OpenBabel::OBResidueData

OBResidueData Class Reference

Table of common biomolecule residues (for PDB or other files). Can assign atom types and bond orders for arbitrary residues. More...

#include <data.h>

Inheritance diagram for OBResidueData:

Inheritance graph
[legend]
List of all members.

Public Member Functions

 OBResidueData ()
void ParseLine (const char *)
 Specified by particular table classes (parses an individual data line).
unsigned int GetSize ()
 
Returns:
the number of residues in the table

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 ()
 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

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 *  buffer  )  [virtual]

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

Reimplemented from OBGlobalDataBase.

unsigned int GetSize (  )  [inline, virtual]

Returns:
the number of residues in the table

Reimplemented from OBGlobalDataBase.

bool SetResName ( const std::string &   ) 

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 &   ) 

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 &  ,
const std::string &   
)

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

bool LookupType ( const std::string &  ,
std::string &  ,
int &   
)

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 &  ,
OBBitVec &   
)

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: