OBResidueData Class Reference

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

#include <openbabel/data.h>

Inheritance diagram for OBResidueData:

Inheritance graph
[legend]

List of all members.

Public Member Functions

 OBResidueData ()
void ParseLine (const char *)
unsigned int 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.

unsigned int 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

Referenced by OBResidueData::AssignBonds().

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

Referenced by OBResidueData::AssignBonds().

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

Referenced by OBResidueData::AssignBonds().

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.

Referenced by OBAromaticTyper::AssignAromaticFlags(), OBResidueData::AssignBonds(), OBBondTyper::AssignFunctionalGroupBonds(), OBAtomTyper::AssignHyb(), OBAtomTyper::AssignImplicitValence(), OBPhModel::AssignSeedPartialCharge(), OBRingTyper::AssignTypes(), OBAtomTyper::AssignTypes(), OBAtomTyper::CorrectAromaticNitrogens(), OBElementTable::CorrectedBondRad(), OBElementTable::CorrectedVdwRad(), OBPhModel::CorrectForPH(), OBElementTable::GetAllredRochowElectroNeg(), OBElementTable::GetAtomicNum(), OBElementTable::GetCovalentRad(), OBElementTable::GetElectronAffinity(), OBElementTable::GetElectroNeg(), OBIsotopeTable::GetExactMass(), OBTypeTable::GetFromType(), OBElementTable::GetIonization(), OBElementTable::GetMass(), OBElementTable::GetMaxBonds(), OBElementTable::GetName(), OBElementTable::GetNumberOfElements(), OBElementTable::GetRGB(), OBRotorRules::GetRotorIncrements(), OBElementTable::GetSymbol(), OBTypeTable::GetToType(), OBElementTable::GetVdwRad(), OBTypeTable::SetFromType(), OBResidueData::SetResName(), OBTypeTable::SetToType(), and OBTypeTable::Translate().

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.

Referenced by OBAromaticTyper::AssignAromaticFlags(), OBResidueData::AssignBonds(), OBBondTyper::AssignFunctionalGroupBonds(), OBAtomTyper::AssignHyb(), OBAtomTyper::AssignImplicitValence(), OBPhModel::AssignSeedPartialCharge(), OBRingTyper::AssignTypes(), OBAtomTyper::AssignTypes(), OBAtomTyper::CorrectAromaticNitrogens(), OBElementTable::CorrectedBondRad(), OBElementTable::CorrectedVdwRad(), OBPhModel::CorrectForPH(), OBElementTable::GetAllredRochowElectroNeg(), OBElementTable::GetAtomicNum(), OBElementTable::GetCovalentRad(), OBElementTable::GetElectronAffinity(), OBElementTable::GetElectroNeg(), OBIsotopeTable::GetExactMass(), OBTypeTable::GetFromType(), OBElementTable::GetIonization(), OBElementTable::GetMass(), OBElementTable::GetMaxBonds(), OBElementTable::GetName(), OBElementTable::GetNumberOfElements(), OBElementTable::GetRGB(), OBRotorRules::GetRotorIncrements(), OBElementTable::GetSymbol(), OBTypeTable::GetToType(), OBElementTable::GetVdwRad(), OBGlobalDataBase::Init(), OBAromaticTyper::OBAromaticTyper(), OBAtomTyper::OBAtomTyper(), OBBondTyper::OBBondTyper(), OBElementTable::OBElementTable(), OBIsotopeTable::OBIsotopeTable(), OBPhModel::OBPhModel(), OBResidueData::OBResidueData(), OBRingTyper::OBRingTyper(), OBRotorRules::OBRotorRules(), OBTypeTable::OBTypeTable(), OBTypeTable::SetFromType(), OBResidueData::SetResName(), OBTypeTable::SetToType(), and OBTypeTable::Translate().

const char* _dataptr [protected, inherited]

Default data table if file is unreadable.

Referenced by OBGlobalDataBase::Init(), OBAromaticTyper::OBAromaticTyper(), OBAtomTyper::OBAtomTyper(), OBBondTyper::OBBondTyper(), OBElementTable::OBElementTable(), OBIsotopeTable::OBIsotopeTable(), OBPhModel::OBPhModel(), OBResidueData::OBResidueData(), OBRotorRules::OBRotorRules(), and OBTypeTable::OBTypeTable().

std::string _filename [protected, inherited]

File to search for.

Referenced by OBGlobalDataBase::Init(), OBAromaticTyper::OBAromaticTyper(), OBAtomTyper::OBAtomTyper(), OBBondTyper::OBBondTyper(), OBElementTable::OBElementTable(), OBIsotopeTable::OBIsotopeTable(), OBPhModel::OBPhModel(), OBResidueData::OBResidueData(), OBRingTyper::OBRingTyper(), OBRotorRules::OBRotorRules(), and OBTypeTable::OBTypeTable().

std::string _dir [protected, inherited]

Data directory for file if _envvar fails.

Referenced by OBAromaticTyper::OBAromaticTyper(), OBAtomTyper::OBAtomTyper(), OBBondTyper::OBBondTyper(), OBElementTable::OBElementTable(), OBIsotopeTable::OBIsotopeTable(), OBPhModel::OBPhModel(), OBResidueData::OBResidueData(), OBRingTyper::OBRingTyper(), OBRotorRules::OBRotorRules(), and OBTypeTable::OBTypeTable().

std::string _subdir [protected, inherited]

Subdirectory (if using environment variable).

Referenced by OBAromaticTyper::OBAromaticTyper(), OBAtomTyper::OBAtomTyper(), OBBondTyper::OBBondTyper(), OBElementTable::OBElementTable(), OBIsotopeTable::OBIsotopeTable(), OBPhModel::OBPhModel(), OBResidueData::OBResidueData(), OBRingTyper::OBRingTyper(), OBRotorRules::OBRotorRules(), and OBTypeTable::OBTypeTable().

std::string _envvar [protected, inherited]

Environment variable to check first.

Referenced by OBGlobalDataBase::Init(), OBAromaticTyper::OBAromaticTyper(), OBAtomTyper::OBAtomTyper(), OBBondTyper::OBBondTyper(), OBElementTable::OBElementTable(), OBIsotopeTable::OBIsotopeTable(), OBPhModel::OBPhModel(), OBResidueData::OBResidueData(), OBRingTyper::OBRingTyper(), OBRotorRules::OBRotorRules(), and OBTypeTable::OBTypeTable().

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