OBAtomTyper Class Reference

#include <openbabel/typer.h>

Inheritance diagram for OBAtomTyper:

Public Member Functions
	OBAtomTyper ()
	OBAtomTyper (const OBAtomTyper &rhs)
	~OBAtomTyper ()
const OBAtomTyper &	operator= (const OBAtomTyper &rhs)
void	ParseLine (const char *)
size_t	GetSize ()
void	AssignHyb (OBMol &)
void	AssignTypes (OBMol &)
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 atom types, hybridization, and formal charges.

The OBAtomTyper class is designed to read in a list of atom typing rules and apply them to molecules. The code that performs atom typing is not usually used directly as atom typing, hybridization assignment, and charge are all done automatically when their corresponding values are requested of atoms:

atom->GetType();
atom->GetFormalCharge();
atom->GetHyb();

Constructor & Destructor Documentation

OBAtomTyper() [1/2]

OBAtomTyper

(

)

OBAtomTyper() [2/2]

OBAtomTyper ( const OBAtomTyper &  rhs )

inline

~OBAtomTyper()

~OBAtomTyper

(

)

Member Function Documentation

operator=()

const OBAtomTyper& operator= ( const OBAtomTyper &  rhs )

inline

ParseLine()

void ParseLine ( const char *  )

virtual

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

Reimplemented from OBGlobalDataBase.

GetSize()

size_t GetSize ( )

inlinevirtual

Returns

the number of internal hybridization rules

Reimplemented from OBGlobalDataBase.

AssignHyb()

void AssignHyb

(

OBMol &

mol

)

Assign atomic hybridization (1 = sp, 2 = sp2, 3 = sp3...)

AssignTypes()

void AssignTypes

(

OBMol &

mol

)

Assign external atomic types (i.e., EXTTYP lines in atomtyp.txt)

Init()

void Init ( )

inherited

Read in the data file, falling back as needed.

Referenced by OBRotorList::Init().

SetReadDirectory()

void SetReadDirectory ( char *  dir )

inlineinherited

Set the directory before calling Init()

SetEnvironmentVariable()

void SetEnvironmentVariable ( char *  var )

inlineinherited

Set the environment variable to use before calling Init()

Member Data Documentation

_init

bool _init

protectedinherited

Whether the data been read already.

_dataptr

const char* _dataptr

protectedinherited

Default data table if file is unreadable.

_filename

std::string _filename

protectedinherited

File to search for.

_dir

std::string _dir

protectedinherited

Data directory for file if _envvar fails.

_subdir

std::string _subdir

protectedinherited

Subdirectory (if using environment variable)

_envvar

std::string _envvar

protectedinherited

Environment variable to check first.

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

• typer.h
• typer.cpp