| SimTK::AcetylResidue | Widely used acetyl protein N-terminal end cap |
| SimTK::AdenineBase | |
| SimTK::AlcoholOHGroup | AlcoholOHGroup is OH group for attachment to aliphatic carbon |
| SimTK::AliphaticCarbon | AliphaticCarbon is a tetrahedral sp3 carbon atom for bonding to four other things |
| SimTK::AliphaticHydrogen | AliphaticHydrogen is a hydrogen atom for bonding to AliphaticCarbon atoms (see below) |
| SimTK::Amber99ForceSubsystem | This class is just a DuMMForceFieldSubsystem for which the constructor pre-loads the definitions of the Amber99 force field |
| SimTK::AminoAcidResidue | Amino acid residue building block for protein polypeptide chain molecules |
| SimTK::AminoAcidResidue::Alanine | |
| SimTK::AminoAcidResidue::Arginine | |
| SimTK::AminoAcidResidue::Asparagine | |
| SimTK::AminoAcidResidue::Aspartate | |
| SimTK::AminoAcidResidue::BetaBranchedAminoAcidResidue | |
| SimTK::AminoAcidResidue::BetaUnbranchedAminoAcidResidue | |
| SimTK::AminoAcidResidue::Cysteine | |
| SimTK::AminoAcidResidue::Glutamate | |
| SimTK::AminoAcidResidue::Glutamine | |
| SimTK::AminoAcidResidue::Glycine | |
| SimTK::AminoAcidResidue::Histidine | |
| SimTK::AminoAcidResidue::HNAminoAcidResidue | AminoAcidResidue differs from HNAminoAcidResidue in lacking "HN" proton, so Proline can be derived |
| SimTK::AminoAcidResidue::Isoleucine | |
| SimTK::AminoAcidResidue::Leucine | |
| SimTK::AminoAcidResidue::Lysine | |
| SimTK::AminoAcidResidue::Methionine | |
| SimTK::AminoAcidResidue::Phenylalanine | |
| SimTK::AminoAcidResidue::Proline | |
| SimTK::AminoAcidResidue::Serine | |
| SimTK::AminoAcidResidue::Threonine | |
| SimTK::AminoAcidResidue::Tryptophan | |
| SimTK::AminoAcidResidue::Tyrosine | |
| SimTK::AminoAcidResidue::Valine | |
| SimTK::Argon | The noble gas argon, which does not bond with other atoms |
| SimTK::AromaticSixMemberedCHGroup | Two atom C-H group in six membered aromatic rings |
| SimTK::AtomSubsystem | |
| SimTK::AtomSubsystem::Atom | |
| SimTK::AtomSubsystem::AtomsByBody | |
| SimTK::AtomSubsystem::Bond | |
| SimTK::AtomSubsystem::PairIterator | |
| SimTK::Biopolymer | The base class for DNA, RNA, and Protein molecules |
| SimTK::BiopolymerResidue | |
| SimTK::Biotype | |
| SimTK::BivalentAtom | Base class for atoms having exactly two covalent bonds |
| SimTK::CalciumIon | Ca2+ calcium ion with +2 charge |
| SimTK::CarboxylateGroup | CaboxylateGroup is COO- for attachment to tetrahedral carbon |
| SimTK::CesiumIon | Cs+ cesium ion with +1 charge |
| SimTK::ChlorideIon | Cl- chloride ion with -1 charge |
| SimTK::Clonable | |
| SimTK::Compound | The base class for atoms, molecules, and chemical groups |
| SimTK::Compound::SingleAtom | Base class for single-atom Compound building blocks |
| SimTK::CompoundModeler | Turns a compound into a multibody system |
| SimTK::CompoundModeler::AtomBonding | |
| SimTK::CompoundModeler::RigidUnit | |
| SimTK::CompoundSystem | Derived class of MolecularMechanicsSystem that knows how to model molmodel Compounds |
| SimTK::CompoundSystem::CompoundIndex | Compound::Index type is an integer index into subcompounds of a Compound |
| SimTK::CytosineBase | |
| SimTK::DuMM::AtomClassIndex | This is a unique integer associated with each "atom class", assigned by the user when the atom class is first introduced via defineAtomClass() |
| SimTK::DuMM::AtomIndex | This is the unique integer index that DuMM assigns to atoms as they are added via addAtom() |
| SimTK::DuMM::BondIndex | This is the unique integer index that DuMM assigns to bonds as they are added via addBond() |
| SimTK::DuMM::ChargedAtomTypeIndex | This is a unique integer associated with each "charged atom type", assigned by the user when the charged atom type is first introduced via defineChargedAtomType() |
| SimTK::DuMM::ClusterIndex | This is the unique integer index that DuMM assigns to clusters as they are created via createCluster() |
| SimTK::DuMM::CustomBondBend | Abstract base class for custom bond bend functions, that is, functional forms that apply an angle-based torque between the two lines formed by a 1-2-3 triple of bonded atoms |
| SimTK::DuMM::CustomBondStretch | Abstract base class for custom bond stretch terms, that is, functional forms that apply a distance-based force along a 1-2 bond between a pair of atoms |
| SimTK::DuMM::CustomBondTorsion | Abstract base class for custom torsion functions, that is, functional forms that apply a dihedral-angle based torque about the middle bond of a 1-2-3-4 quadruple of bonded atoms |
| SimTK::DuMM::IncludedAtomIndex | This is the unique integer index that DuMM assigns to atoms that are to be included in force calculations. These represent a subset of all the atoms and you can map from an IncludedAtomIndex to the corresponding AtomIndex |
| SimTK::DuMM::NonbondAtomIndex | This is the unique integer index that DuMM assigns to included atoms that are involved in nonbonded force calculations (Coulomb, van der Waals, and/or GBSA). These represent a subset of all the included atoms and you can map from a NonbondAtomIndex to the corresponding IncludedAtomIndex |
| SimTK::DuMMForceFieldSubsystem | This is a concrete subsystem that provides basic molecular mechanics functionality for coarse-grained molecules built in the SimTK framework |
| SimTK::Element | |
| SimTK::Element::Actinium | |
| SimTK::Element::Aluminum | |
| SimTK::Element::Americium | |
| SimTK::Element::Antimony | |
| SimTK::Element::Argon | |
| SimTK::Element::Arsenic | |
| SimTK::Element::Astatine | |
| SimTK::Element::Barium | |
| SimTK::Element::Berkelium | |
| SimTK::Element::Beryllium | |
| SimTK::Element::Bismuth | |
| SimTK::Element::Bohrium | |
| SimTK::Element::Boron | |
| SimTK::Element::Bromine | |
| SimTK::Element::Cadmium | |
| SimTK::Element::Calcium | |
| SimTK::Element::Californium | |
| SimTK::Element::Carbon | |
| SimTK::Element::Cerium | |
| SimTK::Element::Cesium | |
| SimTK::Element::Chlorine | |
| SimTK::Element::Chromium | |
| SimTK::Element::Cobalt | |
| SimTK::Element::Copper | |
| SimTK::Element::Curium | |
| SimTK::Element::Darmstadtium | |
| SimTK::Element::Deuterium | |
| SimTK::Element::Dubnium | |
| SimTK::Element::Dysprosium | |
| SimTK::Element::Einsteinium | |
| SimTK::Element::Erbium | |
| SimTK::Element::Europium | |
| SimTK::Element::Fermium | |
| SimTK::Element::Fluorine | |
| SimTK::Element::Francium | |
| SimTK::Element::Gadolinium | |
| SimTK::Element::Gallium | |
| SimTK::Element::Germanium | |
| SimTK::Element::Gold | |
| SimTK::Element::Hafnium | |
| SimTK::Element::Hassium | |
| SimTK::Element::Helium | |
| SimTK::Element::Holmium | |
| SimTK::Element::Hydrogen | |
| SimTK::Element::Indium | |
| SimTK::Element::Iodine | |
| SimTK::Element::Iridium | |
| SimTK::Element::Iron | |
| SimTK::Element::Krypton | |
| SimTK::Element::Lanthanum | |
| SimTK::Element::Lawrencium | |
| SimTK::Element::Lead | |
| SimTK::Element::Lithium | |
| SimTK::Element::Lutetium | |
| SimTK::Element::Magnesium | |
| SimTK::Element::Manganese | |
| SimTK::Element::Meitnerium | |
| SimTK::Element::Mendelevium | |
| SimTK::Element::Mercury | |
| SimTK::Element::Molybdenum | |
| SimTK::Element::Neodymium | |
| SimTK::Element::Neon | |
| SimTK::Element::Neptunium | |
| SimTK::Element::Nickel | |
| SimTK::Element::Niobium | |
| SimTK::Element::Nitrogen | |
| SimTK::Element::Nobelium | |
| SimTK::Element::Osmium | |
| SimTK::Element::Oxygen | |
| SimTK::Element::Palladium | |
| SimTK::Element::Phosphorus | |
| SimTK::Element::Platinum | |
| SimTK::Element::Plutonium | |
| SimTK::Element::Polonium | |
| SimTK::Element::Potassium | |
| SimTK::Element::Praseodymium | |
| SimTK::Element::Promethium | |
| SimTK::Element::Protactinium | |
| SimTK::Element::Radium | |
| SimTK::Element::Radon | |
| SimTK::Element::Rhenium | |
| SimTK::Element::Rhodium | |
| SimTK::Element::Roentgenium | |
| SimTK::Element::Rubidium | |
| SimTK::Element::Ruthenium | |
| SimTK::Element::Rutherfordium | |
| SimTK::Element::Samarium | |
| SimTK::Element::Scandium | |
| SimTK::Element::Seaborgium | |
| SimTK::Element::Selenium | |
| SimTK::Element::Silicon | |
| SimTK::Element::Silver | |
| SimTK::Element::Sodium | |
| SimTK::Element::Strontium | |
| SimTK::Element::Sulfur | |
| SimTK::Element::Tantalum | |
| SimTK::Element::Technetium | |
| SimTK::Element::Tellurium | |
| SimTK::Element::Terbium | |
| SimTK::Element::Thallium | |
| SimTK::Element::Thorium | |
| SimTK::Element::Thulium | |
| SimTK::Element::Tin | |
| SimTK::Element::Titanium | |
| SimTK::Element::Tungsten | |
| SimTK::Element::Ununbium | |
| SimTK::Element::Ununhexium | |
| SimTK::Element::Ununpentium | |
| SimTK::Element::Ununquadium | |
| SimTK::Element::Ununtrium | |
| SimTK::Element::Uranium | |
| SimTK::Element::Vanadium | |
| SimTK::Element::Xenon | |
| SimTK::Element::Ytterbium | |
| SimTK::Element::Yttrium | |
| SimTK::Element::Zinc | |
| SimTK::Element::Zirconium | |
| SimTK::Ethane | The small hydrocarbon ethane, C2H6, which has a single torsion degree of freedom |
| SimTK::Exception::DuplicatePdbResidue | |
| SimTK::Exception::UndefinedAminoAcidResidue | |
| SimTK::Exception::UndefinedPdbChainId | |
| SimTK::FivePrimeRnaHydroxylGroup | Phosphate group at 5' end (beginning) of RNA |
| SimTK::FivePrimeRnaPhosphateGroup | Phosphate group at 5' end (beginning) of RNA |
| SimTK::GrinPointer< PointeeType > | |
| SimTK::GuanineBase | |
| SimTK::Kabsch78 | |
| SimTK::LigandDroplet | |
| SimTK::LithiumIon | Li+ lithium ion with +1 charge |
| SimTK::MagnesiumIon | Mg2+ magnesium ion with +2 charge |
| SimTK::MassCenterMotionRemover | This is an event handler that can remove from a molecular system any unwanted "rigid body" motion of the sytem as a whole |
| SimTK::Methane | The simplest hydrocarbon methane, CH4 |
| SimTK::MethyleneGroup | MethyleneGroup is -CH2- group for bonding to aliphatic carbon and a second something |
| SimTK::MethylGroup | MethylGroup is CH3 for attaching to aliphatic carbon |
| SimTK::MolecularMechanicsSystem | This is a particular kind of MultibodySystem, one intended for use in molecular mechanics (MM) |
| SimTK::Molecule | Base class for complete covalently connected molecules |
| SimTK::NMethylAmideResidue | Neutral C-terminal protein cap |
| SimTK::NoseHooverThermostat | |
| SimTK::P12 | |
| SimTK::PdbAtom | One atom, which may have more than one location, in the case of static or dynamic disorder in an X-ray structure |
| SimTK::PdbAtomLocation | Location information for a PdbAtom, corresponding to one altLoc for a PdbAtom |
| SimTK::PdbChain | One molecule in a PDB structure |
| SimTK::PdbModel | PDB structure containing one or more molecules (chains), corresponding to one member of an NMR ensemble of alternate structures, or to one frame of a molecular dynamics simulation |
| SimTK::PDBReader | This class parses PDB files, then constructs Systems and States based on them for use in Simbody |
| SimTK::PdbResidue | One residue in a protein or nucleic acid, or a single molecule in the case of non-polymer structures |
| SimTK::PdbResidueId | Composite key for residue within a chain, composed of residue number and insertion code |
| SimTK::PdbStructure | Complete PDB file, possibly including multiple MODELS, in the case of NMR structures or molecular dynamics trajectories |
| SimTK::PeriodicPdbWriter | Writes atomic coordinates in PDB format to a file stream at specified intervals during a simulation |
| SimTK::PeriodicVmdReporter | Writes atomic coordinates in PDB format to a file stream at specified intervals during a simulation |
| SimTK::PotassiumIon | K+ potassium ion with +1 charge |
| SimTK::PrimaryAmineGroup | PrimaryAmineGroup is NH3+ for attachment to tetrahedral carbon |
| SimTK::Protein | |
| SimTK::PseudorotationMobilizer | |
| SimTK::PurineBaseCore | |
| SimTK::PyrimidineBaseCore | |
| SimTK::QuadrivalentAtom | Base class for atoms having exactly four covalent bonds |
| SimTK::ResidueInfo | |
| SimTK::ResidueInfo::AtomInfo | |
| SimTK::RibonucleosideResidue | |
| SimTK::RibonucleotideResidue | |
| SimTK::RibonucleotideResidue::Adenylate | |
| SimTK::RibonucleotideResidue::Cytidylate | |
| SimTK::RibonucleotideResidue::Guanylate | |
| SimTK::RibonucleotideResidue::TwoNMethylGuanylate | |
| SimTK::RibonucleotideResidue::Uridylate | |
| SimTK::RiboseCore | |
| SimTK::RiboseNu3Mobilizer | |
| SimTK::RNA | |
| SimTK::RnaPhosphodiesterLinkage | |
| SimTK::RubidiumIon | Rb+ rubidium ion with +1 charge |
| SimTK::SinusoidFunction | Implements a simple functional relationship, y = amplitude * sin(x - phase) |
| SimTK::SodiumIon | Na+ sodium ion with +1 charge |
| SimTK::ThreePrimeRnaHydroxylGroup | Phosphate group at 3' end (beginning) of RNA |
| SimTK::ThreePrimeRnaPhosphateGroup | Phosphate group at 3' end (end) of RNA |
| SimTK::TransformAndResidual | |
| SimTK::TrivalentAtom | Base class for atoms having exactly three covalent bonds |
| SimTK::TwoNMethylGuanidineGroup | |
| SimTK::TwoNMethylGuanineBaseGroup | |
| SimTK::UnivalentAtom | Base class for atoms with exaclty one covalent bond partner |
| SimTK::UracilBase | |
| SimTK::VanDerWaalsForce | |
| SimTK::VanDerWaalsForce::ForceAndEnergy | |
| SimTK::VanDerWaalsForce::VdwAtom | |
| SimTK::VanDerWaalsForce::WallSphere | |
| SimTK::VanderWallSphere | |
| SimTK::Vec3Pair | Matched pair of 3D vectors to be used in least-squares superposition |
| SimTK::VelocityRescalingThermostat | This is an event handler that acts as a thermostat for controlling the temperature of a simulation efficiently, and in a qualitatively reasonable manner although not with the correct statistical temperature distribution |
| SimTK::VmdConnection | |
| SimTK::VmdFloat3 | |
| SimTK::VoxelHash< T > | |
| SimTK::VoxelHash< T >::VoxelIndex | |
| SimTK::Water | |
| SimTK::WaterDroplet | |
| SimTK::ZeroFunction | Function f(x) = 0 for all x |
| SimTK::ZincIon | Zn2+ zinc ion with +2 charge |
1.7.3
