#include <openbabel/data.h>
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 |
Can assign atom types and bond orders for arbitrary residues
OBResidueData | ( | ) |
void ParseLine | ( | const char * | ) | [virtual] |
Specified by particular table classes (parses an individual data line).
Reimplemented from OBGlobalDataBase.
unsigned int GetSize | ( | ) | [inline, virtual] |
bool SetResName | ( | const std::string & | s | ) |
Sets the table to access the residue information for a specified residue name
Referenced by OBResidueData::AssignBonds().
int LookupBO | ( | const std::string & | s | ) |
Referenced by OBResidueData::AssignBonds().
int LookupBO | ( | const std::string & | s1, | |
const std::string & | s2 | |||
) |
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
Referenced by OBResidueData::AssignBonds().
Assign bond orders, atom types and residues for the supplied OBMol based on the residue information assigned to atoms
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().
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().