Compound.h File Reference

#include "SimTKsimbody.h"
#include "molmodel/internal/common.h"
#include "TinkerDuMMForceFieldSubsystem.h"
#include "molmodel/internal/Pdb.h"
#include "molmodel/internal/Superpose.h"
#include "molmodel/internal/units.h"
#include <map>
#include <iosfwd>

Go to the source code of this file.

Namespaces
namespace	SimTK
namespace	SimTK::BondMobility
Classes
class	Compound
	The base class for atoms, molecules, and chemical groups. More...
class	Compound::SingleAtom
	Base class for single-atom Compound building blocks. More...
class	UnivalentAtom
	Base class for atoms with exaclty one covalent bond partner. More...
class	BivalentAtom
	Base class for atoms having exactly two covalent bonds. More...
class	TrivalentAtom
	Base class for atoms having exactly three covalent bonds. More...
class	QuadrivalentAtom
	Base class for atoms having exactly four covalent bonds. More...
class	AliphaticHydrogen
	AliphaticHydrogen is a hydrogen atom for bonding to AliphaticCarbon atoms (see below). More...
class	AliphaticCarbon
	AliphaticCarbon is a tetrahedral sp3 carbon atom for bonding to four other things. More...
class	MethyleneGroup
	MethyleneGroup is -CH2- group for bonding to aliphatic carbon and a second something. More...
class	MethylGroup
	MethylGroup is CH3 for attaching to aliphatic carbon. More...
class	AromaticSixMemberedCHGroup
	Two atom C-H group in six membered aromatic rings. More...
class	AlcoholOHGroup
	AlcoholOHGroup is OH group for attachment to aliphatic carbon. More...
class	PrimaryAmineGroup
	PrimaryAmineGroup is NH3+ for attachment to tetrahedral carbon. More...
class	CarboxylateGroup
	CaboxylateGroup is COO- for attachment to tetrahedral carbon. More...
class	Molecule
	Base class for complete covalently connected molecules. More...
class	Argon
	The noble gas argon, which does not bond with other atoms. More...
class	Methane
	The simplest hydrocarbon methane, CH4. More...
class	Ethane
	The small hydrocarbon ethane, C2H6, which has a single torsion degree of freedom. More...
class	BiopolymerResidue
class	Biopolymer
	The base class for DNA, RNA, and Protein molecules. More...
Enumerations
enum	Mobility { Free = 1, Torsion = 2, Rigid = 3 }
	Which motions are allowed for a particular covalent bond. More...
Functions
std::ostream &	operator<< (std::ostream &o, const Compound &c)
	Dump debugging information about compound structure to a stream.