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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
 
void SetObsolete (bool obsolete)
 
bool GetObsolete () const
 
void SetReplacedBy (const String &replaced_by)
 
const StringGetReplacedBy () 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 AtomSpecListGetAtomSpecs () const
 
int GetAtomSpecIndex (const String &name) const
 
const StringGetName ()
 
void SetName (const String &name)
 
void SetFormula (const String &formula)
 
const StringGetFormula ()
 
void SetInchi (const String &inchi)
 
const StringGetInchi ()
 
void SetInchiKey (const String &inchikey)
 
const StringGetInchiKey ()
 
void SetSMILES (const String &smiles)
 
const StringGetSMILES ()
 
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 139 of file compound.hh.

Member Enumeration Documentation

enum Dialect
Enumerator
PDB 
CHARMM 
OPLS 
AMBER 

Definition at line 141 of file compound.hh.

Constructor & Destructor Documentation

Compound ( const String id)
inline

Definition at line 148 of file compound.hh.

Member Function Documentation

void AddAtom ( const AtomSpec atom)
inline

Definition at line 247 of file compound.hh.

void AddBond ( const BondSpec bond)
inline

Definition at line 251 of file compound.hh.

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

Definition at line 255 of file compound.hh.

const BondSpecList& GetBondSpecs ( ) const
inline

Definition at line 281 of file compound.hh.

mol::ChemClass GetChemClass ( ) const
inline

Definition at line 207 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 235 of file compound.hh.

const Date& GetCreationDate ( ) const
inline

Definition at line 288 of file compound.hh.

Dialect GetDialect ( ) const
inline

Definition at line 172 of file compound.hh.

String GetDialectAsString ( ) const
inline

Definition at line 174 of file compound.hh.

const String& GetFormula ( )
inline

Definition at line 267 of file compound.hh.

const String& GetID ( ) const
inline

three-letter code that is unique for every compound

Definition at line 169 of file compound.hh.

const String& GetInchi ( )
inline

Definition at line 271 of file compound.hh.

const String& GetInchiKey ( )
inline

Definition at line 275 of file compound.hh.

const Date& GetModificationDate ( ) const
inline

Definition at line 284 of file compound.hh.

const String& GetName ( )
inline

Definition at line 261 of file compound.hh.

bool GetObsolete ( ) const
inline

Definition at line 215 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 199 of file compound.hh.

const String& GetReplacedBy ( ) const
inline

Definition at line 223 of file compound.hh.

const String& GetSMILES ( )
inline

Definition at line 279 of file compound.hh.

bool IsNucleotideLinking ( ) const
inline

Definition at line 243 of file compound.hh.

bool IsPeptideLinking ( ) const
inline

Definition at line 239 of file compound.hh.

void SetChemClass ( mol::ChemClass  chem_class)
inline

Definition at line 203 of file compound.hh.

void SetChemType ( mol::ChemType  chem_type)
inline

Definition at line 227 of file compound.hh.

void SetCreationDate ( const Date creation_date)
inline

Definition at line 298 of file compound.hh.

void SetDialect ( Dialect  dialect)
inline

Definition at line 188 of file compound.hh.

void SetFormula ( const String formula)
inline

Definition at line 265 of file compound.hh.

void SetInchi ( const String inchi)
inline

Definition at line 269 of file compound.hh.

void SetInchiKey ( const String inchikey)
inline

Definition at line 273 of file compound.hh.

void SetModificationDate ( const Date mod_date)
inline

Definition at line 293 of file compound.hh.

void SetName ( const String name)
inline

Definition at line 263 of file compound.hh.

void SetObsolete ( bool  obsolete)
inline

Definition at line 211 of file compound.hh.

void SetOneLetterCode ( char  olc)
inline

Definition at line 190 of file compound.hh.

void SetReplacedBy ( const String replaced_by)
inline

Definition at line 219 of file compound.hh.

void SetSMILES ( const String smiles)
inline

Definition at line 277 of file compound.hh.


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