OBResidueData Class Reference

#include <openbabel/data.h>

Inheritance diagram for OBResidueData:

Public Member Functions
	OBResidueData ()
void	ParseLine (const char *)
size_t	GetSize ()
bool	SetResName (const std::string &)
int	LookupBO (const std::string &)
int	LookupBO (const std::string &, const std::string &)
bool	LookupType (const std::string &, std::string &, int &)
bool	AssignBonds (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

Table of common biomolecule residues (for PDB or other files).

Can assign atom types and bond orders for arbitrary residues

Constructor & Destructor Documentation

OBResidueData()

OBResidueData

(

)

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 residues in the table

Reimplemented from OBGlobalDataBase.

SetResName()

bool SetResName

(

const std::string &

s

)

Sets the table to access the residue information for a specified residue name

Returns

whether this residue name is in the table

LookupBO() [1/2]

int LookupBO

(

const std::string &

s

)

Returns

the bond order for the bond specified in the current residue

Deprecated:

Easier to use the two-argument form

LookupBO() [2/2]

int LookupBO	(	const std::string &	s1,
		const std::string &	s2
	)

Returns

the bond order for the bond specified between the two specified atom labels

LookupType()

bool LookupType	(	const std::string &	atmid,
		std::string &	type,
		int &	hyb
	)

Look up the atom type and hybridization for the atom label specified in the first argument for the current residue

Returns

whether the atom label specified is found in the current residue

AssignBonds()

bool AssignBonds

(

OBMol &

mol

)

Assign bond orders, atom types and residues for the supplied OBMol based on the residue information assigned to atoms

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