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 String &	GetID () 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
void	SetObsolete (bool obsolete)
bool	GetObsolete () const
void	SetReplacedBy (const String &replaced_by)
const String &	GetReplacedBy () const
void	SetChemType (mol::ChemType chem_type)
mol::ChemType	GetChemType () const
bool	IsPeptideLinking () const
bool	IsNucleotideLinking () const
void	AddAtom (const AtomSpec &atom)
void	AddBond (const BondSpec &bond)
const AtomSpecList &	GetAtomSpecs () const
int	GetAtomSpecIndex (const String &name) const
const String &	GetName ()
void	SetName (const String &name)
void	SetFormula (const String &formula)
const String &	GetFormula ()
void	SetInchi (const String &inchi)
const String &	GetInchi ()
void	SetInchiKey (const String &inchikey)
const String &	GetInchiKey ()
void	SetSMILES (const String &smiles)
const String &	GetSMILES ()
const BondSpecList &	GetBondSpecs () const
const Date &	GetModificationDate () const
const Date &	GetCreationDate () 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 139 of file compound.hh.

Member Enumeration Documentation

Dialect

enum Dialect

Enumerator
PDB
CHARMM
OPLS
AMBER

Definition at line 141 of file compound.hh.

Constructor & Destructor Documentation

Compound()

Compound ( const String &  id )

inline

Definition at line 148 of file compound.hh.

Member Function Documentation

AddAtom()

void AddAtom ( const AtomSpec &  atom )

inline

Definition at line 247 of file compound.hh.

AddBond()

void AddBond ( const BondSpec &  bond )

inline

Definition at line 251 of file compound.hh.

GetAtomSpecIndex()

int GetAtomSpecIndex

(

const String &

name

)

const

GetAtomSpecs()

const AtomSpecList& GetAtomSpecs ( ) const

inline

Definition at line 255 of file compound.hh.

GetBondSpecs()

const BondSpecList& GetBondSpecs ( ) const

inline

Definition at line 281 of file compound.hh.

GetChemClass()

mol::ChemClass GetChemClass ( ) const

inline

Definition at line 207 of file compound.hh.

GetChemType()

mol::ChemType GetChemType ( ) const

inline

PDB ligand classification from component dictionary.

The PDB classifies all compounds into 7 categories. This classification is extracted from the PDB component dictionary (field: pdbx_type)

Definition at line 235 of file compound.hh.

GetCreationDate()

const Date& GetCreationDate ( ) const

inline

Definition at line 288 of file compound.hh.

GetDialect()

Dialect GetDialect ( ) const

inline

Definition at line 172 of file compound.hh.

GetDialectAsString()

String GetDialectAsString ( ) const

inline

Definition at line 174 of file compound.hh.

GetFormula()

const String& GetFormula ( )

inline

Definition at line 267 of file compound.hh.

GetID()

const String& GetID ( ) const

inline

three-letter code that is unique for every compound

Definition at line 169 of file compound.hh.

GetInchi()

const String& GetInchi ( )

inline

Definition at line 271 of file compound.hh.

GetInchiKey()

const String& GetInchiKey ( )

inline

Definition at line 275 of file compound.hh.

GetModificationDate()

const Date& GetModificationDate ( ) const

inline

Definition at line 284 of file compound.hh.

GetName()

const String& GetName ( )

inline

Definition at line 261 of file compound.hh.

GetObsolete()

bool GetObsolete ( ) const

inline

Definition at line 215 of file compound.hh.

GetOneLetterCode()

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 199 of file compound.hh.

GetReplacedBy()

const String& GetReplacedBy ( ) const

inline

Definition at line 223 of file compound.hh.

GetSMILES()

const String& GetSMILES ( )

inline

Definition at line 279 of file compound.hh.

IsNucleotideLinking()

bool IsNucleotideLinking ( ) const

inline

Definition at line 243 of file compound.hh.

IsPeptideLinking()

bool IsPeptideLinking ( ) const

inline

Definition at line 239 of file compound.hh.

SetChemClass()

void SetChemClass ( mol::ChemClass  chem_class )

inline

Definition at line 203 of file compound.hh.

SetChemType()

void SetChemType ( mol::ChemType  chem_type )

inline

Definition at line 227 of file compound.hh.

SetCreationDate()

void SetCreationDate ( const Date &  creation_date )

inline

Definition at line 298 of file compound.hh.

SetDialect()

void SetDialect ( Dialect  dialect )

inline

Definition at line 188 of file compound.hh.

SetFormula()

void SetFormula ( const String &  formula )

inline

Definition at line 265 of file compound.hh.

SetInchi()

void SetInchi ( const String &  inchi )

inline

Definition at line 269 of file compound.hh.

SetInchiKey()

void SetInchiKey ( const String &  inchikey )

inline

Definition at line 273 of file compound.hh.

SetModificationDate()

void SetModificationDate ( const Date &  mod_date )

inline

Definition at line 293 of file compound.hh.

SetName()

void SetName ( const String &  name )

inline

Definition at line 263 of file compound.hh.

SetObsolete()

void SetObsolete ( bool  obsolete )

inline

Definition at line 211 of file compound.hh.

SetOneLetterCode()

void SetOneLetterCode ( char  olc )

inline

Definition at line 190 of file compound.hh.

SetReplacedBy()

void SetReplacedBy ( const String &  replaced_by )

inline

Definition at line 219 of file compound.hh.

SetSMILES()

void SetSMILES ( const String &  smiles )

inline

Definition at line 277 of file compound.hh.

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

• build-dev-doc/stage/include/ost/conop/compound.hh