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 ()
size_t	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

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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

size_t 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)

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 Improved by Fabian (fab5) in 2009 -- PR#2889708

Parameters:

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

void ExcludeSmallRing

(

OBMol &

mol )

Remove 3-member rings from consideration.

void CheckAromaticity	(	OBAtom *	root,
		int	searchDepth
	)

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

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.

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()

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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.

std::string _filename [protected, inherited]

File to search for.

std::string _dir [protected, inherited]

Data directory for file if _envvar fails.

std::string _subdir [protected, inherited]

Subdirectory (if using environment variable)

std::string _envvar [protected, inherited]

Environment variable to check first.

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

• typer.h
• typer.cpp