RiboseMobilizer.h

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/* -------------------------------------------------------------------------- *
 *                      SimTK Core: SimTK Simbody(tm)                         *
 * -------------------------------------------------------------------------- *
 * This is part of the SimTK Core biosimulation toolkit originating from      *
 * Simbios, the NIH National Center for Physics-Based Simulation of           *
 * Biological Structures at Stanford, funded under the NIH Roadmap for        *
 * Medical Research, grant U54 GM072970. See https://simtk.org.               *
 *                                                                            *
 * Portions copyright (c) 2008 Stanford University and the Authors.           *
 * Authors: Christopher Bruns                                                 *
 * Contributors: Ajay Seth                                                    *
 *                                                                            *
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 * copy of this software and associated documentation files (the "Software"), *
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 * Software is furnished to do so, subject to the following conditions:       *
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 * The above copyright notice and this permission notice shall be included in *
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 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
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#ifndef SimTK_RIBOSE_MOBILIZER_H_
#define SimTK_RIBOSE_MOBILIZER_H_

#include "SimTKsimbody.h"
#include "molmodel/internal/common.h"
#include "molmodel/internal/units.h"
#include <cmath>

namespace SimTK {

class ZeroFunction : public Function::Constant {
public:
    ZeroFunction() : Function::Constant(0, 0) {}
};

class SimTK_MOLMODEL_EXPORT SinusoidFunction : public Function {
private:
    Angle amplitude;
    Angle phase;
public:

    //Default constructor
    SinusoidFunction()
        : amplitude(1.0), phase(0.0*Deg2Rad) {}
    
    //Convenience constructor to specify the slope and Y-intercept of the linear r
    SinusoidFunction(Angle amp, Angle phi)
    : amplitude(amp), phase(phi) {}
    
    Real calcValue(const Vector& x) const{
        return amplitude*std::sin(x[0] - phase);
    }
    
    Real calcDerivative(const Array_<int>& derivComponents, const Vector& x) const{
        Real deriv = 0;
    
        assert(1 == x.size());
        
        // Derivatives 1, 5, 9, 13, ... are cos()
        if      ( 1 == (derivComponents.size() % 4) ){
            deriv = amplitude*std::cos(x[0] - phase);
        }
        // Derivatives 2, 6, 10, 14, ... are -sin()
        else if ( 2 == (derivComponents.size() % 4) ){
            deriv = -amplitude*std::sin(x[0] - phase);
        }
        // Derivatives 3, 7, 11, 15, ... are -cos()
        else if ( 3 == (derivComponents.size() % 4) ){
            deriv = -amplitude*std::cos(x[0] - phase);
        }
        // Derivatives 0, 4, 8, 12, ... are sin()
        else if ( 0 == (derivComponents.size() % 4) ){
            deriv = amplitude*std::sin(x[0] - phase);
        }
        else assert(false);
        
        return deriv;
    }
    
    int getArgumentSize() const{
        return 1;
    }
    
    int getMaxDerivativeOrder() const{
        return 1000;
    }
};
    
class SimTK_MOLMODEL_EXPORT PseudorotationMobilizer : public MobilizedBody::FunctionBased
{
public:
    PseudorotationMobilizer(
            MobilizedBody& parent,
            const Transform& inbFrame,
            const Body& body,
            const Transform& outbFrame,
            Angle amplitude,
            Angle phase
            )
    : MobilizedBody::FunctionBased(
            parent,
            inbFrame,
            body,
            outbFrame,
            1,
            createFunctions(amplitude, phase),
            createCoordIndices() // TODO ask Ajay
            )
    {}  
    
private:
    
    static std::vector< const Function* > createFunctions(Angle amplitude, Angle phase);
    static std::vector< std::vector<int> > createCoordIndices();    
    
};


class SimTK_MOLMODEL_EXPORT RiboseNu3Mobilizer : public PseudorotationMobilizer
{
public:
    RiboseNu3Mobilizer(
            MobilizedBody& parent,
            const Transform& inbFrame,
            const Body& body,
            const Transform& outbFrame)
    : PseudorotationMobilizer(
            parent,
            inbFrame,
            body,
            outbFrame,
            36.4*Deg2Rad,
            124.8*Deg2Rad)
    {}
            
};

} // namespace SimTK

#endif