OpenBabel::OBAtomTyper

OBAtomTyper Class Reference

Assigns atom types, hybridization, implicit valence and formal charges. More...

#include <typer.h>

Inheritance diagram for OBAtomTyper:

Inheritance graph
[legend]
List of all members.

Public Member Functions

 OBAtomTyper ()
 ~OBAtomTyper ()
void ParseLine (const char *)
 Specified by particular table classes (parses an individual data line).
unsigned int GetSize ()
 
Returns:
the number of implicit valence rules

void AssignHyb (OBMol &)
 Assign atomic hybridization (1 = sp, 2 = sp2, 3 = sp3...).
void AssignTypes (OBMol &)
 Assign external atomic types (i.e., EXTTYP lines in atomtyp.txt).
void AssignImplicitValence (OBMol &)
void CorrectAromaticNitrogens (OBMol &)
 Correct typing, valence, and hybridization for aromatic nitrogen atoms.
void Init ()
 Read in the data file, falling back as needed.
void SetReadDirectory (char *dir)
 Set the directory before calling Init().
void SetEnvironmentVariable (char *var)
 Set the environment variable to use before calling Init().

Protected Attributes

bool _init
 whether the data been read already
const char * _dataptr
 default data table if file is unreadable
std::string _filename
 file to search for
std::string _dir
 data directory for file if _envvar fails
std::string _subdir
 subdirectory (if using environment variable)
std::string _envvar
 environment variable to check first

Detailed Description

Assigns atom types, hybridization, implicit valence 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, implicit valence 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 (  ) 

~OBAtomTyper (  ) 

Member Function Documentation

void ParseLine ( const char *  buffer  )  [virtual]

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

Reimplemented from OBGlobalDataBase.

unsigned int GetSize (  )  [inline, virtual]

Returns:
the number of implicit valence rules

Reimplemented from OBGlobalDataBase.

void AssignHyb ( OBMol &   ) 

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

void AssignTypes ( OBMol &   ) 

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

void AssignImplicitValence ( OBMol &   ) 

Assign implicit valence (i.e., given an atomic type, what is the expected number of bonds to this atom

void CorrectAromaticNitrogens ( OBMol &   ) 

Correct typing, valence, and hybridization for aromatic nitrogen atoms.

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

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

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