| _DlsMat | |
| _generic_N_Vector | |
| _generic_N_Vector_Ops | |
| _N_VectorContent_Parallel | |
| _N_VectorContent_Serial | |
| _SpgmrMemRec | |
| AbstractMeasure | This is the base class for all Measure handle classes |
| AbstractValue | Abstract base class representing an arbitrary value of self-describing type |
| AcetylResidue | Widely used acetyl protein N-terminal end cap |
| Actinium | |
| AdenineBase | |
| Adenylate | |
| Alanine | |
| AlcoholOHGroup | AlcoholOHGroup is OH group for attachment to aliphatic carbon |
| AliphaticCarbon | AliphaticCarbon is a tetrahedral sp3 carbon atom for bonding to four other things |
| AliphaticHydrogen | AliphaticHydrogen is a hydrogen atom for bonding to AliphaticCarbon atoms (see below) |
| Aluminum | |
| Amber99ForceSubsystem | This class is just a DuMMForceFieldSubsystem for which the constructor pre-loads the definitions of the Amber99 force field |
| Americium | |
| AminoAcidResidue | Amino acid residue building block for protein polypeptide chain molecules |
| AnalyticBrick | This is a rectangular solid |
| AnalyticCircle | An analytic circle has only a radius |
| AnalyticCurve | |
| AnalyticCylinder | The coordinate frame of the central cross section is the same as for a circle; that is, x and z are radial and y points along the cylinder's axis |
| AnalyticGeometry | This abstract class represents a piece of high-quality geometry that can be used for valid physical simulation |
| AnalyticLine | An analytic line has only a length |
| AnalyticSphere | |
| AnalyticSurface | |
| AnalyticVolume | |
| Antimony | |
| APIArgcheckFailed | This is for reporting problems detected by checking the caller's supplied arguments to a SimTK API method |
| Arginine | |
| Argon | The noble gas argon, which does not bond with other atoms |
| Argon | |
| AromaticSixMemberedCHGroup | Two atom C-H group in six membered aromatic rings |
| Array_< T, X > | The SimTK::Array_<T> container class is a plug-compatible replacement for the C++ standard template library (STL) std::vector<T> class, but with some important advantages in performance, and functionality, and binary compatibility |
| ArrayIndexTraits< X > | This templatized type is used by the Array_<T,X> classes to obtain the information they need to use the class X as an index class for the array |
| ArrayIndexTraits< bool > | Specialization of ArrayIndexTraits for bool used as an index |
| ArrayIndexTraits< char > | Specialization of ArrayIndexTraits for char used as an index |
| ArrayIndexTraits< int > | Specialization of ArrayIndexTraits for (signed) int used as an index |
| ArrayIndexTraits< long > | Specialization of ArrayIndexTraits for (signed) long used as an index |
| ArrayIndexTraits< long long > | Specialization of ArrayIndexTraits for long long used as an index |
| ArrayIndexTraits< short > | Specialization of ArrayIndexTraits for (signed) short used as an index |
| ArrayIndexTraits< signed char > | Specialization of ArrayIndexTraits for signed char used as an index |
| ArrayIndexTraits< unsigned > | Specialization of ArrayIndexTraits for unsigned (that is, unsigned int) used as an index |
| ArrayIndexTraits< unsigned char > | Specialization of ArrayIndexTraits for unsigned char used as an index |
| ArrayIndexTraits< unsigned long > | Specialization of ArrayIndexTraits for unsigned long used as an index |
| ArrayIndexTraits< unsigned long long > | Specialization of ArrayIndexTraits for unsigned long long used as an index |
| ArrayIndexTraits< unsigned short > | Specialization of ArrayIndexTraits for unsigned short used as an index |
| ArrayView_< T, X > | This Array_ helper class is the base class for Array_, extending ArrayViewConst_ to add the ability to modify elements, but not the ability to change size or reallocate |
| ArrayViewConst_< T, X > | This Array_ helper class is the base class for ArrayView_ which is the base class for Array_; here we provide only the minimal read-only "const" functionality required by any Array_ object, and shallow copy semantics |
| Arsenic | |
| ArticulatedInertia_< P > | An articulated body inertia (ABI) matrix P(q) contains the spatial inertia properties that a body appears to have when it is the free base body of an articulated multibody tree in a given configuration q |
| Asparagine | |
| Aspartate | |
| Assembler | This Study attempts to find a configuration (set of joint coordinates q) of a Simbody MultibodySystem that satisfies the System's position Constraints plus optional additional assembly conditions |
| AssemblyCondition | Define an assembly condition consisting of a scalar goal and/or a related set of assembly error equations (that is, an objective and/or some constraints) |
| Assert | This is for reporting internally-detected bugs only, not problems induced by confused users (that is, it is for confused developers instead) |
| Astatine | |
| Atom | |
| AtomBonding | |
| AtomicInteger | This class functions exactly like an int, except that the following operators are atomic: ++, --, +=, -=, *=, /=, =, &=, |=, ^=, <<=, and >>= |
| AtomInfo | |
| AtomsByBody | |
| AtomSubsystem | |
| Attribute | Elements can have attributes, which are name="value" pairs that appear within the element start tag in an XML document; this class represents the in-memory representation of one of those attributes and can be used to examine or modify the name or value |
| attribute_iterator | This is a bidirectional iterator suitable for moving forward or backward within a list of Attributes within an Element, for writable access |
| Ball | Three constraint equations |
| Ball | Three mobilities -- unrestricted orientation modeled with a quaternion which is never singular |
| Barium | |
| Base | |
| BendStretch | Two mobilities: The z axis of the parent's F frame is used for rotation (and that is always aligned with the M frame z axis) |
| Berkelium | |
| Beryllium | |
| BetaBranchedAminoAcidResidue | |
| BetaUnbranchedAminoAcidResidue | |
| Biopolymer | The base class for DNA, RNA, and Protein molecules |
| BiopolymerResidue | |
| Biotype | |
| Bismuth | |
| BivalentAtom | Base class for atoms having exactly two covalent bonds |
| Body | Reference frame that can be used to describe mass properties and geometry |
| Bohrium | |
| Bond | |
| Boron | |
| BrokenContact | This subclass of Contact represents a pair of contact surfaces that were in contact (meaning within cutoff range) but have now gone out of range |
| BrokenContactImpl | This is the internal implementation class for BrokenContact |
| Bromine | |
| CacheEntryOutOfDate | |
| Cadmium | |
| Calcium | |
| CalciumIon | Ca2+ calcium ion with +2 charge |
| Californium | |
| Cant | |
| Carbon | |
| CarboxylateGroup | CaboxylateGroup is COO- for attachment to tetrahedral carbon |
| Cause | These are all the possible causes for events |
| Cerium | |
| Cesium | |
| CesiumIon | Cs+ cesium ion with +1 charge |
| ChlorideIon | Cl- chloride ion with -1 charge |
| Chlorine | |
| Chromium | |
| CircularPointContact | This subclass of Contact represents a contact between two non-conforming surfaces 1 and 2 that initially meet at a point where each surface has a uniform radius of curvature in all directions (R1 and R2), like a sphere (inside or outside) or a halfspace, resulting in a contact region with circular symmetry |
| CircularPointContactImpl | This is the internal implementation class for CircularPointContact |
| Clonable | |
| CNT< K > | Specialized information about Composite Numerical Types which allows us to define appropriate templatized classes using them |
| CNT< complex< R > > | Specializations of CNT for numeric types |
| CNT< conjugate< R > > | |
| CNT< double > | |
| CNT< float > | |
| CNT< long double > | |
| Cobalt | |
| CollisionDetectionAlgorithm | A CollisionDetectionAlgorithm implements an algorithm for detecting overlaps between pairs of ContactGeometry objects, and creating Contact objects based on them |
| Comment | A comment contains only uninterpreted text |
| CompliantContactSubsystem | This is a force subsystem that implements a compliant contact model to respond to Contact objects as detected by a ContactTrackerSubsystem |
| Compound | The base class for atoms, molecules, and chemical groups |
| CompoundModeler | Turns a compound into a multibody system |
| CompoundSystem | Derived class of MolecularMechanicsSystem that knows how to model molmodel Compounds |
| Concretize< T > | Wrap a pointer to an abstract base class in a way that makes it behave like a concrete class (sometimes called a "ClonePtr") |
| conjugate< R > | SimTK::conjugate<R> should be instantiated only for float, double, long double |
| conjugate< double > | |
| conjugate< float > | |
| conjugate< long double > | |
| Constant | This is a Function_ subclass which simply returns a fixed value, independent of its arguments |
| Constant | This creates a Measure whose value is a Topology-stage constant of any type T |
| ConstantAcceleration | One acceleration-only constraint equation |
| ConstantAngle | This constraint consists of a single constraint equation that enforces that a unit vector v1 fixed to one body (the "base body") must maintain a fixed angle theta with respect to a unit vector v2 fixed on the other body (the "follower body") |
| ConstantForce | A constant force applied to a body station |
| ConstantOrientation | Three constraint equations |
| ConstantSpeed | One non-holonomic constraint equation |
| ConstantTorque | A constant torque to a body |
| Constraint | This is the base class for all Constraint classes, which is just a handle for the underlying hidden implementation |
| Contact | A Contact contains information about two surfaces that are in contact with each other |
| ContactDetail | This provides deformed geometry and force details for one element of a contact patch that may be composed of many elements |
| ContactForce | This is a simple class containing the basic force information for a single contact between deformable surfaces S1 and S2 mounted on rigid bodies B1 and B2 |
| ContactForceGenerator | A ContactForceGenerator implements an algorithm for responding to overlaps or potential overlaps between pairs of ContactSurface objects, as detected by a ContactTrackerSubsystem |
| ContactGeometry | A ContactGeometry object describes the physical shape of a body |
| ContactGeometryImpl | |
| ContactImpl | This is the internal implementation base class for Contact |
| ContactMaterial | Define the physical properties of the material from which a contact surface is made, including properties needed by a variety of contact response techniques that might be applied during contact |
| ContactPatch | A ContactPatch is the description of the forces and the deformed shape of the contact surfaces that result from compliant contact interactions |
| ContactSnapshot | Objects of this class represent collections of surface-pair interactions that are being tracked at a particular instant during a simulation |
| ContactSurface | This class combines a piece of ContactGeometry with a ContactMaterial to make an object suitable for attaching to a body which can then engage in contact behavior with other contact surfaces |
| ContactTracker | A ContactTracker implements an algorithm for detecting overlaps or potential overlaps between pairs of ContactGeometry objects, and managing Contact objects that track individual contacts as they evolve through time |
| ContactTrackerSubsystem | This subsystem identifies and tracks potential contacts between bodies of a multibody system, but does not generate any physical responses to those contacts |
| ConvergedFailed | |
| CoordinateAxis | |
| CoordinateCoupler | This is a subclass of Constraint::Custom which uses a Function object to define a holonomic (position) constraint |
| Copper | |
| CPodes | This is a straightforward translation of the Sundials CPODES C interface into C++ |
| CPodesIntegrator | This is an Integrator based on the CPODES library |
| CPodesSystem | This abstract class defines the system to be integrated with SimTK CPodes |
| Curium | |
| Custom | The handle class Constraint::Custom (dataless) and its companion class Constraint::Custom::Implementation can be used together to define new Constraint types with arbitrary properties |
| Custom | This class can be used to define new forces |
| Custom | The handle class MobilizedBody::Custom (dataless) and its companion class MobilizedBody::Custom::Implementation can be used together to define new MobilizedBody types with arbitrary properties |
| Custom | This class can be used to define new motions |
| 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 |
| 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 |
| 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 |
| CVadjCheckPointRec | |
| Cylinder | Two mobilities -- rotation and translation along the common z axis of the inboard and outboard mobilizer frames |
| Cysteine | |
| Cytidylate | |
| CytosineBase | |
| Darmstadtium | |
| DeadMatrixView_< ELT > | This is a MatrixView_ with the additional property that we are about to delete it |
| DecorationSubsystem | This is the client-side handle class encapsulating the hidden implementation of the DecorationSubsystem |
| DecorativeBrick | This defines a rectangular solid centered at the origin and aligned with the local frame axes |
| DecorativeCircle | This defines a circle in the x-y plane, centered at the origin |
| DecorativeCylinder | This defines a cylinder centered on the origin and aligned in the y direction |
| DecorativeEllipsoid | This defines an ellipsoidal solid centered at the origin and aligned with the local frame axes |
| DecorativeFrame | This defines geometry to represent a coordinate frame |
| DecorativeGeometry | This is an abstract handle class using the PIMPL design pattern to hide the private implementation |
| DecorativeGeometryImplementation | Use this abstract class to connect your implementation of decorative geometry to the implementation-independent classes above |
| DecorativeLine | A line between two points |
| DecorativeMesh | This defines a polygonal mesh |
| DecorativeSphere | This defines a sphere centered at the origin |
| DecorativeText | This defines a text label with its base at the origin |
| DeepCopy | |
| DefaultSystemSubsystem | This is a concrete Subsystem that is part of every System |
| Deuterium | |
| DiagonalView | |
| Differentiate | This Measure operator returns the time derivative of its operand measure, or a numerical approximation of the time derivative if an analytic one is not available |
| Differentiator | Given a function f(y), where f, y or both can be vectors, calculate the derivative (gradient, Jacobian) df/dy |
| DoNothing | This ContactForceGenerator silently does nothing |
| Dubnium | |
| DuMMForceFieldSubsystem | This is a concrete subsystem that provides basic molecular mechanics functionality for coarse-grained molecules built in the SimTK framework |
| DuplicatePdbResidue | |
| Dysprosium | |
| Edge | |
| Eigen | Class to compute Eigen values and Eigen vectors of a matrix |
| Einsteinium | |
| ElasticFoundation | This ContactForceGenerator handles contact between a TriangleMesh and a variety of other geometric objects, all of which produce a TriangleMeshContact tracking object |
| ElasticFoundationForce | This class implements an elastic foundation or "bed of springs" contact model |
| Element | |
| Element | An element has (1) a tagword, (2) a map of (name,value) pairs called attributes, and (3) a list of child nodes |
| element_iterator | This is a bidirectional iterator suitable for moving forward or backward within a list of Element nodes, for writable access |
| Ellipsoid | Three mobilities -- coordinated rotation and translation along the surface of an ellipsoid fixed to the parent (inboard) body |
| EltResult< P > | |
| EltResult< P > | |
| EltResult< P > | |
| EltResult< P > | |
| EltResult< P > | |
| EltResult< P > | |
| EltResult< P > | |
| Enumeration< T > | This class defines an enumerated type |
| EnumerationSet< T > | This class provides an efficient implementation of a set for storing values of an enumerated type defined with Enumeration |
| EnumerationSetRep | This class is the internal implementation of EnumerationSet |
| Erbium | |
| ErrorCheck | This is for reporting errors occurring during execution of SimTK core methods, beyond those caused by mere improper API arguments, which should be reported with APIArgcheck instead |
| Ethane | The small hydrocarbon ethane, C2H6, which has a single torsion degree of freedom |
| Europium | |
| Event | An Event is "something that happens" during a Study that is advancing through time |
| EventHandler | An EventHandler is an object that defines an event that can occur within a system |
| EventReporter | An EventReporter is an object that defines an event that can occur within a system |
| EventTriggerInfo | This class is used to communicate between the System and an Integrator regarding the properties of a particular event trigger function |
| ExplicitEulerIntegrator | This is an Integrator based on the explicit Euler algorithm |
| Face | |
| Factor | Abstract class for performing matrix factorizations |
| FactorLU | Class for performing LU matrix factorizations |
| FactorQTZ | Class to perform a QTZ (linear least squares) factorization |
| FactorSVD | Class to compute a singular value decomposition of a matrix |
| Fermium | |
| FivePrimeRnaHydroxylGroup | Phosphate group at 5' end (beginning) of RNA |
| FivePrimeRnaPhosphateGroup | Phosphate group at 5' end (beginning) of RNA |
| Fluorine | |
| Force | This is the base class from which all Force element handle classes derive |
| ForceAndEnergy | |
| ForceSubsystem | This is logically an abstract class, more specialized than "Subsystem" but not yet concrete |
| Francium | |
| Free | Unrestricted motion for a rigid body (six mobilities) |
| FreeLine | Five mobilities, representing unrestricted motion for a body which is inertialess along its own z axis |
| Function | This abstract class defines a function to be differentiated (repeatedly) by a Differentiator object |
| Function_< T > | This abstract class represents a mathematical function that calculates a value of arbitrary type based on M real arguments |
| FunctionBased | This is a subclass of MobilizedBody::Custom which uses a set of Function objects to define the behavior of the MobilizedBody |
| Gadolinium | |
| Gallium | |
| Gaussian | This is a subclass of Random that generates numbers according to a Gaussian distribution with a specified mean and standard deviation |
| GCVSPLUtil | This class provides entry points for using the GCVSPL algorithm in terms of SimTK data types |
| GeneralContactSubsystem | This class performs collision detection for use in contact modeling |
| GeneralForceSubsystem | This is a concrete subsystem which can apply arbitrary forces to a MultibodySystem |
| Germanium | |
| Gimbal | Three mobilities -- unrestricted orientation modeled as a 1-2-3 body-fixed Euler angle sequence |
| GlobalDamper | A general energy "drain" on the system |
| Glutamate | |
| Glutamine | |
| Glycine | |
| Gold | |
| GradientFunction | Derive a concrete class from this one if you have a scalar function of multiple variables that you want to differentiate |
| Gravity | This force element represents a uniform gravitational field applied to a set of bodies |
| GrinPointer< PointeeType > | |
| Ground | This is a Body representing something immobile, of effectively infinite mass and inertia, that cannot be modified to be anything else |
| Ground | This is a special type of "mobilized" body used as a placeholder for Ground in the 0th slot for a MatterSubsystem's mobilized bodies |
| GuanineBase | |
| Guanylate | |
| Guts | This is the declaration for the Study::Guts class, the abstract object to which a Study handle points |
| Guts | The abstract parent of all Subsystem "Guts" implementation classes |
| Guts | This is the declaration for the System::Guts class, the abstract object to which a System handle points |
| Guts | Public declaration of internals for ForceSubsystem extension |
| Gyration_< P > | A Gyration matrix is a unit-mass inertia matrix; you can convert it to an Inertia by multiplying it by the actual body mass |
| Hafnium | |
| HalfSpace | This ContactGeometry subclass represents an object that occupies the entire half-space x>0 |
| HalfSpaceImpl | |
| HalfSpaceSphere | This algorithm detects contacts between a ContactGeometry::HalfSpace and a ContactGeometry::Sphere |
| HalfSpaceSphere | This ContactTracker handles contacts between a ContactGeometry::HalfSpace and a ContactGeometry::Sphere, in that order |
| HalfSpaceTriangleMesh | This algorithm detects contacts between a ContactGeometry::HalfSpace and a ContactGeometry::TriangleMesh |
| HalfSpaceTriangleMesh | This ContactTracker handles contacts between a ContactGeometry::HalfSpace and a ContactGeometry::TriangleMesh, in that order |
| Hassium | |
| Helium | |
| Hermitian | This is the default commitment for a Hermitian (*not* symmetric) matrix |
| HertzCircular | This ContactForceGenerator handles contact between non-conforming objects that meet at a point and generate a circular contact patch; those generate a PointContact tracking object |
| Histidine | |
| HNAminoAcidResidue | AminoAcidResidue differs from HNAminoAcidResidue in lacking "HN" proton, so Proline can be derived |
| Holmium | |
| HuntCrossleyContact | This is a concrete subsystem that handles simple, frictionless contact situations with a model due to Hunt & Crossley: K |
| HuntCrossleyForce | This class models the forces generated by simple point contacts, such as between two spheres, or a sphere and a half space |
| Hydrogen | |
| IllegalLapackArg | |
| Implementation | The abstract parent of all Measure Implementation classes |
| Implementation | This is the base Implementation class for all Measures whose value type is known |
| Implementation | |
| Implementation | |
| Implementation | |
| Implementation | |
| Implementation | |
| Implementation | |
| Implementation | |
| Implementation | |
| Implementation | |
| Implementation | |
| Implementation | |
| Implementation | This is the abstract base class for Custom Motion implementations |
| Implementation | |
| Implementation | |
| Implementation | |
| IncompatibleValues | |
| IncorrectArrayLength | |
| IndexOutOfRange | |
| Indium | |
| Inertia_< P > | The physical meaning of an inertia is the distribution of a rigid body's mass about a particular point |
| Integrate | |
| Integrator | An Integrator is an object that can simulate the behavior of a System through time |
| InverseRotation_< P > | ----------------------------------------------------------------------------- This InverseRotation class is the inverse of a Rotation See the Rotation class for information |
| InverseTransform_< P > | Transform from frame B to frame F, but with the internal representation inverted |
| Iodine | |
| Iridium | |
| Iron | |
| Isoleucine | |
| iterator | This class provides an interface for iterating over the content of an EnumerationSet |
| iterator | This class provides an interface for iterating over the set of all possible enumerated values |
| JacobianFunction | Derive a concrete class from this one if you have a set of functions (i.e., a vector-valued function) of multiple variables that you want to differentiate |
| Kabsch78 | |
| Krypton | |
| Lanthanum | |
| Lapack | |
| LapackFull | Predefined MatrixCharacter for an ordinary Lapack-style full matrix of a particular dimension m x n (nrows X ncols) |
| Lawrencium | |
| Lead | |
| Leucine | |
| LigandDroplet | |
| Linear | This is a rigid body in the shape of a line, which is inherently inertialess about its axis |
| Linear | This is a Function_ subclass whose output value is a linear function of its arguments: f(x, y, |
| LinearBushing | This force element represents a bushing acting to connect a frame F fixed on one body (B1) to a frame M fixed on a second body (B2), by a massless, compliant element with linear stiffness and damping properties |
| LineOrientation | Two mobilities, representing unrestricted orientation for a body which is inertialess along its own z axis |
| Lithium | |
| LithiumIon | Li+ lithium ion with +1 charge |
| LocalEnergyMinimizer | This class performs local potential energy minimization of a MultibodySystem |
| Lutetium | |
| Lysine | |
| Magnesium | |
| MagnesiumIon | Mg2+ magnesium ion with +2 charge |
| Manganese | |
| Markers | This AssemblyCondition specifies a correspondence between stations on mobilized bodies ("markers") and fixed ground-frame locations ("observations") |
| Mask | |
| Mask | Use this class to represent sets of acceptable values for each of the storage attributes (packing, position, order, diagonal) |
| Mask | |
| Mask | Use this class to represent a set of acceptable Condition values |
| Mask | This class collects masks of each characteristic type for representing sets of accceptable characteristics |
| MassCenterMotionRemover | This is an event handler that can remove from a molecular system any unwanted "rigid body" motion of the sytem as a whole |
| Massless | This is a Body that is constitutively massless (and inertialess); meaning that no amount of fiddling with it will ever give it any mass or inertia |
| MassProperties | This class contains the mass, center of mass, and inertia of a rigid body B |
| Mat< M, N, ELT, CS, RS > | CS is total spacing between columns in memory (default M) RS is total spacing between rows in memory (default 1) |
| Matrix_< ELT > | This is the Matrix class intended to appear in user code |
| MatrixBase< ELT > | Variable-size 2d matrix of Composite Numerical Type (ELT) elements |
| MatrixCharacter | A MatrixCharacter is a set containing a value for each of the matrix characteristics except element type, which is part of the templatized declaration of a Matrix, Vector, or RowVector handle |
| MatrixCommitment | A MatrixCommitment provides a set of acceptable matrix characteristics |
| MatrixCondition | Matrix "condition" is a statement about the numerical characteristics of a Matrix |
| MatrixHelper< S > | Here we define class MatrixHelper<S>, the scalar-type templatized helper class for the more general, composite numerical type-templatized class MatrixBase<ELT> |
| MatrixOutline | Matrix "outline" refers to the characteristic relationship between the number of rows and columns of a matrix, without necessarily specifying the absolute dimensions |
| MatrixStorage | Matrix "storage" refers to the physical layout of data in the computer’s memory |
| MatrixStructure | Matrix "structure" refers to an inherent mathematical (or at least algorithmic) characteristic of the matrix rather than a storage strategy |
| MatrixView_< ELT > | This class is identical to a Matrix_; it is used only to manage the C++ rules for when copy constructors are called by introducing a separate type to prevent certain allowed optimizations from occuring when we don't want them |
| Measure_< T > | This is the base handle class for all Measures whose value type is known |
| Measure_Differentiate_Result< T > | |
| Meitnerium | |
| Mendelevium | |
| Mercury | |
| Methane | The simplest hydrocarbon methane, CH4 |
| Methionine | |
| MethyleneGroup | MethyleneGroup is -CH2- group for bonding to aliphatic carbon and a second something |
| MethylGroup | MethylGroup is CH3 for attaching to aliphatic carbon |
| Minimum | This Measure tracks the minimum value attained by its source operand since the last initialize() call |
| Minus | This Measure is the difference of two Measures of the same type T |
| MobilityConstantForce | A constant (scalar) "force" f applied to a mobility |
| MobilityLinearDamper | A linear damper on a mobility coordinate |
| MobilityLinearSpring | A linear spring along or around a mobility coordinate |
| MobilizedBody | This is the base class for all MobilizedBody classes, just a handle for the underlying hidden implementation |
| MolecularMechanicsSystem | This is a particular kind of MultibodySystem, one intended for use in molecular mechanics (MM) |
| Molecule | Base class for complete covalently connected molecules |
| Molybdenum | |
| Motion | A Motion object belongs to a particular mobilizer and specifies how the associated motion is to be calculated |
| MultibodyDynamicsStudy | |
| MultibodySystem | The job of the MultibodySystem class is to coordinate the activities of various subsystems which can be part of a multibody system |
| N_Vector_Ops_SimTK | |
| N_Vector_SimTK | |
| N_VectorContent_SimTK | |
| Narrowest< R1, R2 > | This class is specialized for all 36 combinations of standard types (that is, real and complex types in each of three precisions) and has typedefs "Type" which is the appropriate "narrowed" type for use when R1 & R2 appear in an operation together where the result must be of the narrower precision, and "Precision" which is the expected precision of the result (float, double, long double) |
| Narrowest< complex< R1 >, complex< R2 > > | |
| Narrowest< complex< R1 >, R2 > | |
| Narrowest< double, double > | |
| Narrowest< double, float > | |
| Narrowest< double, long double > | |
| Narrowest< float, double > | |
| Narrowest< float, float > | |
| Narrowest< float, long double > | |
| Narrowest< long double, double > | |
| Narrowest< long double, float > | |
| Narrowest< long double, long double > | |
| Narrowest< R1, complex< R2 > > | |
| negator< NUMBER > | Negator<N>, where N is a number type (real, complex, conjugate), is represented in memory identically to N, but behaves as though multiplied by -1, though at zero cost |
| Neodymium | |
| Neon | |
| Neptunium | |
| Nickel | |
| Niobium | |
| Nitrogen | |
| NMethylAmideResidue | Neutral C-terminal protein cap |
| Nobelium | |
| Node | Abstract handle for holding any kind of node in an XML tree |
| node_iterator | This is a bidirectional iterator suitable for moving forward or backward within a list of Nodes, for writable access |
| NoseHooverThermostat | |
| NoSlip1D | One non-holonomic constraint equation |
| NotPositiveDefinite | |
| NTraits< N > | |
| NTraits< complex< R > > | Partial specialization for complex numbers -- underlying real R is still a template parameter |
| NTraits< conjugate< R > > | |
| OBBTreeNode | This class represents a node in the Oriented Bounding Box Tree for a TriangleMesh |
| OBBTreeNodeImpl | |
| ObservedPointFitter | This class attempts to find the configuration of an internal coordinate model which best fits a set of observed data |
| One | This creates a Measure::Constant whose value is always T(1) and can't be changed |
| OperationNotAllowedOnNonconstReadOnlyView | |
| OperationNotAllowedOnOwner | |
| OperationNotAllowedOnView | |
| Optimizer | API for SimTK Simmath's optimizers |
| OptimizerFailed | |
| OptimizerSystem | Abstract class which defines an objective/cost function which is optimized by and Optimizer object |
| OrientedBoundingBox | This class represents a rectangular box with arbitrary position and orientation |
| Osmium | |
| Oxygen | |
| P12 | |
| PairIterator | |
| Palladium | |
| Parallel2DExecutor | This class is used for performing multithreaded computations over two dimensional ranges |
| ParallelExecutor | This class is used for performing multithreaded computations |
| Particle | This kind of body can only represent an inertialess point mass, with mass center at (0,0,0) in the local frame |
| Pathname | This class encapsulates the handling of file and directory pathnames in a platform-independent manner |
| PdbAtom | One atom, which may have more than one location, in the case of static or dynamic disorder in an X-ray structure |
| PdbAtomLocation | Location information for a PdbAtom, corresponding to one altLoc for a PdbAtom |
| PdbChain | One molecule in a PDB structure |
| 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 |
| PDBReader | This class parses PDB files, then constructs Systems and States based on them for use in Simbody |
| PdbResidue | One residue in a protein or nucleic acid, or a single molecule in the case of non-polymer structures |
| PdbResidueId | Composite key for residue within a chain, composed of residue number and insertion code |
| PdbStructure | Complete PDB file, possibly including multiple MODELS, in the case of NMR structures or molecular dynamics trajectories |
| PeriodicEventHandler | PeriodicEventHandler is a subclass of ScheduledEventHandler which generates a series of uniformly spaced events at regular intervals |
| PeriodicEventReporter | PeriodicEventReporter is a subclass of ScheduledEventReporter which generates a series of uniformly spaced events at regular intervals |
| PeriodicPdbWriter | Writes atomic coordinates in PDB format to a file stream at specified intervals during a simulation |
| PeriodicVmdReporter | Writes atomic coordinates in PDB format to a file stream at specified intervals during a simulation |
| Phenylalanine | |
| PhiMatrix | |
| PhiMatrixTranspose | |
| Phosphorus | |
| PIMPLHandle< HANDLE, IMPL, PTR > | This class provides some infrastructure useful in making SimTK Private Implementation (PIMPL) classes |
| PIMPLImplementation< HANDLE, IMPL > | This class provides some infrastructure useful in creating PIMPL Implementation classes (the ones referred to by Handles) |
| Pin | One mobility -- rotation about the common z axis of the inboard and outboard mobilizer frames |
| Planar | Three mobilities -- z rotation and x,y translation |
| Platinum | |
| Plugin | This is the base class for representing a runtime-linked dynamic library, also known as a "plugin", in a platform-independent manner |
| Plus | This Measure is the sum of two Measures of the same type T |
| Plutonium | |
| PointContact | This subclass of Contact represents a symmetric contact centered at a single point, such as between two spheres or a sphere and a half space |
| PointContactImpl | This is the internal implementation class for PointContact |
| PointInPlane | One constraint equation |
| PointOnLine | Two constraint equations |
| Polonium | |
| PolygonalMesh | This class provides a description of a mesh made of polygonal faces |
| Polynomial | This is a Function_ subclass whose output value is a polynomial of its argument: f(x) = ax^n+bx^(n-1)+ |
| PolynomialRootFinder | This class provides static methods for finding the roots of polynomials |
| Potassium | |
| PotassiumIon | K+ potassium ion with +1 charge |
| Praseodymium | |
| PrescribedMotion | This is a subclass of Constraint::Custom which uses a Function to prescribe the behavior of a single generalized coordinate as a function of time |
| PrimaryAmineGroup | PrimaryAmineGroup is NH3+ for attachment to tetrahedral carbon |
| ProjectOptions | |
| Proline | |
| Promethium | |
| Protactinium | |
| Protein | |
| PseudorotationMobilizer | |
| pthread_once_t_ | |
| ptw32_cleanup_t | |
| ptw32_handle_t | |
| PurineBaseCore | |
| PyrimidineBaseCore | |
| QuadrivalentAtom | Base class for atoms having exactly four covalent bonds |
| Quaternion_< P > | A Quaternion is a Vec4 with the following behavior:
- its length is always 1 (or else it is all NaN)
- it is equivalent to an angle/axis rotation for angle a, axis unit vector v, as: q = [ cos(a/2) sin(a/2)*v ] A quaternion is in "canonical form" when its first element is nonnegative
|
| QValue | This AssemblyCondition requests that a particular generalized coordinate end up with a specified value |
| Radium | |
| Radon | |
| Random | This class defines the interface for pseudo-random number generators |
| RealizeCheckFailed | |
| RealizeTopologyMustBeCalledFirst | |
| ResidueInfo | |
| Result< P > | |
| Result< P > | |
| Result< P > | |
| Result< P > | |
| Result< P > | |
| Result< P > | |
| Result< P > | |
| Result< P > | |
| Rhenium | |
| Rhodium | |
| RibonucleosideResidue | |
| RibonucleotideResidue | |
| RiboseCore | |
| RiboseNu3Mobilizer | |
| Rigid | A general rigid body |
| RigidUnit | |
| RNA | |
| RnaPhosphodiesterLinkage | |
| Rod | This constraint consists of one constriant equation that enforces a constant distance between a point on one body and a point on another body |
| Roentgenium | |
| Rotation_< P > | The Rotation class is a Mat33 that guarantees that the matrix is a legitimate 3x3 array associated with the relative orientation of two right-handed, orthogonal, unit vector bases |
| Row< N, ELT, STRIDE > | Generic Row |
| RowVector | This is the default commitment for a row vector |
| RowVector | Predefined MatrixCharacter for an ordinary row vector of a particular size |
| RowVector_< ELT > | RowVectors are much less common than Vectors |
| RowVectorBase< ELT > | This is a dataless rehash of the MatrixBase class to specialize it for RowVectors |
| RowVectorView_< ELT > | This class is identical to a RowVector_; it is used only to manage the C++ rules for when copy constructors are called by introducing a separate type to prevent certain allowed optimizations from occuring when we don't want them |
| RTraits< R > | RTraits is a helper class for NTraits |
| RTraits< double > | |
| RTraits< float > | |
| RTraits< long double > | |
| Rubidium | |
| RubidiumIon | Rb+ rubidium ion with +1 charge |
| RungeKutta3Integrator | This is a 3rd order Runge-Kutta Integrator using coefficents from J.C |
| RungeKuttaFeldbergIntegrator | |
| RungeKuttaMersonIntegrator | |
| Ruthenium | |
| Rutherfordium | |
| Samarium | |
| SampleAndHold | This is a Measure operator which, upon occurrence of a designated event, samples its source Measure and then holds its value in a discrete state variable until the next occurrence of the event |
| ScalarFunction | Derive a concrete class from this one if you have a scalar function of a single scalar variable that you want to differentiate |
| Scale | This Measure multiplies some other Measure by a Real scale factor |
| Scandium | |
| sched_param | |
| ScheduledEventHandler | ScheduledEventHandler is a subclass of EventHandler for events that occur at a particular time that is known in advance |
| ScheduledEventReporter | ScheduledEventReporter is a subclass of EventReporter for events that occur at a particular time that is known in advance |
| Screw | One mobility -- coordinated rotation and translation along the common z axis of the inboard and outboard mobilizer frames |
| Seaborgium | |
| Selenium | |
| Serine | |
| SetHandle | |
| ShallowCopy | |
| Silicon | |
| Silver | |
| SimbodyMatterSubsystem | The Simbody low-level multibody tree interface |
| SimbodyMatterSubtree | A SimbodyMatterSubtree is a view of a connected subgraph of the tree of mobilized bodies in a SimbodyMatterSubsystem |
| SimbodyMatterSubtreeResults | |
| SimTK_double_complex | |
| SimTK_float_complex | |
| SingleAtom | Base class for single-atom Compound building blocks |
| SingularMatrix | |
| Sinusoid | This measure produces a sinusoidal function of time: |
| Sinusoid | Prescribe position, velocity, or acceleration motion as a sinusoidal function of time, m(t) = a * sin( w*t + p ) |
| SinusoidFunction | Implements a simple functional relationship, y = amplitude * sin(x - phase) |
| SizeOutOfRange | |
| SizeWasNegative | |
| SkewHermitian | This is the default commitment for a skew Hermitian (*not* skew symmetric) matrix |
| SkewSymmetric | This is the default commitment for skew symmetric (*not* skew Hermitian) matrix |
| Slider | One mobility -- translation along the common x axis of the inboard and outboard mobilizer frames |
| Sodium | |
| SodiumIon | Na+ sodium ion with +1 charge |
| SpatialInertia_< P > | A spatial inertia contains the mass, center of mass point, and inertia matrix for a rigid body |
| SpbcgMemRec | |
| SpeedCoupler | This is a subclass of Constraint::Custom which uses a Function object to define a nonholonomic (velocity) constraint |
| Sphere | This ContactGeometry subclass represents a sphere centered at the origin |
| SphereImpl | |
| SphereSphere | This ContactTracker handles contacts between two ContactGeometry::Sphere objects |
| SphereSphere | This algorithm detects contacts between two ContactGeometry::Sphere objects |
| SphereTriangleMesh | This algorithm detects contacts between a ContactGeometry::Sphere and a ContactGeometry::TriangleMesh |
| SphereTriangleMesh | This ContactTracker handles contacts between a ContactGeometry::Sphere and a ContactGeometry::TriangleMesh, in that order |
| SphericalCoords | Three mobilities -- body fixed 3-2 (z-y) rotation followed by translation along body z or body x |
| Spline_< T > | This class implements a non-uniform B-spline curve |
| SplineFitter< T > | Given a set of data points, this class creates a Spline_ which interpolates or approximates them |
| SplineFitterImpl | |
| SplineImpl | |
| SptfqmrMemRec | |
| StableArray< T > | StableArray<T> is like std::vector<T> (or SimTK::Array_<T>) but more stable in two ways:
- the addresses of the inserted items never change, even if the array has to be resized, and
- the index of an inserted item never changes either
|
| Stage | This class is basically a glorified enumerated type, type-safe and range checked but permitting convenient (if limited) arithmetic |
| StageIsWrong | |
| StageOutOfRange | |
| StageTooHigh | |
| StageTooLow | |
| State | This is the handle class for the hidden State implementation |
| Steady | This non-holonomic Motion object imposes a constant rate on all mobilities |
| Step | This is a Function_ subclass whose output value y=f(x) is smoothly stepped from y=y0 to y1 as its input argument goes from x=x0 to x1 |
| String | SimTK::String is a plug-compatible std::string replacement (plus some additional functionality) intended to be suitable for passing through the SimTK API without introducing binary compatibility problems the way std::string does, especially on Windows |
| Strontium | |
| Study | |
| SubMat< MM, NN > | |
| Substitute< P > | |
| Substitute< P > | |
| Substitute< P > | |
| Substitute< P > | |
| Substitute< P > | |
| Substitute< P > | |
| Substitute< P > | |
| Substitute< P > | |
| Subsystem | The abstract parent of all Subsystems |
| Subtest | Internal utility class for generating test messages for subtests |
| Sulfur | |
| SymMat< M, ELT, RS > | RS is total spacing between rows in memory (default 1) |
| Symmetric | This is the default commitment for a symmetric (*not* Hermitian) matrix |
| System | The handle class which serves as the abstract parent of all System handles |
| Tantalum | |
| Task | Concrete subclasses of this abstract class represent tasks that can be executed by a ParallelExecutor |
| Task | Concrete subclasses of this abstract class represent tasks that can be executed by a Parallel2DExecutor |
| Technetium | |
| Tellurium | |
| Terbium | |
| Test | This is the main class to support testing |
| Text | This is the "leaf" content of an element |
| TextDataEventReporter | This is an EventReporter which prints out numeric data at regular intervals in tabular form |
| Thallium | |
| Thermostat | This is a feedback-controlled force that uses Nose'-Hoover chains to maintain a particular temperature Tb, as though the system were immersed in an infinite heat bath at that temperature |
| Thorium | |
| ThreadLocal< T > | This class represents a "thread local" variable: one which has a different value on each thread |
| ThreePrimeRnaHydroxylGroup | Phosphate group at 3' end (beginning) of RNA |
| ThreePrimeRnaPhosphateGroup | Phosphate group at 3' end (end) of RNA |
| Threonine | |
| ThrowError | This ContactForceGenerator throws an error if it is every invoked |
| Thulium | |
| Time | This creates a Measure::Time whose value is always T(time) |
| timespec | |
| TimeStepper | This class uses an Integrator to advance a System through time |
| Tin | |
| Titanium | |
| Transform_< P > | This class represents the rotate-and-shift transform which gives the location and orientation of a new frame F in a base (reference) frame B |
| TransformAndResidual | |
| Translation | Three translational mobilities |
| TransposeView | |
| TriangleMesh | This ContactGeometry subclass represents an arbitrary shape described by a mesh of triangular faces |
| TriangleMeshContact | This subclass of Contact is used when one or both of the ContactGeometry objects is a TriangleMesh |
| TriangleMeshContactImpl | This is the internal implementation class for TriangleMeshContact |
| TriangleMeshImpl | |
| TriangleMeshTriangleMesh | This algorithm detects contacts between two ContactGeometry::TriangleMesh objects |
| TriangleMeshTriangleMesh | This ContactTracker handles contacts between two ContactGeometry::TriangleMesh surfaces |
| Triangular | This is the default commitment for a triangular matrix |
| TriggeredEventHandler | TriggeredEventHandler is a subclass of EventHandler for events that occur when some condition is satisfied within the system |
| TriggeredEventReporter | TriggeredEventReporter is a subclass of EventReporter for events that occur when some condition is satisfied within the system |
| TrivalentAtom | Base class for atoms having exactly three covalent bonds |
| Tryptophan | |
| Tungsten | |
| TwoNMethylGuanidineGroup | |
| TwoNMethylGuanineBaseGroup | |
| TwoNMethylGuanylate | |
| TwoPointConstantForce | A constant force f (a signed scalar) which acts along the line between two points, specified as a station on each of two bodies |
| TwoPointLinearDamper | A force which resists changes in the distance between two points, acting along the line between those points |
| TwoPointLinearSpring | A linear spring between two points, specified as a station on each of two bodies |
| Tyrosine | |
| UndefinedAminoAcidResidue | |
| UndefinedPdbChainId | |
| Uniform | This is a subclass of Random that generates numbers uniformly distributed within a specified range |
| UniformGravity | A uniform gravitational force applied to every body in the system |
| UnimplementedVirtualMethod | |
| UnitRow< P, S > | This type is used for the transpose of UnitVec, and as the returned row type of a Rotation |
| UnitVec< P, S > | This class is a Vec3 plus an ironclad guarantee either that:
- the length is one (to within a very small tolerance), or
- all components are NaN
|
| UnivalentAtom | Base class for atoms with exaclty one covalent bond partner |
| Universal | Two mobilities -- rotation about the x axis, followed by a rotation about the new y axis |
| Unknown | This is something we don't understand but can carry around |
| UnrecognizedParameter | |
| UntrackedContact | This subclass of Contact represents a pair of contact surfaces that are not yet being tracked; there is no ContactId for them |
| UntrackedContactImpl | This is the internal implementation class for UntrackedContact |
| Ununbium | |
| Ununhexium | |
| Ununpentium | |
| Ununquadium | |
| Ununtrium | |
| UracilBase | |
| Uranium | |
| Uridylate | |
| UserFunction< T > | This template class defines a standard interface for objects that calculate a function based on a System and State for use in a TextDataEventReporter |
| Valine | |
| Value< T > | Templatized version of the abstract class, providing generic type-specific functionality that does not require specialization, with automatic conversion to the underlying type |
| ValueOutOfRange | |
| ValueWasNegative | |
| Vanadium | |
| VanDerWaalsForce | |
| VanderWallSphere | |
| Variable | This creates a Measure whose value is a discrete State variable of any type T |
| VdwAtom | |
| Vec< M, ELT, STRIDE > | Generic Vec |
| Vec3Pair | Matched pair of 3D vectors to be used in least-squares superposition |
| Vector | This is the default commitment for a column vector |
| Vector | Predefined MatrixCharacter for an ordinary column vector of a particular size |
| Vector_< ELT > | This is the Vector class intended to appear in user code |
| VectorBase< ELT > | This is a dataless rehash of the MatrixBase class to specialize it for Vectors |
| VectorIterator< ELT, VECTOR_CLASS > | This is an iterator for iterating over the elements of a Vector |
| VectorView_< ELT > | This class is identical to a Vector_; it is used only to manage the C++ rules for when copy constructors are called by introducing a separate type to prevent certain allowed optimizations from occuring when we don't want them |
| 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 |
| VerletIntegrator | This is an Integrator based on the velocity Verlet algorithm |
| Vertex | |
| VmdConnection | |
| VmdFloat3 | |
| VoxelHash< T > | |
| VoxelIndex | |
| VTKEventReporter | This is an EventReporter that makes it easy to generate on-screen movies of any simulation |
| VTKVisualizer | |
| WallSphere | |
| Water | |
| WaterDroplet | |
| Weld | Six constraint equations |
| Weld | Zero mobilities |
| Wider< R1, R2 > | |
| Wider< double, double > | |
| Wider< double, float > | |
| Wider< double, long double > | |
| Wider< float, double > | |
| Wider< float, float > | |
| Wider< float, long double > | |
| Wider< long double, double > | |
| Wider< long double, float > | |
| Wider< long double, long double > | |
| Widest< R1, R2 > | This class is specialized for all 36 combinations of standard types (that is, real and complex types in each of three precisions) and has typedefs "Type" which is the appropriate "widened" type for use when R1 & R2 appear in an operation together, and "Precision" which is the wider precision (float,double,long double) |
| Widest< complex< R1 >, complex< R2 > > | |
| Widest< complex< R1 >, R2 > | |
| Widest< double, double > | |
| Widest< double, float > | |
| Widest< double, long double > | |
| Widest< float, double > | |
| Widest< float, float > | |
| Widest< float, long double > | |
| Widest< long double, double > | |
| Widest< long double, float > | |
| Widest< long double, long double > | |
| Widest< R1, complex< R2 > > | |
| XCoordinateAxis | |
| Xenon | |
| Xml | This class provides a minimalist capability for reading and writing XML documents, as files or strings |
| XTypeAxis | |
| YCoordinateAxis | |
| Ytterbium | |
| Yttrium | |
| YTypeAxis | |
| ZCoordinateAxis | |
| Zero | This creates a Measure::Constant whose value is always T(0) and can't be changed |
| ZeroFunction | Function f(x) = 0 for all x |
| ZeroLeadingCoefficient | This is an exception which is thrown by all of the PolynomialRootFinder::findRoots() methods |
| Zinc | |
| ZincIon | Zn2+ zinc ion with +2 charge |
| Zirconium | |
| ZTypeAxis | |
