OBResidueData Class Reference

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

#include <openbabel/data.h>

Inheritance diagram for OBResidueData:
OBGlobalDataBase

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]
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:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines