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	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 ()
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 136 of file compound.hh.

Member Enumeration Documentation

enum Dialect

Enumerator
PDB
CHARMM
OPLS
AMBER

Definition at line 138 of file compound.hh.

Constructor & Destructor Documentation

Compound ( const String &  id )

inline

Definition at line 145 of file compound.hh.

Member Function Documentation

void AddAtom ( const AtomSpec &  atom )

inline

Definition at line 225 of file compound.hh.

void AddBond ( const BondSpec &  bond )

inline

Definition at line 229 of file compound.hh.

int GetAtomSpecIndex

(

const String &

name

)

const

const AtomSpecList& GetAtomSpecs ( ) const

inline

Definition at line 233 of file compound.hh.

const BondSpecList& GetBondSpecs ( ) const

inline

Definition at line 255 of file compound.hh.

mol::ChemClass GetChemClass ( ) const

inline

Definition at line 201 of file compound.hh.

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 213 of file compound.hh.

const Date& GetCreationDate ( ) const

inline

Definition at line 262 of file compound.hh.

Dialect GetDialect ( ) const

inline

Definition at line 166 of file compound.hh.

String GetDialectAsString ( ) const

inline

Definition at line 168 of file compound.hh.

const String& GetFormula ( )

inline

Definition at line 245 of file compound.hh.

const String& GetID ( ) const

inline

three-letter code that is unique for every compound

Definition at line 163 of file compound.hh.

const String& GetInchi ( )

inline

Definition at line 249 of file compound.hh.

const String& GetInchiKey ( )

inline

Definition at line 253 of file compound.hh.

const Date& GetModificationDate ( ) const

inline

Definition at line 258 of file compound.hh.

const String& GetName ( )

inline

Definition at line 239 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 193 of file compound.hh.

bool IsNucleotideLinking ( ) const

inline

Definition at line 221 of file compound.hh.

bool IsPeptideLinking ( ) const

inline

Definition at line 217 of file compound.hh.

void SetChemClass ( mol::ChemClass  chem_class )

inline

Definition at line 197 of file compound.hh.

void SetChemType ( mol::ChemType  chem_type )

inline

Definition at line 205 of file compound.hh.

void SetCreationDate ( const Date &  creation_date )

inline

Definition at line 272 of file compound.hh.

void SetDialect ( Dialect  dialect )

inline

Definition at line 182 of file compound.hh.

void SetFormula ( const String &  formula )

inline

Definition at line 243 of file compound.hh.

void SetInchi ( const String &  inchi )

inline

Definition at line 247 of file compound.hh.

void SetInchiKey ( const String &  inchikey )

inline

Definition at line 251 of file compound.hh.

void SetModificationDate ( const Date &  mod_date )

inline

Definition at line 267 of file compound.hh.

void SetName ( const String &  name )

inline

Definition at line 241 of file compound.hh.

void SetOneLetterCode ( char  olc )

inline

Definition at line 184 of file compound.hh.

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

• stage/include/ost/conop/compound.hh