Open Babel  3.0
Public Member Functions | Protected Attributes | List of all members
OBResidueData Class Reference

#include <openbabel/data.h>

Inheritance diagram for OBResidueData:
OBGlobalDataBase

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()

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.


The documentation for this class was generated from the following files: