(), OBAromaticTyper::OBAromaticTyper(), OBAtomTyper::OBAtomTyper(), OBBondTyper::OBBondTyper(), OBElementTable::OBElementTable(), OBIsotopeTable::OBIsotopeTable(), OBPhModel::OBPhModel(), OBResidueData::OBResidueData(), OBRingTyper::OBRingTyper(), OBRotorRules::OBRotorRules(), and OBTypeTable::OBTypeTable().

std::string _dir [protected, inherited]

Data directory for file if _envvar fails.

Referenced by OBAromaticTyper::OBAromaticTyper(), OBAtomTyper::OBAtomTyper(), OBBondTyper::OBBondTyper(), OBElementTable::OBElementTable(), OBIsotopeTable::OBIsotopeTable(), OBPhModel::OBPhModel(), OBResidueData::OBResidueData(), OBRingTyper::OBRingTyper(), OBRotorRules::OBRotorRules(), and OBTypeTable::OBTypeTable().

std::string _subdir [protected, inherited]

Subdirectory (if using environment variable).

Referenced by OBAromaticTyper::OBAromaticTyper(), OBAtomTyper::OBAtomTyper(), OBBondTyper::OBBondTyper(), OBElementTable::OBElementTable(), OBIsotopeTable::OBIsotopeTable(), OBPhModel::OBPhModel(), OBResidueData::OBResidueData(), OBRingTyper::OBRingTyper(), OBRotorRules::OBRotorRules(), and OBTypeTable::OBTypeTable().

std::string _envvar [protected, inherited]

Environment variable to check first.

Referenced by OBGlobalDataBase::Init(), OBAromaticTyper::OBAromaticTyper(), OBAtomTyper::OBAtomTyper(), OBBondTyper::OBBondTyper(), OBElementTable::OBElementTable(), OBIsotopeTable::OBIsotopeTable(), OBPhModel::OBPhModel(), OBResidueData::OBResidueData(), OBRingTyper::OBRingTyper(), OBRotorRules::OBRotorRules(), and OBTypeTable::OBTypeTable().

The documentation for this class was generated from the following files:


Public Member Functions
	OBAromaticTyper ()
	~OBAromaticTyper ()
unsigned int	GetSize ()
void	ParseLine (const char *)
void	AssignAromaticFlags (OBMol &)
void	PropagatePotentialAromatic (OBAtom *)
void	SelectRootAtoms (OBMol &, bool avoidInnerRingAtoms=true)
void	ExcludeSmallRing (OBMol &)
void	CheckAromaticity (OBAtom *root, int searchDepth)
bool	TraverseCycle (OBAtom root, OBAtom atom, OBBond *prev, std::pair< int, int > &er, int depth)
void	Init ()
void	SetReadDirectory (char *dir)
void	SetEnvironmentVariable (char *var)
Protected Attributes
bool	_init
const char *	_dataptr
std::string	_filename
std::string	_dir
std::string	_subdir
std::string	_envvar