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Molmodel
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Molmodel
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#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 | SimTK::Compound |
| The base class for atoms, molecules, and chemical groups. More... | |
| class | SimTK::Compound::SingleAtom |
| Base class for single-atom Compound building blocks. More... | |
| class | SimTK::UnivalentAtom |
| Base class for atoms with exaclty one covalent bond partner. More... | |
| class | SimTK::BivalentAtom |
| Base class for atoms having exactly two covalent bonds. More... | |
| class | SimTK::TrivalentAtom |
| Base class for atoms having exactly three covalent bonds. More... | |
| class | SimTK::QuadrivalentAtom |
| Base class for atoms having exactly four covalent bonds. More... | |
| class | SimTK::AliphaticHydrogen |
| AliphaticHydrogen is a hydrogen atom for bonding to AliphaticCarbon atoms (see below) More... | |
| class | SimTK::AliphaticCarbon |
| AliphaticCarbon is a tetrahedral sp3 carbon atom for bonding to four other things. More... | |
| class | SimTK::MethyleneGroup |
| MethyleneGroup is -CH2- group for bonding to aliphatic carbon and a second something. More... | |
| class | SimTK::MethylGroup |
| MethylGroup is CH3 for attaching to aliphatic carbon. More... | |
| class | SimTK::AromaticSixMemberedCHGroup |
| Two atom C-H group in six membered aromatic rings. More... | |
| class | SimTK::AlcoholOHGroup |
| AlcoholOHGroup is OH group for attachment to aliphatic carbon. More... | |
| class | SimTK::PrimaryAmineGroup |
| PrimaryAmineGroup is NH3+ for attachment to tetrahedral carbon. More... | |
| class | SimTK::CarboxylateGroup |
| CaboxylateGroup is COO- for attachment to tetrahedral carbon. More... | |
| class | SimTK::Molecule |
| Base class for complete covalently connected molecules. More... | |
| class | SimTK::Argon |
| The noble gas argon, which does not bond with other atoms. More... | |
| class | SimTK::Methane |
| The simplest hydrocarbon methane, CH4 More... | |
| class | SimTK::Ethane |
| The small hydrocarbon ethane, C2H6, which has a single torsion degree of freedom. More... | |
| class | SimTK::BiopolymerResidue |
| class | SimTK::ResidueInfo |
| class | SimTK::ResidueInfo::AtomInfo |
| class | SimTK::Biopolymer |
| The base class for DNA, RNA, and Protein molecules. More... | |
Namespaces | |
| namespace | SimTK |
| namespace | SimTK::BondMobility |
Namespace for description of allowed bond motions. | |
Enumerations | |
| enum | SimTK::BondMobility::Mobility { SimTK::BondMobility::Free = 1, SimTK::BondMobility::Torsion = 2, SimTK::BondMobility::Rigid = 3 } |
Which motions are allowed for a particular covalent bond. More... | |
Functions | |
| SimTK_MOLMODEL_EXPORT std::ostream & | SimTK::operator<< (std::ostream &o, const Compound &c) |
| Dump debugging information about compound structure to a stream. | |
Variables | |
| static Mobility | SimTK::BondMobility::Default = Torsion |
1.7.3