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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 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 ()
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 116 of file compound.hh.


Member Enumeration Documentation

enum Dialect
Enumerator:
PDB 
CHARMM 
OPLS 
AMBER 

Definition at line 118 of file compound.hh.


Constructor & Destructor Documentation

Compound ( const String id)
inline

Definition at line 125 of file compound.hh.


Member Function Documentation

void AddAtom ( const AtomSpec atom)
inline

Definition at line 192 of file compound.hh.

void AddBond ( const BondSpec bond)
inline

Definition at line 196 of file compound.hh.

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

Definition at line 200 of file compound.hh.

const BondSpecList& GetBondSpecs ( ) const
inline

Definition at line 214 of file compound.hh.

mol::ChemClass GetChemClass ( ) const
inline

Definition at line 168 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 180 of file compound.hh.

const Date& GetCreationDate ( ) const
inline

Definition at line 221 of file compound.hh.

Dialect GetDialect ( ) const
inline

Definition at line 133 of file compound.hh.

String GetDialectAsString ( ) const
inline

Definition at line 135 of file compound.hh.

const String& GetFormula ( )
inline

Definition at line 212 of file compound.hh.

const String& GetID ( ) const
inline

three-letter code that is unique for every compound

Definition at line 130 of file compound.hh.

const Date& GetModificationDate ( ) const
inline

Definition at line 217 of file compound.hh.

const String& GetName ( )
inline

Definition at line 206 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 160 of file compound.hh.

bool IsNucleotideLinking ( ) const
inline

Definition at line 188 of file compound.hh.

bool IsPeptideLinking ( ) const
inline

Definition at line 184 of file compound.hh.

void SetChemClass ( mol::ChemClass  chem_class)
inline

Definition at line 164 of file compound.hh.

void SetChemType ( mol::ChemType  chem_type)
inline

Definition at line 172 of file compound.hh.

void SetCreationDate ( const Date creation_date)
inline

Definition at line 231 of file compound.hh.

void SetDialect ( Dialect  dialect)
inline

Definition at line 149 of file compound.hh.

void SetFormula ( const String formula)
inline

Definition at line 210 of file compound.hh.

void SetModificationDate ( const Date mod_date)
inline

Definition at line 226 of file compound.hh.

void SetName ( const String name)
inline

Definition at line 208 of file compound.hh.

void SetOneLetterCode ( char  olc)
inline

Definition at line 151 of file compound.hh.


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