OBResidueData Class Reference
Table of common biomolecule residues (for PDB or other files). More...
#include <openbabel/data.h>

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
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: