Biotype Class Reference

#include <Biotype.h>

List of all members.

Public Member Functions
const Element &	getElement () const
int	getValence () const
BiotypeIndex	getIndex () const
TinkerBiotypeIndex	getTinkerBiotypeIfAny () const
Biotype &	setTinkerBiotypeIndex (TinkerBiotypeIndex tIx)
	Biotype ()
const String &	getAtomName () const
const String &	getResidueName () const
Ordinality::Residue	getOrdinality () const
std::ostream &	generateSelfCode (std::ostream &os) const
Static Public Member Functions
static const Biotype &	Argon ()
static const Biotype &	MethaneH ()
static const Biotype &	MethaneC ()
static const Biotype &	EthaneH ()
static const Biotype &	EthaneC ()
static const Biotype &	SerineN ()
static const Biotype &	SerineHN ()
static const Biotype &	SerineCA ()
static const Biotype &	SerineHA ()
static const Biotype &	SerineC ()
static const Biotype &	SerineO ()
static const Biotype &	SerineCB ()
static const Biotype &	SerineHB ()
static const Biotype &	SerineOG ()
static const Biotype &	SerineHG ()
static void	initializePopularBiotypes ()
static const Biotype &	get (BiotypeIndex biotypeIndex)
static const Biotype &	get (TinkerBiotypeIndex tinkerBiotypeIndex)
static const Biotype &	get (const char *residueName, const char *atomName, Ordinality::Residue ordinality=Ordinality::Any)
static Biotype &	upd (BiotypeIndex biotypeIndex)
static Biotype &	upd (TinkerBiotypeIndex tinkerBiotypeIndex)
static Biotype &	upd (const char *residueName, const char *atomName, Ordinality::Residue ordinality=Ordinality::Any)
static bool	exists (const char *residueName, const char *atomName, Ordinality::Residue ordinality=Ordinality::Any)
static bool	exists (BiotypeIndex biotypeIndex)
static BiotypeIndex	defineBiotype (const Element &element, int valence, const char *residueName, const char *atomName, Ordinality::Residue ordinality=Ordinality::Any)
static BiotypeIndex	defineTinkerBiotype (TinkerBiotypeIndex tinkerBiotypeIndex, const Element &element, int valence, const char *residueName, const char *atomName, Ordinality::Residue ordinality=Ordinality::Any)
static std::ostream &	generateAllBiotypeCode (std::ostream &os)

---

Constructor & Destructor Documentation

Biotype

(

)

---

Member Function Documentation

static const Biotype& Argon

(

)

[static]

Referenced by Argon::Argon().

static BiotypeIndex defineBiotype	(	const Element &	element,
		int	valence,
		const char *	residueName,
		const char *	atomName,
		Ordinality::Residue	ordinality = Ordinality::Any
	)			[inline, static]

Referenced by RnaPhosphodiesterLinkage::instantiateBiotypes(), SodiumIon::instantiateBiotypes(), RubidiumIon::instantiateBiotypes(), MagnesiumIon::instantiateBiotypes(), CesiumIon::instantiateBiotypes(), CalciumIon::instantiateBiotypes(), FivePrimeRnaHydroxylGroup::instantiateBiotypes(), ThreePrimeRnaPhosphateGroup::instantiateBiotypes(), FivePrimeRnaPhosphateGroup::instantiateBiotypes(), TwoNMethylGuanidineGroup::instantiateBiotypes(), LithiumIon::instantiateBiotypes(), ZincIon::instantiateBiotypes(), PotassiumIon::instantiateBiotypes(), ChlorideIon::instantiateBiotypes(), ThreePrimeRnaHydroxylGroup::instantiateBiotypes(), Compound::setAtomBiotype(), and Water::Water().

static BiotypeIndex defineTinkerBiotype	(	TinkerBiotypeIndex	tinkerBiotypeIndex,
		const Element &	element,
		int	valence,
		const char *	residueName,
		const char *	atomName,
		Ordinality::Residue	ordinality = Ordinality::Any
	)			[static]

static const Biotype& EthaneC

(

)

[static]

Referenced by Ethane::Ethane().

static const Biotype& EthaneH

(

)

[static]

Referenced by Ethane::Ethane().

static bool exists

(

BiotypeIndex

biotypeIndex

)

[static]

static bool exists	(	const char *	residueName,
		const char *	atomName,
		Ordinality::Residue	ordinality = Ordinality::Any
	)			[static]

Referenced by RnaPhosphodiesterLinkage::instantiateBiotypes(), SodiumIon::instantiateBiotypes(), RubidiumIon::instantiateBiotypes(), MagnesiumIon::instantiateBiotypes(), CesiumIon::instantiateBiotypes(), CalciumIon::instantiateBiotypes(), FivePrimeRnaHydroxylGroup::instantiateBiotypes(), ThreePrimeRnaPhosphateGroup::instantiateBiotypes(), FivePrimeRnaPhosphateGroup::instantiateBiotypes(), TwoNMethylGuanidineGroup::instantiateBiotypes(), LithiumIon::instantiateBiotypes(), ZincIon::instantiateBiotypes(), PotassiumIon::instantiateBiotypes(), ChlorideIon::instantiateBiotypes(), ThreePrimeRnaHydroxylGroup::instantiateBiotypes(), RNA::RNA(), Compound::setAtomBiotype(), and Water::Water().

static std::ostream& generateAllBiotypeCode

(

std::ostream &

os

)

[static]

std::ostream& generateSelfCode

(

std::ostream &

os

)

const

static const Biotype& get	(	const char *	residueName,
		const char *	atomName,
		Ordinality::Residue	ordinality = Ordinality::Any
	)			[static]

static const Biotype& get

(

TinkerBiotypeIndex

tinkerBiotypeIndex

)

[static]

static const Biotype& get

(

BiotypeIndex

biotypeIndex

)

[static]

Referenced by CalciumIon::CalciumIon(), CesiumIon::CesiumIon(), ChlorideIon::ChlorideIon(), FivePrimeRnaHydroxylGroup::FivePrimeRnaHydroxylGroup(), FivePrimeRnaPhosphateGroup::FivePrimeRnaPhosphateGroup(), LithiumIon::LithiumIon(), MagnesiumIon::MagnesiumIon(), P12::P12(), PotassiumIon::PotassiumIon(), RNA::RNA(), RnaPhosphodiesterLinkage::RnaPhosphodiesterLinkage(), RubidiumIon::RubidiumIon(), ZincIon::setAmberLikeParameters(), ChlorideIon::setAmberLikeParameters(), CalciumIon::setAmberLikeParameters(), LithiumIon::setAmberLikeParameters(), CesiumIon::setAmberLikeParameters(), MagnesiumIon::setAmberLikeParameters(), PotassiumIon::setAmberLikeParameters(), SodiumIon::setAmberLikeParameters(), RubidiumIon::setAmberLikeParameters(), Compound::setAtomBiotype(), SodiumIon::SodiumIon(), ThreePrimeRnaHydroxylGroup::ThreePrimeRnaHydroxylGroup(), ThreePrimeRnaPhosphateGroup::ThreePrimeRnaPhosphateGroup(), TwoNMethylGuanidineGroup::TwoNMethylGuanidineGroup(), TwoNMethylGuanylate::TwoNMethylGuanylate(), Water::Water(), and ZincIon::ZincIon().

const String& getAtomName

(

)

const

const Element& getElement

(

)

const

Referenced by Compound::setAtomBiotype().

BiotypeIndex getIndex

(

)

const

Referenced by ChlorideIon::setAmberLikeParameters(), ZincIon::setAmberLikeParameters(), CalciumIon::setAmberLikeParameters(), MagnesiumIon::setAmberLikeParameters(), CesiumIon::setAmberLikeParameters(), RubidiumIon::setAmberLikeParameters(), PotassiumIon::setAmberLikeParameters(), SodiumIon::setAmberLikeParameters(), LithiumIon::setAmberLikeParameters(), and Compound::setAtomBiotype().

Ordinality::Residue getOrdinality

(

)

const

const String& getResidueName

(

)

const

TinkerBiotypeIndex getTinkerBiotypeIfAny

(

)

const

int getValence

(

)

const

Referenced by Compound::setAtomBiotype().

static void initializePopularBiotypes

(

)

[static]

Referenced by Protein::initialize(), and RNA::RNA().

static const Biotype& MethaneC

(

)

[static]

Referenced by Methane::Methane().

static const Biotype& MethaneH

(

)

[static]

Referenced by Methane::Methane().

static const Biotype& SerineC

(

)

[static]

Referenced by Serine::Serine().

static const Biotype& SerineCA

(

)

[static]

Referenced by Serine::Serine().

static const Biotype& SerineCB

(

)

[static]

static const Biotype& SerineHA

(

)

[static]

Referenced by Serine::Serine().

static const Biotype& SerineHB

(

)

[static]

static const Biotype& SerineHG

(

)

[static]

Referenced by Serine::Serine().

static const Biotype& SerineHN

(

)

[static]

Referenced by Serine::Serine().

static const Biotype& SerineN

(

)

[static]

Referenced by Serine::Serine().

static const Biotype& SerineO

(

)

[static]

Referenced by Serine::Serine().

static const Biotype& SerineOG

(

)

[static]

Referenced by Serine::Serine().

Biotype& setTinkerBiotypeIndex

(

TinkerBiotypeIndex

tIx

)

static Biotype& upd	(	const char *	residueName,
		const char *	atomName,
		Ordinality::Residue	ordinality = Ordinality::Any
	)			[static]

static Biotype& upd

(

TinkerBiotypeIndex

tinkerBiotypeIndex

)

[static]

static Biotype& upd

(

BiotypeIndex

biotypeIndex

)

[static]

---

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

• Biotype.h