OBTypeTable Class Reference

#include <openbabel/data.h>

Inheritance diagram for OBTypeTable:

Public Member Functions
	OBTypeTable (void)
	~OBTypeTable ()
void	ParseLine (const char *)
size_t	GetSize ()
bool	SetFromType (const char *)
bool	SetToType (const char *)
bool	Translate (char *to, const char *from)
bool	Translate (std::string &to, const std::string &from)
std::string	Translate (const std::string &from)
std::string	GetFromType ()
std::string	GetToType ()
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

Atom Type Translation Table.

Molecular file formats frequently store information about atoms in an atom type field. Some formats store only the element for each atom, while others include hybridization and local environments, such as the Sybyl mol2 atom type field. The OBTypeTable class acts as a translation table to convert atom types between a number of different molecular file formats. The constructor for OBTypeTable automatically reads the text file types.txt. An instance of OBTypeTable (ttab) is declared external in data.cpp and is referenced as extern OBTypeTable ttab in mol.h. The following code demonstrates how to use the OBTypeTable class to translate the internal representation of atom types in an OBMol Internal to Sybyl Mol2 atom types.

ttab.SetFromType("INT");
ttab.SetToType("SYB");
OBAtom *atom;
vector<OBAtom*>::iterator i;
string src,dst;
for (atom = mol.BeginAtom(i);atom;atom = mol.EndAtom(i))
{
   src = atom->GetType();
   ttab.Translate(dst,src);
   cout << "atom number " << atom->GetIdx() << "has mol2 type " << dst << endl;
}

Current atom types include (defined in the top line of the data file types.txt):

• INT (Open Babel internal codes)
• ATN (atomic numbers)
• HYB (hybridization)
• MMD (MacroModel)
• MM2 (MM2 force field)
• XYZ (element symbols from XYZ file format)
• ALC (Alchemy)
• HAD (H added)
• MCML (MacMolecule)
• C3D (Chem3D)
• SYB (Sybyl mol2)
• MOL (Sybyl mol)
• MAP (Gasteiger partial charge types)
• DRE (Dreiding)
• XED (XED format)
• DOK (Dock)
• M3D (Molecular Arts M3D)
• SBN (Sybyl descriptor types for MPD files)
• PCM (PC Model)

Constructor & Destructor Documentation

OBTypeTable()

OBTypeTable

(

void

)

~OBTypeTable()

~OBTypeTable ( )

inline

Member Function Documentation

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 atom types in the translation table

Reimplemented from OBGlobalDataBase.

SetFromType()

bool SetFromType

(

const char *

from

)

Set the initial atom type to be translated.

SetToType()

bool SetToType

(

const char *

to

)

Set the destination atom type for translation.

Translate() [1/3]

bool Translate	(	char *	to,
		const char *	from
	)

Translate atom types.

Translates atom types (to, from), checking for size of destination string and null-terminating as needed

Deprecated:

Because there is no guarantee on the length of an atom type you should consider using std::string instead

Translate() [2/3]

bool Translate	(	std::string &	to,
		const std::string &	from
	)

Translate atom types

Returns

whether the translation was successful

Translate() [3/3]

std::string Translate

(

const std::string &

from

)

Translate atom types

Returns

the translated atom type, or an empty string if not possible

GetFromType()

std::string GetFromType

(

)

Returns

the initial atom type to be translated

GetToType()

std::string GetToType

(

)

Returns

the destination atom type for translation

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:

• data.h
• data.cpp