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

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]
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

whether this residue name is in the table
int LookupBO ( const std::string &  s )
the bond order for the bond specified in the current residue
Easier to use the two-argument form
int LookupBO ( const std::string &  s1,
const std::string &  s2 
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

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

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:
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