OBResidueData Class Reference

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

#include <openbabel/data.h>

Inheritance diagram for OBResidueData:

List of all members.

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 &, OBBitVec &)
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

(

)

---

Member Function Documentation

void ParseLine

(

const char *

)

[virtual]

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

Reimplemented from OBGlobalDataBase.

size_t GetSize

(

)

[inline, virtual]

Returns:

the number of residues in the table

Reimplemented from OBGlobalDataBase.

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

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

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

Returns:

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

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

bool AssignBonds	(	OBMol &	mol,
		OBBitVec &	bv
	)

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

Deprecated:

second OBBitVec argument is ignored

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:

• data.h
• data.cpp