RNA.h

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#ifndef SimTK_MOLMODEL_RNA_H_
#define SimTK_MOLMODEL_RNA_H_

/* -------------------------------------------------------------------------- *
 *                      SimTK Core: SimTK Molmodel                            *
 * -------------------------------------------------------------------------- *
 * 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) 2007 Stanford University and the Authors.           *
 * Authors: Michael Sherman, Christopher Bruns                                *
 * Contributors: Samuel Flores                                                *
 *                                                                            *
 * Permission is hereby granted, free of charge, to any person obtaining a    *
 * copy of this software and associated documentation files (the "Software"), *
 * to deal in the Software without restriction, including without limitation  *
 * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
 * and/or sell copies of the Software, and to permit persons to whom the      *
 * Software is furnished to do so, subject to the following conditions:       *
 *                                                                            *
 * The above copyright notice and this permission notice shall be included in *
 * all copies or substantial portions of the Software.                        *
 *                                                                            *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
 * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
 * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
 * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
 * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
 * -------------------------------------------------------------------------- */


#include "molmodel/internal/common.h"
#include "molmodel/internal/Compound.h"

namespace SimTK {

// RiboseCore leaves 4 bond centers open:
// 1) inboard center at O5* atom, for binding 5' phosphate
// 2) 
class SimTK_MOLMODEL_EXPORT RiboseCore : public BiopolymerResidue {
public:
    RiboseCore(const String& name, const String& tlc, char olc) 
        : BiopolymerResidue(name, tlc, olc)
    {
        setBaseAtom(BivalentAtom("O5*", Element::Oxygen(), 120.90*Deg2Rad));

        bondAtom(AliphaticCarbon("C5*"), "O5*/bond2", 0.1423, 180*Deg2Rad);
        bondAtom(AliphaticHydrogen("H5*1"), "C5*/bond4");
        bondAtom(AliphaticHydrogen("H5*2"), "C5*/bond3");

        bondAtom(AliphaticCarbon("C4*"), "C5*/bond2", 0.1510); // length from (Gelbin et al 1996)
        bondAtom(AliphaticHydrogen("H4*"), "C4*/bond4");

        bondAtom(BivalentAtom("O4*", Element::Oxygen(), 112.0*Deg2Rad), "C4*/bond2", 0.1453);

        bondAtom(AliphaticCarbon("C3*"), "C4*/bond3", 0.1524);
        bondAtom(AliphaticHydrogen("H3*"), "C3*/bond4");

        bondAtom(BivalentAtom("O3*", Element::Oxygen(), 119.7*Deg2Rad), "C3*/bond2", 0.1423);
 
        bondAtom(AliphaticCarbon("C2*"), "C3*/bond3", 0.1525);
        bondAtom(AliphaticHydrogen("H2*"), "C2*/bond3");

        bondAtom(AliphaticCarbon("C1*"), "C2*/bond2", 0.1528);
        bondAtom(AliphaticHydrogen("H1*"), "C1*/bond4");

        addRingClosingBond("C1*/bond2", "O4*/bond2", 0.1414);

        // Ring strain reduces ring bond angles
        setDefaultBondAngle(109.6*Deg2Rad, "C1*", "O4*", "C4*"); 
        setDefaultBondAngle(105.5*Deg2Rad, "O4*", "C4*", "C3*"); 
        setDefaultBondAngle(102.7*Deg2Rad, "C4*", "C3*", "C2*"); 
        setDefaultBondAngle(101.5*Deg2Rad, "C3*", "C2*", "C1*"); 
        setDefaultBondAngle(106.4*Deg2Rad, "C2*", "C1*", "O4*");

        nameBondCenter("bondO5", "O5*/bond1");
        nameBondCenter("bondO3", "O3*/bond2");
        nameBondCenter("bondC1", "C1*/bond3");

        // RNA backbone dihedral angles
        // defineDihedralAngle("alpha", "bondO5", ""); // TODO requires phosphate
        //defineDihedralAngle("beta", "bondO5", "C5*/bond2");
        //defineDihedralAngle("gamma", "O5*", "C5*", "C4*", "C3*");
        //defineDihedralAngle("delta", "C5*", "C4*", "C3*", "C2*");
        //defineDihedralAngle("epsilon", "bondO3", "C3*/bond1");
        // TODO zeta requires next phosphate

        // ribose ring dihedral angles
        defineDihedralAngle( "nu0", "C4*", "O4*", "C1*", "C2*" );
        defineDihedralAngle( "nu1", "O4*", "C1*", "C2*", "C3*" );
        defineDihedralAngle( "nu2", "C1*", "C2*", "C3*", "C4*" );
        defineDihedralAngle( "nu3", "C2*", "C3*", "C4*", "O4*" );
        defineDihedralAngle( "nu4", "C3*", "C4*", "O4*", "C1*" );

        // Guestimated from Figure 2 of 
        // Schneider, B; Moravek, Z; and Berman, H.M. (2004)
        // "RNA conformational classes"
        // Nucleic Acids Research 32(5): 1666-1677
        // setDefaultDihedralAngle("alpha", -60*Deg2Rad);
        //setDefaultDihedralAngle("beta", 180*Deg2Rad);
        //setDefaultDihedralAngle("gamma", 60*Deg2Rad);
        //setDefaultDihedralAngle("delta", 80*Deg2Rad);
        //setDefaultDihedralAngle("epsilon", 190*Deg2Rad);
        // setDefaultDihedralAngle("zeta", -70*Deg2Rad);

        // nu angles selected from resdue U52 of 1EHZ
        setDefaultDihedralAngle("nu0", 2.2*Deg2Rad);
        setDefaultDihedralAngle("nu1", -24.5*Deg2Rad);
        setDefaultDihedralAngle("nu2", 35.8*Deg2Rad);
        setDefaultDihedralAngle("nu3", -35.9*Deg2Rad); // same bond as delta, different reference atoms
        setDefaultDihedralAngle("nu4", 21.6*Deg2Rad);

        nameBondCenter("bondNext", "bondO3");
        nameBondCenter("bondPrevious", "bondO5");

        setDefaultInboardBondLength(0.16100);

        // alternate atom names
        nameAtom("O5'", "O5*");
        nameAtom("C5'", "C5*");
        nameAtom("H5'", "H5*1");
        nameAtom("H5''", "H5*2");
        nameAtom("C4'", "C4*");
        nameAtom("H4'", "H4*");
        nameAtom("O4'", "O4*");
        nameAtom("C3'", "C3*");
        nameAtom("H3'", "H3*");
        nameAtom("O3'", "O3*");
        nameAtom("C2'", "C2*");
        nameAtom("H2'", "H2*");
        nameAtom("C1'", "C1*");
        nameAtom("H1'", "H1*");
    }

};


class SimTK_MOLMODEL_EXPORT FivePrimeRnaHydroxylGroup : public BiopolymerResidue
{
public:
    FivePrimeRnaHydroxylGroup(String name, String threeLetterCode = "Unk", char oneLetterCode = '?') 
    : BiopolymerResidue(name, threeLetterCode, oneLetterCode)
    {
        instantiateBiotypes();
        
        setBaseAtom( UnivalentAtom("H5T", Element::Hydrogen()) );
        
        nameBondCenter("bondNext", "H5T/bond");

        setBiotypeIndex( "H5T", Biotype::get("Hydroxyl, RNA", "H5T", SimTK::Ordinality::Initial).getIndex() );
    }
    
    static void instantiateBiotypes() 
    {
        if ( ! Biotype::exists("Hydroxyl, RNA", "H5T", SimTK::Ordinality::Initial) )
            Biotype::defineBiotype(Element::Hydrogen(), 1, "Hydroxyl, RNA", "H5T", SimTK::Ordinality::Initial);
        
        // This oxygen biotype should get applied to the 5' oxygen of the nucleotide this hydroxyl attaches to
        if ( ! Biotype::exists("Hydroxyl, RNA", "O5*", SimTK::Ordinality::Initial) )
            Biotype::defineBiotype(Element::Oxygen(), 2, "Hydroxyl, RNA", "O5*", SimTK::Ordinality::Initial);
    }
    
};


class SimTK_MOLMODEL_EXPORT FivePrimeRnaPhosphateGroup : public BiopolymerResidue
{
public:
    FivePrimeRnaPhosphateGroup(String name, String threeLetterCode = "Unk", char oneLetterCode = '?') 
    : BiopolymerResidue(name, threeLetterCode, oneLetterCode)
    {
        instantiateBiotypes();
        
        setBaseAtom( QuadrivalentAtom("P", Element::Phosphorus()) );
        
        bondAtom(UnivalentAtom("OP1", Element::Oxygen()), "P/bond4", 0.14800);
        bondAtom(UnivalentAtom("OP2", Element::Oxygen()), "P/bond3", 0.14800);
        bondAtom(UnivalentAtom("OP3", Element::Oxygen()), "P/bond2", 0.14800);
        
        nameBondCenter("bondNext", "P/bond1");

        setBiotypeIndex( "P", Biotype::get("Phosphate, RNA", "P", SimTK::Ordinality::Initial).getIndex() );
        setBiotypeIndex( "OP1", Biotype::get("Phosphate, RNA", "OP", SimTK::Ordinality::Initial).getIndex() );
        setBiotypeIndex( "OP2", Biotype::get("Phosphate, RNA", "OP", SimTK::Ordinality::Initial).getIndex() );
        setBiotypeIndex( "OP3", Biotype::get("Phosphate, RNA", "OP", SimTK::Ordinality::Initial).getIndex() );
    }
    
    static void instantiateBiotypes() 
    {
        if ( ! Biotype::exists("Phosphate, RNA", "P", SimTK::Ordinality::Initial) )
            Biotype::defineBiotype(Element::Phosphorus(), 4, "Phosphate, RNA", "P", SimTK::Ordinality::Initial);
        if ( ! Biotype::exists("Phosphate, RNA", "OP", SimTK::Ordinality::Initial) )
            Biotype::defineBiotype(Element::Oxygen(), 1, "Phosphate, RNA", "OP", SimTK::Ordinality::Initial);
    }
    
};


// Phosphodiester linkage between two RNA nucleotides
class SimTK_MOLMODEL_EXPORT RnaPhosphodiesterLinkage : public BiopolymerResidue
{
public:
    RnaPhosphodiesterLinkage(String name, String threeLetterCode = "Unk", char oneLetterCode = '?') 
        : BiopolymerResidue(name, threeLetterCode, oneLetterCode)
    {
        instantiateBiotypes();

        // TODO - set bond angles: 102.6 between ether oxygens, 119.9 between lone oxygen, 108.23 between mismatched pairs
        setBaseAtom( QuadrivalentAtom("P", Element::Phosphorus() 
                   ,  104.0*Deg2Rad // 03'-P-O5' from Gelbin et al
                   ,  107.9*Deg2Rad // 03'-P-OP? from Gelbin et al
                   ,  107.9*Deg2Rad // 03'-P-OP? from Gelbin et al
                   , -108.15*Deg2Rad // to make OP1-P-OP2 angle 119.6
                   ,  108.15*Deg2Rad // to make OP1-P-OP2 angle 119.6
                   ) );

        bondAtom(UnivalentAtom("OP1", Element::Oxygen()), "P/bond3", 0.14800);
        bondAtom(UnivalentAtom("OP2", Element::Oxygen()), "P/bond4", 0.14800);

        nameBondCenter("bondPrevious", "P/bond1");
        nameBondCenter("bondNext", "P/bond2");

        setDefaultInboardBondLength(0.16100);

        addCompoundSynonym("Phosphodiester, RNA");

        setBiotypeIndex("P", Biotype::get("Phosphodiester, RNA", "P").getIndex() );
        setBiotypeIndex("OP1", Biotype::get("Phosphodiester, RNA", "OP").getIndex() );
        setBiotypeIndex("OP2", Biotype::get("Phosphodiester, RNA", "OP").getIndex() );
    }
    
    
    static void instantiateBiotypes() 
    {
        if ( ! Biotype::exists("Phosphodiester, RNA", "P") )
            Biotype::defineBiotype(Element::Phosphorus(), 4, "Phosphodiester, RNA", "P");
        if ( ! Biotype::exists("Phosphodiester, RNA", "OP") )
            Biotype::defineBiotype(Element::Oxygen(), 1, "Phosphodiester, RNA", "OP");
    }
};


class SimTK_MOLMODEL_EXPORT ThreePrimeRnaHydroxylGroup : public BiopolymerResidue
{
public:
    ThreePrimeRnaHydroxylGroup(String name, String threeLetterCode = "Unk", char oneLetterCode = '?') 
    : BiopolymerResidue(name, threeLetterCode, oneLetterCode)
    {
        instantiateBiotypes();
        
        setBaseAtom( UnivalentAtom("H3T", Element::Hydrogen()) );
        
        nameBondCenter("bondNext", "H3T/bond");

        setBiotypeIndex( "H3T", Biotype::get("Hydroxyl, RNA", "H3T", SimTK::Ordinality::Final).getIndex() );
    }
    
    static void instantiateBiotypes() 
    {
        if ( ! Biotype::exists("Hydroxyl, RNA", "H3T", SimTK::Ordinality::Final) )
            Biotype::defineBiotype(Element::Hydrogen(), 1, "Hydroxyl, RNA", "H3T", SimTK::Ordinality::Final);
        
        // This oxygen biotype should get applied to the 3' oxygen of the nucleotide this hydroxyl attaches to
        if ( ! Biotype::exists("Hydroxyl, RNA", "O3*", SimTK::Ordinality::Final) )
            Biotype::defineBiotype(Element::Oxygen(), 2, "Hydroxyl, RNA", "O3*", SimTK::Ordinality::Final);
    }
    
};

class SimTK_MOLMODEL_EXPORT ThreePrimeRnaPhosphateGroup : public BiopolymerResidue
{
public:
    ThreePrimeRnaPhosphateGroup(String name, String threeLetterCode = "Unk", char oneLetterCode = '?') 
    : BiopolymerResidue(name, threeLetterCode, oneLetterCode)
    {
        instantiateBiotypes();
        
        setBaseAtom( QuadrivalentAtom("P", Element::Phosphorus()) );
        
        bondAtom(UnivalentAtom("OP1", Element::Oxygen()), "P/bond4", 0.14800);
        bondAtom(UnivalentAtom("OP2", Element::Oxygen()), "P/bond3", 0.14800);
        bondAtom(UnivalentAtom("OP3", Element::Oxygen()), "P/bond2", 0.14800);
        
        nameBondCenter("bondNext", "P/bond1");

        setBiotypeIndex( "P", Biotype::get("Phosphate, RNA", "P", SimTK::Ordinality::Final).getIndex() );
        setBiotypeIndex( "OP1", Biotype::get("Phosphate, RNA", "OP", SimTK::Ordinality::Final).getIndex() );
        setBiotypeIndex( "OP2", Biotype::get("Phosphate, RNA", "OP", SimTK::Ordinality::Final).getIndex() );
        setBiotypeIndex( "OP3", Biotype::get("Phosphate, RNA", "OP", SimTK::Ordinality::Final).getIndex() );
    }
    
    static void instantiateBiotypes() 
    {
        if ( ! Biotype::exists("Phosphate, RNA", "P", SimTK::Ordinality::Final) )
            Biotype::defineBiotype(Element::Phosphorus(), 4, "Phosphate, RNA", "P", SimTK::Ordinality::Final);
        if ( ! Biotype::exists("Phosphate, RNA", "OP", SimTK::Ordinality::Final) )
            Biotype::defineBiotype(Element::Oxygen(), 1, "Phosphate, RNA", "OP", SimTK::Ordinality::Final);
    }
    
};


// Nucleoside has sugar and base but not phosphate
class SimTK_MOLMODEL_EXPORT RibonucleosideResidue : public RiboseCore {
public:
    RibonucleosideResidue(String name, String threeLetterCode = "Unk", char oneLetterCode = '?')
        : RiboseCore(name, threeLetterCode, oneLetterCode)
    {
        // 2' hydroxyl group present in RNA but not in DNA
        bondAtom(BivalentAtom("O2*", Element::Oxygen(), 108.50*Deg2Rad), "C2*/bond4", 0.1413, -60*Deg2Rad);
        bondAtom(UnivalentAtom("2HO*", Element::Hydrogen()), "O2*/bond2", 0.0960);

        // alternate atom name
        nameAtom("O2'", "O2*");
        nameAtom("HO2'", "2HO*");
    }
    
    // Create larger residue with phosphodiester prepended
    BiopolymerResidue withPhosphodiester() const 
    {
        const RibonucleosideResidue& residue = *this;
        
        RnaPhosphodiesterLinkage po2(residue.getCompoundName(), residue.getPdbResidueName(), residue.getOneLetterCode());
        po2.bondCompound("nucleoside", residue, "bondNext");
        po2.inheritAtomNames("nucleoside");
        po2.inheritCompoundSynonyms(residue);
        po2.nameBondCenter("bondNext", "nucleoside/bondNext");

        po2.setPdbResidueNumber(residue.getPdbResidueNumber());
        po2.setPdbChainId(residue.getPdbChainId());

        po2.defineDihedralAngle("alpha", "bondPrevious", "O5*/bond2");
        po2.setDefaultDihedralAngle("alpha", 295.0*Deg2Rad); // A-RNA (Schneider et al 2004)

        return po2;
    }
};

// Nucleotide has sugar and base and phosphate
class SimTK_MOLMODEL_EXPORT RibonucleotideResidue : public RibonucleosideResidue {
public:
    // Factory method
    static RibonucleotideResidue create(char oneLetterCode);
    static RibonucleotideResidue create(const PdbResidue& pdbResidue, char chainId = ' ');

    RibonucleotideResidue(String name, String threeLetterCode = "Unk", char oneLetterCode = '?')
        : RibonucleosideResidue(name, threeLetterCode, oneLetterCode)
    {
        defineDihedralAngle("beta", "O5*/bond1", "C5*/bond2");
        setDefaultDihedralAngle("beta", 173.0*Deg2Rad); //  A-RNA (Schneider et al 2004)

        defineDihedralAngle("gamma", "C5*/bond1", "C4*/bond3");
        setDefaultDihedralAngle("gamma", 54.0*Deg2Rad); //  A-RNA (Schneider et al 2004)

        defineDihedralAngle("delta", "C4*/bond1", "C3*/bond2");
        setDefaultDihedralAngle("delta", 80.0*Deg2Rad); //  A-RNA (Schneider et al 2004)

        defineDihedralAngle("epsilon", "C3*/bond1", "O3*/bond2");
        setDefaultDihedralAngle("epsilon", 210.0*Deg2Rad); //  A-RNA (Schneider et al 2004)

        nameBondCenter("bondBase", "C1*/bond3");
    }


    class Adenylate;
    class Cytidylate;
    class Guanylate;
    class Uridylate;
    
    // Modified residues from tRNA
    class TwoNMethylGuanylate;
};


// PurineBaseCore represents the atoms in common among purine bases such as Adenine and Guanine
class PurineBaseCore : public Compound {
public:
    PurineBaseCore()
    {
        setBaseAtom( TrivalentAtom("N9",  Element::Nitrogen(), 125.8*Deg2Rad, 128.8*Deg2Rad));

        bondAtom( TrivalentAtom("C8",  Element::Carbon(),   113.9*Deg2Rad, 123.05*Deg2Rad),  "N9/bond3", 0.13710, 180*Deg2Rad,   BondMobility::Rigid );

        bondAtom( UnivalentAtom("H8",  Element::Hydrogen()),                                 "C8/bond3",  0.10800 );
        bondAtom(  BivalentAtom("N7",  Element::Nitrogen(), 103.8*Deg2Rad),                  "C8/bond2",  0.13040, 0*Deg2Rad,    BondMobility::Rigid );
        bondAtom( TrivalentAtom("C5",  Element::Carbon(),   110.4*Deg2Rad, 132.40*Deg2Rad),  "N7/bond2",  0.13910, 0*Deg2Rad,    BondMobility::Rigid );
        
        bondAtom( TrivalentAtom("C4",  Element::Carbon(),   126.2*Deg2Rad, 106.2*Deg2Rad),   "N9/bond2",  0.13740, 0*Deg2Rad,    BondMobility::Rigid );

        addRingClosingBond("C5/bond2",                                                       "C4/bond3",  0.13700, 0*Deg2Rad,    BondMobility::Rigid );

        // 114.30 is average between amber angle for guanine(111.30) and adenine(117.30)
        bondAtom( TrivalentAtom("C6",  Element::Carbon(), 114.30*Deg2Rad, 122.85*Deg2Rad),   "C5/bond3",  0.14040, 180*Deg2Rad,  BondMobility::Rigid );

        bondAtom(  BivalentAtom("N3",  Element::Nitrogen(), 118.60*Deg2Rad),                 "C4/bond2",  0.13540, 180*Deg2Rad,  BondMobility::Rigid );
        bondAtom( TrivalentAtom("C2",  Element::Carbon()),                                   "N3/bond2",  0.13240, 0*Deg2Rad,    BondMobility::Rigid );

        // Two bond centers open, inboard (N9), and C6
        nameBondCenter("bondC6", "C6/bond3");
        nameBondCenter("bondC2", "C2/bond3");
    }
};


class AdenineBase : public PurineBaseCore
{
public:
    AdenineBase()
    {
        // Lone pair on N1
        bondAtom(  BivalentAtom("N1",  Element::Nitrogen(), 118.60*Deg2Rad), "C6/bond2",  0.13390, 0*Deg2Rad, BondMobility::Rigid );
        addRingClosingBond("N1/bond2",                                       "C2/bond2",  0.13240, 0*Deg2Rad, BondMobility::Rigid);

        // Hydrogen on C2
        bondAtom( UnivalentAtom("H2",  Element::Hydrogen()),                 "bondC2",    0.10800,            BondMobility::Rigid );

        // Amine on C6
        bondAtom( TrivalentAtom("N6",  Element::Nitrogen()),                 "bondC6",    0.13400, 0*Deg2Rad, BondMobility::Rigid );
        bondAtom( UnivalentAtom("H61", Element::Hydrogen()),                 "N6/bond2",  0.10100,            BondMobility::Rigid );
        bondAtom( UnivalentAtom("H62", Element::Hydrogen()),                 "N6/bond3",  0.10100,            BondMobility::Rigid );
    }
};

class GuanineBase : public PurineBaseCore
{
public:
    GuanineBase()
    {
        // Hydrogen on N1
        bondAtom( TrivalentAtom("N1",  Element::Nitrogen(), 125.20*Deg2Rad, 116.8*Deg2Rad), "C6/bond2",  0.13880, 0*Deg2Rad, BondMobility::Rigid );
        bondAtom(UnivalentAtom("H1", Element::Hydrogen()),   "N1/bond3", 0.10100, BondMobility::Rigid);
        addRingClosingBond("N1/bond2",                       "C2/bond2",  0.13240, 0*Deg2Rad, BondMobility::Rigid);

        // Amine on C2
        bondAtom( TrivalentAtom("N2",  Element::Nitrogen()), "bondC2",    0.13400, 0*Deg2Rad, BondMobility::Rigid );
        bondAtom( UnivalentAtom("H21", Element::Hydrogen()), "N2/bond2",  0.10100,            BondMobility::Rigid );
        bondAtom( UnivalentAtom("H22", Element::Hydrogen()), "N2/bond3",  0.10100,            BondMobility::Rigid );

        // Carbonyl on C6
        bondAtom( UnivalentAtom("O6",  Element::Oxygen()),   "bondC6",    0.12290,            BondMobility::Rigid );

    }
};

class TwoNMethylGuanineBaseGroup : public PurineBaseCore
{
public:
    TwoNMethylGuanineBaseGroup() {
        addCompoundSynonym("Guanosine"); // for resolving biotypes KLUDGE
        // TODO
    }
};


// PyrimidineBaseCore represents the atoms in common among pyrimidine bases such as Cytosine, Uracil, and Thymine
class PyrimidineBaseCore : public Compound {
public:
    PyrimidineBaseCore()
    {
    }
};


class CytosineBase : public PyrimidineBaseCore
{
public:
    CytosineBase()
    {
        setBaseAtom(   TrivalentAtom("N1",  Element::Nitrogen(), 125.8*Deg2Rad, 128.8*Deg2Rad));
    //scf added temporarily
        //bondAtom( UnivalentAtom("HN1", Element::Hydrogen()), "N1/bond4", 0.1010, 0*Deg2Rad, BondMobility::Rigid);

        bondAtom( TrivalentAtom("C2", Element::Carbon(), 118.6*Deg2Rad, 120.9*Deg2Rad),  "N1/bond2", 0.1383, 180*Deg2Rad,   BondMobility::Rigid );
        bondAtom( UnivalentAtom("O2", Element::Oxygen()), "C2/bond3", 0.1229, 0*Deg2Rad, BondMobility::Rigid);

        bondAtom( BivalentAtom("N3", Element::Nitrogen(), 120.5*Deg2Rad), "C2/bond2", 0.1358, 0*Deg2Rad, BondMobility::Rigid);

        bondAtom( TrivalentAtom("C4", Element::Carbon(), 121.5*Deg2Rad, 119.3*Deg2Rad), "N3/bond2", 0.1339, 0*Deg2Rad, BondMobility::Rigid);
        bondAtom( TrivalentAtom("N4", Element::Nitrogen(), 120.0*Deg2Rad, 120.0*Deg2Rad), "C4/bond3", 0.1340, 0*Deg2Rad, BondMobility::Rigid);
        bondAtom( UnivalentAtom("H41", Element::Hydrogen()), "N4/bond2", 0.1010, 0*Deg2Rad, BondMobility::Rigid);
        bondAtom( UnivalentAtom("H42", Element::Hydrogen()), "N4/bond3", 0.1010, 0*Deg2Rad, BondMobility::Rigid);

        bondAtom( TrivalentAtom("C5", Element::Carbon(), 117.0*Deg2Rad, 119.70*Deg2Rad), "C4/bond2", 0.1433, 0*Deg2Rad, BondMobility::Rigid);
        bondAtom( UnivalentAtom("H5", Element::Hydrogen()), "C5/bond3", 0.1080, 0*Deg2Rad, BondMobility::Rigid);

        bondAtom( TrivalentAtom("C6", Element::Carbon(), 121.20*Deg2Rad, 119.70*Deg2Rad), "C5/bond2", 0.1350, 0*Deg2Rad, BondMobility::Rigid);
        bondAtom( UnivalentAtom("H6", Element::Hydrogen()), "C6/bond3", 0.1080, 0*Deg2Rad, BondMobility::Rigid);

        addRingClosingBond("C6/bond2", "N1/bond3", 0.1365, 0*Deg2Rad, BondMobility::Rigid);
    }
};

class UracilBase : public PyrimidineBaseCore
{
public:
    UracilBase()
    {
        setBaseAtom( TrivalentAtom("N1",  Element::Nitrogen(), 125.8*Deg2Rad, 128.8*Deg2Rad));

        bondAtom( TrivalentAtom("C2", Element::Carbon(), 118.6*Deg2Rad, 120.9*Deg2Rad),  "N1/bond2", 0.1383, 180*Deg2Rad,   BondMobility::Rigid );
        bondAtom( UnivalentAtom("O2", Element::Oxygen()), "C2/bond3", 0.1229, 0*Deg2Rad, BondMobility::Rigid);

        bondAtom(TrivalentAtom("N3", Element::Nitrogen(), 126.4*Deg2Rad, 116.8*Deg2Rad), "C2/bond2", 0.1358, 0*Deg2Rad, BondMobility::Rigid);
        bondAtom(UnivalentAtom("H3", Element::Hydrogen()), "N3/bond3", 0.1010, 0*Deg2Rad, BondMobility::Rigid);

        bondAtom( TrivalentAtom("C4", Element::Carbon(), 114.0*Deg2Rad, 120.6*Deg2Rad),  "N3/bond2", 0.1388, 0*Deg2Rad,   BondMobility::Rigid );
        bondAtom( UnivalentAtom("O4", Element::Oxygen()), "C4/bond3", 0.1229, 0*Deg2Rad, BondMobility::Rigid);

        bondAtom( TrivalentAtom("C5", Element::Carbon(), 120.7*Deg2Rad, 119.70*Deg2Rad), "C4/bond2", 0.1444, 0*Deg2Rad, BondMobility::Rigid);
        bondAtom( UnivalentAtom("H5", Element::Hydrogen()), "C5/bond3", 0.1080, 0*Deg2Rad, BondMobility::Rigid);

        bondAtom( TrivalentAtom("C6", Element::Carbon(), 121.20*Deg2Rad, 119.70*Deg2Rad), "C5/bond2", 0.1350, 0*Deg2Rad, BondMobility::Rigid);
        bondAtom( UnivalentAtom("H6", Element::Hydrogen()), "C6/bond3", 0.1080, 0*Deg2Rad, BondMobility::Rigid);

        addRingClosingBond("C6/bond2", "N1/bond3", 0.1365, 0*Deg2Rad, BondMobility::Rigid);
    }
};

// TODO - these should not be classes, e.g. Adenylate should be an instance of RibonucleotideResidue
class  RibonucleotideResidue::Adenylate : public RibonucleotideResidue {
public:
    Adenylate() : RibonucleotideResidue("adenylate", "A  ", 'A') 
    {
        bondCompound("base", AdenineBase(), "bondBase", 0.14750, 200*Deg2Rad, BondMobility::Torsion);
        inheritAtomNames("base");

        defineDihedralAngle("chi", "O4*", "C1*", "N9", "C4");
        setDefaultDihedralAngle("chi", 199.0*Deg2Rad);

        addCompoundSynonym("Adenosine"); // for resolving biotypes
    }
};

class  RibonucleotideResidue::Guanylate : public RibonucleotideResidue {
public:
    Guanylate() : RibonucleotideResidue("guanylate", "G  ", 'G') 
    {
        bondCompound("base", GuanineBase(), "bondBase", 0.14710, 200*Deg2Rad, BondMobility::Torsion);
        inheritAtomNames("base");

        defineDihedralAngle("chi", "O4*", "C1*", "N9", "C4");
        setDefaultDihedralAngle("chi", 199.0*Deg2Rad);

        addCompoundSynonym("Guanosine"); // for resolving biotypes
    }
};

class  RibonucleotideResidue::Cytidylate : public RibonucleotideResidue {
public:
    Cytidylate() : RibonucleotideResidue("cytidylate", "C  ", 'C') 
    {
        bondCompound("base", CytosineBase(), "bondBase", 0.14710, 200*Deg2Rad, BondMobility::Torsion);
        inheritAtomNames("base");

        defineDihedralAngle("chi", "O4*", "C1*", "N1", "C2");
        setDefaultDihedralAngle("chi", 199.0*Deg2Rad);

        addCompoundSynonym("Cytidine"); // for resolving biotypes
    }
};

class  RibonucleotideResidue::Uridylate : public RibonucleotideResidue {
public:
    Uridylate() : RibonucleotideResidue("uridylate", "U  ", 'U') 
    {
        bondCompound("base", UracilBase(), "bondBase", 0.14710, 200*Deg2Rad, BondMobility::Torsion);
        inheritAtomNames("base");

        defineDihedralAngle("chi", "O4*", "C1*", "N1", "C2");
        setDefaultDihedralAngle("chi", 199.0*Deg2Rad);

        addCompoundSynonym("Uridine"); // for resolving biotypes
    }
};


class TwoNMethylGuanidineGroup : public Compound {
public:
    TwoNMethylGuanidineGroup()
    {
        instantiateBiotypes();

        setPdbResidueName("2MG");

        setCompoundName("TwoNMethylGuanidineGroup");

        setBaseAtom( TrivalentAtom("N9", Element::Nitrogen(), 127.767*Deg2Rad, 112.885*Deg2Rad) );

        bondAtom( TrivalentAtom("C8", Element::Carbon(), 113.564*Deg2Rad, 120.934*Deg2Rad), "N9/bond2", 0.13740, 180.00*Deg2Rad, BondMobility::Rigid );
        bondAtom( BivalentAtom("N7", Element::Nitrogen(), 104.422*Deg2Rad), "C8/bond2", 0.12800, 0.02*Deg2Rad, BondMobility::Rigid );
        bondAtom( TrivalentAtom("C5", Element::Carbon(), 130.918*Deg2Rad, 112.885*Deg2Rad), "N7/bond2", 0.13760, 179.54*Deg2Rad, BondMobility::Rigid );
        bondAtom( TrivalentAtom("C6", Element::Carbon(), 131.213*Deg2Rad, 109.672*Deg2Rad), "C5/bond2", 0.14350, -0.17*Deg2Rad, BondMobility::Rigid );
        bondAtom( UnivalentAtom("O6", Element::Oxygen()), "C6/bond2", 0.11940 );
        bondAtom( TrivalentAtom("N1", Element::Nitrogen(), 126.495*Deg2Rad, 113.649*Deg2Rad), "C6/bond3", 0.14150, 0.32*Deg2Rad, BondMobility::Rigid );
        bondAtom( TrivalentAtom("C2", Element::Carbon(), 116.091*Deg2Rad, 123.417*Deg2Rad), "N1/bond2", 0.13620, 178.30*Deg2Rad, BondMobility::Rigid );
        bondAtom( TrivalentAtom("N2", Element::Nitrogen(), 116.703*Deg2Rad, 120.926*Deg2Rad), "C2/bond2", 0.13550, 20.71*Deg2Rad, BondMobility::Rigid );
        bondAtom( UnivalentAtom("1H2", Element::Hydrogen()), "N2/bond2", 0.09940 );
        bondAtom( QuadrivalentAtom("C10", Element::Carbon()), "N2/bond3", 0.14490, 176.13*Deg2Rad, BondMobility::Torsion );
        bondAtom( UnivalentAtom("H20", Element::Hydrogen()), "C10/bond2", 0.10810 );
        bondAtom( UnivalentAtom("H21", Element::Hydrogen()), "C10/bond3", 0.10850 );
        bondAtom( UnivalentAtom("H22", Element::Hydrogen()), "C10/bond4", 0.10790 );
        bondAtom( BivalentAtom("N3", Element::Nitrogen(), 112.885*Deg2Rad), "C2/bond3", 0.12910, 0.73*Deg2Rad, BondMobility::Rigid );
        bondAtom( TrivalentAtom("C4", Element::Carbon(), 109.368*Deg2Rad, 104.422*Deg2Rad), "N3/bond2", 0.13560, -119.37*Deg2Rad, BondMobility::Rigid );
        bondAtom( UnivalentAtom("H1", Element::Hydrogen()), "N1/bond3", 0.09980 );
        bondAtom( UnivalentAtom("H8", Element::Hydrogen()), "C8/bond3", 0.10710 );

        addRingClosingBond( "C4/bond2", "N9/bond3", 0.15);
        addRingClosingBond( "C4/bond3", "C5/bond3", 0.15);

        setBiotypeIndex( "N9", Biotype::get("TwoNMethylGuanidineGroup", "N9").getIndex());
        setBiotypeIndex( "C8", Biotype::get("TwoNMethylGuanidineGroup", "C8").getIndex());
        setBiotypeIndex( "N7", Biotype::get("TwoNMethylGuanidineGroup", "N7").getIndex());
        setBiotypeIndex( "C5", Biotype::get("TwoNMethylGuanidineGroup", "C5").getIndex());
        setBiotypeIndex( "C6", Biotype::get("TwoNMethylGuanidineGroup", "C6").getIndex());
        setBiotypeIndex( "O6", Biotype::get("TwoNMethylGuanidineGroup", "O6").getIndex());
        setBiotypeIndex( "N1", Biotype::get("TwoNMethylGuanidineGroup", "N1").getIndex());
        setBiotypeIndex( "C2", Biotype::get("TwoNMethylGuanidineGroup", "C2").getIndex());
        setBiotypeIndex( "N2", Biotype::get("TwoNMethylGuanidineGroup", "N2").getIndex());
        setBiotypeIndex( "1H2", Biotype::get("TwoNMethylGuanidineGroup", "1H2").getIndex());
        setBiotypeIndex( "C10", Biotype::get("TwoNMethylGuanidineGroup", "C10").getIndex());
        setBiotypeIndex( "H20", Biotype::get("TwoNMethylGuanidineGroup", "H20").getIndex());
        setBiotypeIndex( "H21", Biotype::get("TwoNMethylGuanidineGroup", "H21").getIndex());
        setBiotypeIndex( "H22", Biotype::get("TwoNMethylGuanidineGroup", "H22").getIndex());
        setBiotypeIndex( "N3", Biotype::get("TwoNMethylGuanidineGroup", "N3").getIndex());
        setBiotypeIndex( "C4", Biotype::get("TwoNMethylGuanidineGroup", "C4").getIndex());
        setBiotypeIndex( "H1", Biotype::get("TwoNMethylGuanidineGroup", "H1").getIndex());
        setBiotypeIndex( "H8", Biotype::get("TwoNMethylGuanidineGroup", "H8").getIndex());

        setDefaultDihedralAngle(0.020*Deg2Rad, "C5", "N7", "C8", "N9");
        setDefaultDihedralAngle(179.544*Deg2Rad, "C6", "C5", "N7", "C8");
        setDefaultDihedralAngle(-0.165*Deg2Rad, "O6", "C6", "C5", "N7");
        setDefaultDihedralAngle(-179.886*Deg2Rad, "N1", "C6", "C5", "N7");
        setDefaultDihedralAngle(0.318*Deg2Rad, "C2", "N1", "C6", "C5");
        setDefaultDihedralAngle(178.303*Deg2Rad, "N2", "C2", "N1", "C6");
        setDefaultDihedralAngle(20.715*Deg2Rad, "1H2", "N2", "C2", "N1");
        setDefaultDihedralAngle(173.145*Deg2Rad, "C10", "N2", "C2", "N1");
        setDefaultDihedralAngle(176.133*Deg2Rad, "H20", "C10", "N2", "C2");
        setDefaultDihedralAngle(-63.298*Deg2Rad, "H21", "C10", "N2", "C2");
        setDefaultDihedralAngle(57.486*Deg2Rad, "H22", "C10", "N2", "C2");
        setDefaultDihedralAngle(-0.550*Deg2Rad, "N3", "C2", "N1", "C6");
        setDefaultDihedralAngle(0.727*Deg2Rad, "C4", "N3", "C2", "N1");
        setDefaultDihedralAngle(176.522*Deg2Rad, "H1", "N1", "C6", "C5");
    } // end constructor TwoNMethylGuanidineGroup 

    static void instantiateBiotypes() {
        if (! Biotype::exists("TwoNMethylGuanidineGroup", "N9") )
            Biotype::defineBiotype(Element::Nitrogen(), 3, "TwoNMethylGuanidineGroup", "N9"); 
        if (! Biotype::exists("TwoNMethylGuanidineGroup", "C8") )
            Biotype::defineBiotype(Element::Carbon(), 3, "TwoNMethylGuanidineGroup", "C8"); 
        if (! Biotype::exists("TwoNMethylGuanidineGroup", "N7") )
            Biotype::defineBiotype(Element::Nitrogen(), 2, "TwoNMethylGuanidineGroup", "N7"); 
        if (! Biotype::exists("TwoNMethylGuanidineGroup", "C5") )
            Biotype::defineBiotype(Element::Carbon(), 3, "TwoNMethylGuanidineGroup", "C5"); 
        if (! Biotype::exists("TwoNMethylGuanidineGroup", "C6") )
            Biotype::defineBiotype(Element::Carbon(), 3, "TwoNMethylGuanidineGroup", "C6"); 
        if (! Biotype::exists("TwoNMethylGuanidineGroup", "O6") )
            Biotype::defineBiotype(Element::Oxygen(), 1, "TwoNMethylGuanidineGroup", "O6"); 
        if (! Biotype::exists("TwoNMethylGuanidineGroup", "N1") )
            Biotype::defineBiotype(Element::Nitrogen(), 3, "TwoNMethylGuanidineGroup", "N1"); 
        if (! Biotype::exists("TwoNMethylGuanidineGroup", "C2") )
            Biotype::defineBiotype(Element::Carbon(), 3, "TwoNMethylGuanidineGroup", "C2"); 
        if (! Biotype::exists("TwoNMethylGuanidineGroup", "N2") )
            Biotype::defineBiotype(Element::Nitrogen(), 3, "TwoNMethylGuanidineGroup", "N2"); 
        if (! Biotype::exists("TwoNMethylGuanidineGroup", "1H2") )
            Biotype::defineBiotype(Element::Hydrogen(), 1, "TwoNMethylGuanidineGroup", "1H2"); 
        if (! Biotype::exists("TwoNMethylGuanidineGroup", "C10") )
            Biotype::defineBiotype(Element::Carbon(), 4, "TwoNMethylGuanidineGroup", "C10"); 
        if (! Biotype::exists("TwoNMethylGuanidineGroup", "H20") )
            Biotype::defineBiotype(Element::Hydrogen(), 1, "TwoNMethylGuanidineGroup", "H20"); 
        if (! Biotype::exists("TwoNMethylGuanidineGroup", "H21") )
            Biotype::defineBiotype(Element::Hydrogen(), 1, "TwoNMethylGuanidineGroup", "H21"); 
        if (! Biotype::exists("TwoNMethylGuanidineGroup", "H22") )
            Biotype::defineBiotype(Element::Hydrogen(), 1, "TwoNMethylGuanidineGroup", "H22"); 
        if (! Biotype::exists("TwoNMethylGuanidineGroup", "N3") )
            Biotype::defineBiotype(Element::Nitrogen(), 2, "TwoNMethylGuanidineGroup", "N3"); 
        if (! Biotype::exists("TwoNMethylGuanidineGroup", "C4") )
            Biotype::defineBiotype(Element::Carbon(), 3, "TwoNMethylGuanidineGroup", "C4"); 
        if (! Biotype::exists("TwoNMethylGuanidineGroup", "H1") )
            Biotype::defineBiotype(Element::Hydrogen(), 1, "TwoNMethylGuanidineGroup", "H1"); 
        if (! Biotype::exists("TwoNMethylGuanidineGroup", "H8") )
            Biotype::defineBiotype(Element::Hydrogen(), 1, "TwoNMethylGuanidineGroup", "H8"); 
    } // end instantiateBiotypes

}; // end class TwoNMethylGuanidineGroup 


class  RibonucleotideResidue::TwoNMethylGuanylate : public RibonucleotideResidue {
public:
    TwoNMethylGuanylate() : RibonucleotideResidue("2-N-methyl-guanylate", "2MG", 'X') 
    {
        bondCompound("base", TwoNMethylGuanidineGroup(), "bondBase", 0.14750, 200*Deg2Rad, BondMobility::Torsion);
        inheritAtomNames("base");

        defineDihedralAngle("chi", "O4*", "C1*", "N9", "C4");
        setDefaultDihedralAngle("chi", 210*Deg2Rad);

        addCompoundSynonym("TwoNMethylGuanidineGroup"); // for resolving biotypes
        
        setBiotypeIndex( "N9", Biotype::get("TwoNMethylGuanidineGroup", "N9").getIndex());
        setBiotypeIndex( "C8", Biotype::get("TwoNMethylGuanidineGroup", "C8").getIndex());
        setBiotypeIndex( "N7", Biotype::get("TwoNMethylGuanidineGroup", "N7").getIndex());
        setBiotypeIndex( "C5", Biotype::get("TwoNMethylGuanidineGroup", "C5").getIndex());
        setBiotypeIndex( "C6", Biotype::get("TwoNMethylGuanidineGroup", "C6").getIndex());
        setBiotypeIndex( "O6", Biotype::get("TwoNMethylGuanidineGroup", "O6").getIndex());
        setBiotypeIndex( "N1", Biotype::get("TwoNMethylGuanidineGroup", "N1").getIndex());
        setBiotypeIndex( "C2", Biotype::get("TwoNMethylGuanidineGroup", "C2").getIndex());
        setBiotypeIndex( "N2", Biotype::get("TwoNMethylGuanidineGroup", "N2").getIndex());
        setBiotypeIndex( "1H2", Biotype::get("TwoNMethylGuanidineGroup", "1H2").getIndex());
        setBiotypeIndex( "C10", Biotype::get("TwoNMethylGuanidineGroup", "C10").getIndex());
        setBiotypeIndex( "H20", Biotype::get("TwoNMethylGuanidineGroup", "H20").getIndex());
        setBiotypeIndex( "H21", Biotype::get("TwoNMethylGuanidineGroup", "H21").getIndex());
        setBiotypeIndex( "H22", Biotype::get("TwoNMethylGuanidineGroup", "H22").getIndex());
        setBiotypeIndex( "N3", Biotype::get("TwoNMethylGuanidineGroup", "N3").getIndex());
        setBiotypeIndex( "C4", Biotype::get("TwoNMethylGuanidineGroup", "C4").getIndex());
        setBiotypeIndex( "H1", Biotype::get("TwoNMethylGuanidineGroup", "H1").getIndex());
        setBiotypeIndex( "H8", Biotype::get("TwoNMethylGuanidineGroup", "H8").getIndex());
        
    }
};






class  RNA : public Biopolymer {
public:

    RNA(const PdbStructure& pdbStructure) 
    {
        // Assume first chain of first model is wanted
        const PdbChain& pdbChain = pdbStructure.getModel(Pdb::ModelIndex(0)).getChain(Pdb::ChainIndex(0));
        initializeFromPdbChain(pdbChain);
    }

    RNA(const PdbChain& pdbChain)
    {
        initializeFromPdbChain(pdbChain);
    }
    RNA(const Sequence& seq, bool useCappingHydroxyls = true) 
    {
        String previousResidueName;
        Biotype::initializePopularBiotypes();

        // TODO - create 5' end cap
        for (int resi = 0; resi < (int)seq.size(); ++resi)
        {
            
            RibonucleotideResidue residue = RibonucleotideResidue::create(seq[resi]);
            residue.assignBiotypes();

            residue.setPdbResidueNumber(resi + 1);

            // Name residue subcompound after its number in the sequence
            // name must be unique within the protein
            String residueName(resi);

            // Cap the 3' end with a hydroxyl group
            if ((resi == seq.size() - 1) && (useCappingHydroxyls)) {
                    residue.bondCompound(
                            "3PrimeHydroxyl", 
                            ThreePrimeRnaHydroxylGroup(residueName, residue.getPdbResidueName(), 'X'), 
                            "bondNext", 
                                    0.0960);
            residue.inheritAtomNames("3PrimeHydroxyl");
                    // Oxygen biotype must be changed for the amber atom types to come out correctly
            if ( (residue.hasAtom("O3*")) && ( Biotype::exists("Hydroxyl, RNA", "O3*", SimTK::Ordinality::Final)) )
                    residue.setBiotypeIndex( "O3*", Biotype::get("Hydroxyl, RNA", "O3*", SimTK::Ordinality::Final).getIndex() );
            }

 if (resi == 0) {
                    // first residue needs end cap
                    residue.convertInboardBondCenterToOutboard();

                            if (useCappingHydroxyls) { // 5' hydroxyl
                            residue.bondCompound(
                                            "5PrimeHydroxyl", 
                                            FivePrimeRnaHydroxylGroup(residueName, residue.getPdbResidueName(), 'X'), 
                                            "bondPrevious", 
                                                    0.0960);
                            residue.inheritAtomNames("5PrimeHydroxyl");
                            if ( (residue.hasAtom("O5*")) && ( Biotype::exists("Hydroxyl, RNA", "O5*", SimTK::Ordinality::Initial)) )
                                    residue.setBiotypeIndex( "O5*", Biotype::get("Hydroxyl, RNA", "O5*", SimTK::Ordinality::Initial).getIndex() );
                            }

                            else { // 5' phosphate
                            residue.bondCompound(
                                            "5PrimePhosphate", 
                                            FivePrimeRnaPhosphateGroup(residueName, residue.getPdbResidueName(), 'X'), 
                                            "bondPrevious");
                            residue.inheritAtomNames("5PrimePhosphate");
                            }

                    appendResidue( residueName, residue );
            }
            else {
                // non-first residue needs phosphodiester linkage
                appendResidue( residueName, residue.withPhosphodiester() );

                // Define zeta angle
                String zetaName = String("zeta") + String(resi - 1);
                defineDihedralAngle(zetaName, previousResidueName + "/O3*/bond1", residueName + "/P/bond2");
                setDefaultDihedralAngle(zetaName, 287.0*Deg2Rad); // (Schneider et al 2004)
            }

            previousResidueName = residueName;
        }
    }
    RNA& setRNABondMobility (BondMobility::Mobility  mobility, ResidueInfo::Index startResidue, ResidueInfo::Index endResidue){
        for (ResidueInfo::Index q =startResidue; q<=endResidue; q++) {
            setResidueBondMobility(q, mobility);
            // (updResidue(ResidueInfo::Index(q))).setCompoundBondMobility(mobility);
            if (q>startResidue) {
                std::stringstream ss1;
                ss1<<q-1<<"/O3*";
                std::stringstream ss2;
                ss2<<q<<"/P";
                setBondMobility(mobility ,ss1.str() ,ss2.str()  ); 
            }
        }
        return *this;
    }
    Vec3 calcRNABaseNormal  (const State & state,int residueNumber, int bodyOrGroundFrame, const SimbodyMatterSubsystem & matter) const {
        const ResidueInfo& myResidue = getResidue(ResidueInfo::Index(residueNumber));
            String myResidueName = myResidue.getPdbResidueName();
        //cout<<"[RNA.h:calcRNABaseNormal] myResidueName ="<<myResidueName<<endl;
            //String myResidueName = (updResidue(Compound::Index(residueNumber))).getPdbResidueName();
        assert((myResidueName.compare("A  ") == 0) || (myResidueName.compare("G  ") == 0)  || (myResidueName.compare("U  ") == 0) || (myResidueName.compare("C  ") == 0));
            String atomName1;
            String atomName1a;
            String atomName1b;
        if ((myResidueName.compare("A  ") == 0) || (myResidueName.compare("G  ") == 0)) {
            atomName1  = "N9";
            atomName1a = "C4";
            atomName1b = "C8";
        } else {
            atomName1  = "N1";
            atomName1a = "C2";
            atomName1b = "C6";
        }
            Compound::AtomIndex myAtomIndex1 = myResidue.getAtomIndex(atomName1 );
            Compound::AtomIndex myAtomIndex1a= myResidue.getAtomIndex(atomName1a);
            Compound::AtomIndex myAtomIndex1b= myResidue.getAtomIndex(atomName1b);
        MobilizedBodyIndex myMobilizedBodyIndex1  = getAtomMobilizedBodyIndex(myAtomIndex1 );
        MobilizedBodyIndex myMobilizedBodyIndex1a = getAtomMobilizedBodyIndex(myAtomIndex1a);
        MobilizedBodyIndex myMobilizedBodyIndex1b = getAtomMobilizedBodyIndex(myAtomIndex1b);
            MobilizedBody body1 = matter.getMobilizedBody(myMobilizedBodyIndex1 );
            MobilizedBody body1a= matter.getMobilizedBody(myMobilizedBodyIndex1a);
            MobilizedBody body1b= matter.getMobilizedBody(myMobilizedBodyIndex1b);
        if (bodyOrGroundFrame == 0 ) {
                Vec3 normalInBodyFrame = (
                    (~(body1.getBodyTransform(state)) * body1a.getBodyTransform(state) * getAtomLocationInMobilizedBodyFrame(myAtomIndex1a)  
                    - getAtomLocationInMobilizedBodyFrame(myAtomIndex1)) %
                    (~(body1.getBodyTransform(state)) * body1b.getBodyTransform(state) * getAtomLocationInMobilizedBodyFrame(myAtomIndex1b)
                    - getAtomLocationInMobilizedBodyFrame(myAtomIndex1)));
        normalInBodyFrame /= normalInBodyFrame.norm();
            return normalInBodyFrame;
        } else if (bodyOrGroundFrame == 1) {
                Vec3 normalInGroundFrame = 
                    (    
                    body1a.getBodyTransform(state) * getAtomLocationInMobilizedBodyFrame(myAtomIndex1a)
                    - body1.getBodyTransform(state) * getAtomLocationInMobilizedBodyFrame(myAtomIndex1)
                    ) % (
                    body1b.getBodyTransform(state) * getAtomLocationInMobilizedBodyFrame(myAtomIndex1b)
                    - body1.getBodyTransform(state) * getAtomLocationInMobilizedBodyFrame(myAtomIndex1)
                    );
                normalInGroundFrame /= normalInGroundFrame.norm();
                return normalInGroundFrame;
        }

    }

private:
    void initializeFromPdbChain(
            const PdbChain& pdbChain, 
            Compound::MatchStratagem matchStratagem = 
                    Compound::Match_TopologyOnly)
    {
        setPdbChainId( pdbChain.getChainId() );
        
        String previousResidueName("");
        
        // TODO end caps
        for (Pdb::ResidueIndex r(0); r < (Pdb::ResidueIndex)pdbChain.getNumResidues(); ++r) 
        {
            const PdbResidue& pdbResidue = pdbChain.getResidue(r);
            String residueName = pdbResidue.getName() + String(pdbResidue.getPdbResidueNumber());
            if (pdbResidue.getInsertionCode() != ' ') // include unusual insertion codes in residue name
                    residueName += pdbResidue.getInsertionCode();
            
            RibonucleotideResidue residue = RibonucleotideResidue::create(pdbResidue, pdbChain.getChainId());
            residue.assignBiotypes();
            
            if (r == 0) { // first residue does not get phosphate
                appendResidue( residueName, residue );
            }
            else {
                // non-first residue needs phosphodiester linkage
                BiopolymerResidue resWithP = residue.withPhosphodiester();
                resWithP.assignBiotypes();
                appendResidue( residueName, resWithP );

                // Define zeta angle
                String zetaName = String("zeta") + String(residue.getPdbResidueNumber());
                defineDihedralAngle(zetaName, previousResidueName + "/O3*/bond1", residueName + "/P/bond2");
                setDefaultDihedralAngle(zetaName, 287.0*Deg2Rad); // (Schneider et al 2004)
            } 
            
            previousResidueName = residueName;            
        }
        
        if (matchStratagem != Compound::Match_TopologyOnly) 
        {
            Compound::AtomTargetLocations atomTargets = 
                    createAtomTargets(pdbChain);
            
            matchDefaultConfiguration(atomTargets, matchStratagem);
        }        
    }
};


} // namespace SimTK

#endif // SimTK_MOLMODEL_RNA_H_