#include "SimTKsimbody.h"#include "molmodel/internal/common.h"#include "DuMMForceFieldSubsystem.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.
Classes | |
| class | Compound |
| The base class for atoms, molecules, and chemical groups. More... | |
| class | 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 | ResidueInfo |
| class | AtomInfo |
| class | Biopolymer |
| The base class for DNA, RNA, and Protein molecules. More... | |
Namespaces | |
| namespace | SimTK |
This is the top-level SimTK namespace into which all SimTK names are placed to avoid collision with other symbols. | |
| namespace | SimTK::BondMobility |
Namespace for description of allowed bond motions. | |
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. | |
1.6.1