Compound Class Reference

Knows about the atoms and bonds of a chemical compounds. More...

#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 ()
void SetInchi (const String &inchi)
const StringGetInchi ()
void SetInchiKey (const String &inchikey)
const StringGetInchiKey ()
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 136 of file compound.hh.

Member Enumeration Documentation

enum Dialect

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.

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