OpenStructure
Public Types | Public Member Functions
Compound Class Reference

#include <compound.hh>

Public Types

enum  Dialect { PDB = 'P', CHARMM = 'C', OPLS = 'O', AMBER = 'A' }

Public Member Functions

 Compound (const String &id)
const StringGetID () const
Dialect GetDialect () const
String GetDialectAsString () const
void SetDialect (Dialect dialect)
void SetOneLetterCode (char olc)
char GetOneLetterCode () const
void SetChemClass (mol::ChemClass chem_class)
mol::ChemClass GetChemClass () const
bool IsPeptideLinking () const
void AddAtom (const AtomSpec &atom)
void AddBond (const BondSpec &bond)
const AtomSpecListGetAtomSpecs () const
int GetAtomSpecIndex (const String &name) const
const StringGetFormula ()
void SetFormula (const String &formula)
const BondSpecListGetBondSpecs () const
const DateGetModificationDate () const
const DateGetCreationDate () const
void SetModificationDate (const Date &mod_date)
void SetCreationDate (const Date &creation_date)

Detailed Description

Knows about the atoms and bonds of a chemical compounds.

Definition at line 113 of file compound.hh.


Member Enumeration Documentation

enum Dialect
Enumerator:
PDB 
CHARMM 
OPLS 
AMBER 

Definition at line 115 of file compound.hh.


Constructor & Destructor Documentation

Compound ( const String id)
inline

Definition at line 122 of file compound.hh.


Member Function Documentation

void AddAtom ( const AtomSpec atom)
inline

Definition at line 172 of file compound.hh.

void AddBond ( const BondSpec bond)
inline

Definition at line 176 of file compound.hh.

int GetAtomSpecIndex ( const String name) const
const AtomSpecList& GetAtomSpecs ( ) const
inline

Definition at line 180 of file compound.hh.

const BondSpecList& GetBondSpecs ( ) const
inline

Definition at line 190 of file compound.hh.

mol::ChemClass GetChemClass ( ) const
inline

Definition at line 165 of file compound.hh.

const Date& GetCreationDate ( ) const
inline

Definition at line 197 of file compound.hh.

Dialect GetDialect ( ) const
inline

Definition at line 130 of file compound.hh.

String GetDialectAsString ( ) const
inline

Definition at line 132 of file compound.hh.

const String& GetFormula ( )
inline

Definition at line 186 of file compound.hh.

const String& GetID ( ) const
inline

three-letter code that is unique for every compound

Definition at line 127 of file compound.hh.

const Date& GetModificationDate ( ) const
inline

Definition at line 193 of file compound.hh.

char GetOneLetterCode ( ) const
inline

one letter code, if available.

For compounds without a defined one-letter code, the code is set to "?". One letter codes are ambigous. For instance, both glycine and guanosine have G as their one-letter code.

Definition at line 157 of file compound.hh.

bool IsPeptideLinking ( ) const
inline

Definition at line 169 of file compound.hh.

void SetChemClass ( mol::ChemClass  chem_class)
inline

Definition at line 161 of file compound.hh.

void SetCreationDate ( const Date creation_date)
inline

Definition at line 207 of file compound.hh.

void SetDialect ( Dialect  dialect)
inline

Definition at line 146 of file compound.hh.

void SetFormula ( const String formula)
inline

Definition at line 188 of file compound.hh.

void SetModificationDate ( const Date mod_date)
inline

Definition at line 202 of file compound.hh.

void SetOneLetterCode ( char  olc)
inline

Definition at line 148 of file compound.hh.


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