Protein.h

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#ifndef SimTK_MOLMODEL_PROTEIN_H_
#define SimTK_MOLMODEL_PROTEIN_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:                                                              *
 *                                                                            *
 * 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"
#include "molmodel/internal/CompoundSystem.h"

namespace SimTK {

class AcetylResidue : public BiopolymerResidue {
public:
    AcetylResidue() : BiopolymerResidue("acetyl", "ACE", 'X')
    {
        setBaseCompound("methyl", MethylGroup());
        nameAtom("CH3", "methyl/C");
        nameAtom("1H", "methyl/H1");
        nameAtom("2H", "methyl/H2");
        nameAtom("3H", "methyl/H3");

        convertInboardBondCenterToOutboard();
        bondAtom(TrivalentAtom("C", Element::Carbon()), "methyl/bond", 0.15520);
        bondAtom(UnivalentAtom("O", Element::Oxygen()), "C/bond2", 0.12290);
        nameBondCenter("bondC", "C/bond3");
        nameBondCenter("bondNext", "bondC");
        
        setAtomBiotype("CH3", "Acetyl", "CH3", SimTK::Ordinality::Initial);
        setAtomBiotype("1H",  "Acetyl", "H", SimTK::Ordinality::Initial);
        setAtomBiotype("2H",  "Acetyl", "H", SimTK::Ordinality::Initial);
        setAtomBiotype("3H",  "Acetyl", "H", SimTK::Ordinality::Initial);
        setAtomBiotype("C",   "Acetyl", "C", SimTK::Ordinality::Initial);
        setAtomBiotype("O",   "Acetyl", "O", SimTK::Ordinality::Initial);    
    }
};


class NMethylAmideResidue : public BiopolymerResidue {
public:
    NMethylAmideResidue() : BiopolymerResidue("N-methyl amide", "NAC", 'X')
    {
        // TODO - set nitrogen bond angles
        setBaseAtom(TrivalentAtom("N", Element::Nitrogen()));
        bondAtom(UnivalentAtom("HN", Element::Hydrogen()), "N/bond3", 0.1010);
        bondAtom(AliphaticCarbon("CH3"), "N/bond2", 0.1449);
        bondAtom(AliphaticHydrogen("1H"), "CH3/bond2");
        bondAtom(AliphaticHydrogen("2H"), "CH3/bond3");
        bondAtom(AliphaticHydrogen("3H"), "CH3/bond4");

        nameBondCenter("bondN", "N/bond1");
        nameBondCenter("bondPrevious", "bondN");

        // Define default bonding geometry to previous residue
        setDefaultInboardBondLength(0.1335);

        // Help with automated biotype resolution
        addCompoundSynonym("N-MeAmide");

        // zero and 180 degrees are poor choices for phi angle because each eclipses either N-H or N-C
        defineDihedralAngle("phi", "bondPrevious", "CH3/bond2", 30*Deg2Rad);
        
        setAtomBiotype("N",   "N-MeAmide", "N",   SimTK::Ordinality::Final);
        setAtomBiotype("HN",  "N-MeAmide", "HN",  SimTK::Ordinality::Final);
        setAtomBiotype("CH3", "N-MeAmide", "CH3", SimTK::Ordinality::Final);
        setAtomBiotype("1H",  "N-MeAmide", "H",   SimTK::Ordinality::Final);
        setAtomBiotype("2H",  "N-MeAmide", "H",   SimTK::Ordinality::Final);
        setAtomBiotype("3H",  "N-MeAmide", "H",   SimTK::Ordinality::Final);    
    }
};

static const Angle DefaultAlphaPhiAngle = -57 * Deg2Rad;
static const Angle DefaultAlphaPsiAngle = -47 * Deg2Rad;
static const Angle DefaultParallelBetaPhiAngle = -119 * Deg2Rad;
static const Angle DefaultParallelBetaPsiAngle =  113 * Deg2Rad;
static const Angle DefaultAntiparallelBetaPhiAngle = -139 * Deg2Rad;
static const Angle DefaultAntiparallelBetaPsiAngle =  135 * Deg2Rad;

class SimTK_MOLMODEL_EXPORT AminoAcidResidue : public BiopolymerResidue {
public:

    static AminoAcidResidue create(
        char oneLetterCode 
        );


    static AminoAcidResidue create(
        const PdbResidue& 
        );
        
    explicit AminoAcidResidue(
        String name, 
        String threeLetterCode = "Unk", 
        char oneLetterCode = '?' 
        )
        : BiopolymerResidue(name, threeLetterCode, oneLetterCode)
    {
        static const mdunits::Length CA_Hdistance = 0.1090;
        static const mdunits::Length N_CAdistance = 0.1449;
        static const mdunits::Length CA_Cdistance = 0.1522;
        static const mdunits::Length  C_Odistance = 0.1229;
        static const mdunits::Length  C_Ndistance = 0.1335; // peptide bond

        // Amino nitrogen
        // We want the inboard bond center to be on the main chain nitrogen peptide bond
        // But we also want the CA and main chain H to be the reference for dihedrals.
        // To reconcile these two requirements, a bit of extra work is required.
        TrivalentAtom nAtom("N", Element::Nitrogen());
        // nAtom.convertInboardBondCenterToOutboard(); // free bond1 for use with HN
        // nAtom.setInboardBondCenter("bond3");  // lowest priority bond becomes inboard

        setBaseAtom(nAtom);

        // Alpha carbon
        bondAtom(QuadrivalentAtom("CA", Element::Carbon()), "N/bond2", N_CAdistance, DefaultAntiparallelBetaPhiAngle + 180*Deg2Rad); // phi
        bondAtom(UnivalentAtom("HA", Element::Hydrogen()), "CA/bond3", CA_Hdistance);
        nameBondCenter("bondCA", "CA/bond4");

        // Carbonyl
        bondAtom(TrivalentAtom("C", Element::Carbon()), "CA/bond2", CA_Cdistance, DefaultAntiparallelBetaPsiAngle + 180*Deg2Rad); // psi
        bondAtom(UnivalentAtom("O", Element::Oxygen()), "C/bond2", C_Odistance);
        nameBondCenter("bondC", "C/bond3");
        nameBondCenter("bondNext", "bondC");

        nameBondCenter("bondN", "N/bond1");
        nameBondCenter("bondPrevious", "bondN");

        // Define default bonding geometry to previous residue
        setDefaultInboardBondLength(C_Ndistance);

        defineDihedralAngle("psi", "N", "CA", "C", "O", 180*Deg2Rad);
        setDefaultPsiAngle(DefaultAntiparallelBetaPsiAngle);

        defineDihedralAngle("phi", "N/bond3", "CA/bond2", 180*Deg2Rad);
        setDefaultPhiAngle(DefaultAntiparallelBetaPhiAngle);
    }


    AminoAcidResidue& setDefaultPhiAngle(Angle phi) {
        setDefaultDihedralAngle("phi", phi);

        return *this;
    }

    AminoAcidResidue& setDefaultPsiAngle(Angle psi) {
        setDefaultDihedralAngle("psi", psi);

        return *this;
    }

    // Make intermediate classes inner classes of AminoAcidResidue
    // to avoid registration order problems in boost.python/Py++ wrapping
    class HNAminoAcidResidue;
    class BetaUnbranchedAminoAcidResidue;
    class BetaBranchedAminoAcidResidue;

    class Alanine;
    class Cysteine;
    class Aspartate;
    class Glutamate;
    class Phenylalanine;
    class Glycine;
    class Histidine;
    class Isoleucine;
    class Lysine;
    class Leucine;
    class Methionine;
    class Asparagine;
    class Proline;
    class Glutamine;
    class Arginine;
    class Serine;
    class Threonine;
    class Valine;
    class Tryptophan;
    class Tyrosine;
};


class  AminoAcidResidue::HNAminoAcidResidue : public AminoAcidResidue {
public:
    explicit HNAminoAcidResidue(String name, String threeLetterCode = "Unk", char oneLetterCode = '?')
        : AminoAcidResidue(name, threeLetterCode, oneLetterCode)
    {
        static const mdunits::Length  H_Ndistance = 0.1010;

        bondAtom(UnivalentAtom("H", Element::Hydrogen()), "N/bond3", H_Ndistance);
        nameAtom("HN", "H"); // synonym

        // defineDihedralAngle("phi", "H", "N", "CA", "C", 180*Deg2Rad); // already defined
    }
};


// BetaunbranchedAminoAcidResidue is base class for AminoAcidResidues
// posessing side chains that do not branch at the beta carbon
class  AminoAcidResidue::BetaUnbranchedAminoAcidResidue : public AminoAcidResidue::HNAminoAcidResidue {
public:
    BetaUnbranchedAminoAcidResidue(String name, String tlc, char olc)
        : AminoAcidResidue::HNAminoAcidResidue(name, tlc, olc) 
    {
        bondCompound("beta methylene", MethyleneGroup(), "bondCA");
        nameAtom("CB", "beta methylene/C");
        nameAtom("1HB", "beta methylene/H1");
        nameAtom("2HB", "beta methylene/H2");
        nameBondCenter("bondCB", "beta methylene/bond2");

        defineDihedralAngle("chi1", "CA/bond1", "beta methylene/bond2");
        setDefaultDihedralAngle("chi1", -60*Deg2Rad); // best for most amino acids
    }
};


// BetaunbranchedAminoAcidResidue is base class for AminoAcidResidues
// posessing side chains that do not branch at the beta carbon
class  AminoAcidResidue::BetaBranchedAminoAcidResidue : public AminoAcidResidue::HNAminoAcidResidue {
public:
    BetaBranchedAminoAcidResidue(String name, String tlc, char olc)
        : AminoAcidResidue::HNAminoAcidResidue(name, tlc, olc) 
    {
        bondAtom(AliphaticCarbon("CB"), "bondCA");

        // To get correct chirality *and* priority in isoleucine and threonine,
        // place hydrogen on bond3

        bondAtom(AliphaticHydrogen("HB"), "CB/bond3");
        nameBondCenter("bondCB1", "CB/bond2");
        nameBondCenter("bondCB2", "CB/bond4");

        defineDihedralAngle("chi1", "CA/bond1", "CB/bond2");
        setDefaultDihedralAngle("chi1", -60*Deg2Rad); // best for most amino acids
    }
};


class  AminoAcidResidue::Alanine : public AminoAcidResidue::BetaUnbranchedAminoAcidResidue {
public:
    Alanine() 
        : AminoAcidResidue::BetaUnbranchedAminoAcidResidue("alanine", "Ala", 'A')
    {
        bondAtom(AliphaticHydrogen("3HB"), "bondCB");
        
        setAtomBiotype("N",   "Alanine", "N");
        setAtomBiotype("H",   "Alanine", "HN");
        setAtomBiotype("CA",  "Alanine", "CA");
        setAtomBiotype("C",   "Alanine", "C");
        setAtomBiotype("O",   "Alanine", "O");
        setAtomBiotype("HA",  "Alanine", "HA");
        setAtomBiotype("CB",  "Alanine", "CB");
        setAtomBiotype("1HB", "Alanine", "HB");    
        setAtomBiotype("2HB", "Alanine", "HB");    
        setAtomBiotype("3HB", "Alanine", "HB");    
    }
};


class  AminoAcidResidue::Cysteine : public AminoAcidResidue::BetaUnbranchedAminoAcidResidue {
public:
    Cysteine() 
        : AminoAcidResidue::BetaUnbranchedAminoAcidResidue("cysteine", "Cys", 'C')
    {
        // From amber99 parameters in Tinker param file amber99.dat
        static const mdunits::Length H_Sdistance = 0.1336;
        static const mdunits::Length S_Cdistance = 0.1810;
        static const Angle H_S_Cangle = 96.0*Deg2Rad;
        static const Angle S_C_Cangle = 108.6*Deg2Rad;

        bondAtom(BivalentAtom("SG", Element::Sulfur(), H_S_Cangle), "bondCB", S_Cdistance, 180*Deg2Rad);
        bondAtom(UnivalentAtom("HG", Element::Hydrogen()), "SG/bond2", H_Sdistance, 180*Deg2Rad);

        defineDihedralAngle("chi2", "HG", "SG", "CB", "CA");

        setDefaultBondAngle(108.60*Deg2Rad, "SG", "CB", "CA");

        // Synonym hints to help resolve biotypes from tinker files
        // eventually, these biotypes will be pre-defined and hard coded
        addCompoundSynonym("CYS (-SH)");
        addCompoundSynonym("cysteine (-SH)");
    }
};

class  AminoAcidResidue::Aspartate : public AminoAcidResidue::BetaUnbranchedAminoAcidResidue {
public:
    Aspartate() 
        : AminoAcidResidue::BetaUnbranchedAminoAcidResidue("aspartate", "Asp", 'D')
    {
        bondCompound("sidechain carboxylate", CarboxylateGroup(), "bondCB");
        nameAtom("CG", "sidechain carboxylate/C");
        nameAtom("OD1", "sidechain carboxylate/O1");
        nameAtom("OD2", "sidechain carboxylate/O2");

        defineDihedralAngle("chi2", "OD1", "CG", "CB", "CA");

        // From Roland Dunbrack's side chain rotamer statistics
        // http://dunbrack.fccc.edu/bbdep/confanalysis.php
        setDefaultDihedralAngle("chi2", -15*Deg2Rad);

        // Synonym hints to help resolve biotypes from tinker files
        // eventually, these biotypes will be pre-defined and hard coded
        addCompoundSynonym("aspartic acid");
    }
};

class  AminoAcidResidue::Glutamate : public AminoAcidResidue::BetaUnbranchedAminoAcidResidue {
public:
    Glutamate() 
        : AminoAcidResidue::BetaUnbranchedAminoAcidResidue("glutamate", "Glu", 'E')
    {
        bondAtom(AliphaticCarbon("CG"), "bondCB");
        bondAtom(AliphaticHydrogen("1HG"), "CG/bond3");
        bondAtom(AliphaticHydrogen("2HG"), "CG/bond4");

        bondCompound("sidechain carboxylate", CarboxylateGroup(), "CG/bond2");
        nameAtom("CD", "sidechain carboxylate/C");
        nameAtom("OE1", "sidechain carboxylate/O1");
        nameAtom("OE2", "sidechain carboxylate/O2");

        defineDihedralAngle("chi2", "CD", "CG", "CB", "CA");
        defineDihedralAngle("chi3", "OE1", "CD", "CG", "CB");

        setDefaultDihedralAngle("chi3", -15*Deg2Rad);

        // Synonym hints to help resolve biotypes from tinker files
        // eventually, these biotypes will be pre-defined and hard coded
        addCompoundSynonym("glutamic acid");
    }
};


class  AminoAcidResidue::Phenylalanine : public AminoAcidResidue::BetaUnbranchedAminoAcidResidue {
public:
    Phenylalanine()
        : AminoAcidResidue::BetaUnbranchedAminoAcidResidue("phenylalanine", "Phe", 'F')
    {
        static const mdunits::Length CB_CGdistance = 0.1510;
        static const mdunits::Length C_Hdistance = 0.1080; // from tinker amber99.dat
        static const mdunits::Length C_Cdistance = 0.1400; // from tinker amber99.dat

        // default angle for TrivalentAtom is 120 degrees, which is what we want
        // for a six-membered ring
        bondAtom( TrivalentAtom("CG", Element::Carbon()), "bondCB", CB_CGdistance, 180*Deg2Rad);

        bondAtom( TrivalentAtom("CD1", Element::Carbon()), "CG/bond2", C_Cdistance, 180*Deg2Rad );
        bondAtom( UnivalentAtom("HD1", Element::Hydrogen()), "CD1/bond3", C_Hdistance );

        // Start using hidedral of zero, to loop ring back to beginning
        bondAtom( TrivalentAtom("CE1", Element::Carbon()), "CD1/bond2", C_Cdistance, 0*Deg2Rad );
        bondAtom( UnivalentAtom("HE1", Element::Hydrogen()), "CE1/bond3", C_Hdistance );

        bondAtom( TrivalentAtom("CZ", Element::Carbon()), "CE1/bond2", C_Cdistance, 0*Deg2Rad );
        bondAtom( UnivalentAtom("HZ", Element::Hydrogen()), "CZ/bond3", C_Hdistance );

        bondAtom( TrivalentAtom("CE2", Element::Carbon()), "CZ/bond2", C_Cdistance, 0*Deg2Rad );
        bondAtom( UnivalentAtom("HE2", Element::Hydrogen()), "CE2/bond3", C_Hdistance );

        bondAtom( TrivalentAtom("CD2", Element::Carbon()), "CE2/bond2", C_Cdistance, 0*Deg2Rad );
        bondAtom( UnivalentAtom("HD2", Element::Hydrogen()), "CD2/bond3", C_Hdistance );

        addRingClosingBond("CD2/bond2", "CG/bond3", C_Cdistance, 0*Deg2Rad);

        defineDihedralAngle("chi2", "CD1", "CG", "CB", "CA");

        setDefaultDihedralAngle("chi2", 90*Deg2Rad); // from Dunbrack site

        setBondMobility(BondMobility::Rigid, "CG", "CD1");
        setBondMobility(BondMobility::Rigid, "CD1", "CE1");
        setBondMobility(BondMobility::Rigid, "CE1", "CZ");
        setBondMobility(BondMobility::Rigid, "CZ", "CE2");
        setBondMobility(BondMobility::Rigid, "CE2", "CD2");
        setBondMobility(BondMobility::Rigid, "CD2", "CG");
    }
};


class  AminoAcidResidue::Glycine : public AminoAcidResidue::HNAminoAcidResidue {
public:
    Glycine() 
        : AminoAcidResidue::HNAminoAcidResidue("glycine", "Gly", 'G')
    {
        bondAtom(AliphaticHydrogen("2HA"), "bondCA");
        nameAtom("1HA", "HA");  // glycine names alpha hydrogen differently than others
    }
};


class  AminoAcidResidue::Histidine : public AminoAcidResidue::BetaUnbranchedAminoAcidResidue {
public:
    Histidine()
        : AminoAcidResidue::BetaUnbranchedAminoAcidResidue("histidine", "His", 'H')
    {
        // use average values for different protonation states
        static const mdunits::Length CB_CGdistance = 0.15040; // from tinker amber99.dat
        static const mdunits::Length CG_NDdistance = 0.13895; // average of protonation states 1385/1394
        static const mdunits::Length N_CEdistance = 0.13390; // average of protonation states 1343/1335
        static const mdunits::Length NE_CDdistance = 0.13875; // avg 1394/1381
        static const mdunits::Length CD_CGdistance = 0.1373; // avg 1371/1375
        static const mdunits::Length H_Cdistance = 0.1080;
        static const mdunits::Length H_Ndistance = 0.1010;

        // set angle to pentagonal angle 108, as amber parameters set 120 degrees as
        // "optimal" and let the forces fight it out.  Such a strategy will not
        // do for simple coordinate generation and for rigid body models.
        static const Angle ringAngle = 108.000 * Deg2Rad; // 108 degrees is exact
        static const Angle outerRingAngle = 180*Deg2Rad - 0.5*ringAngle;

        bondAtom( TrivalentAtom("CG", Element::Carbon(), outerRingAngle, outerRingAngle), "bondCB", CB_CGdistance);

        bondAtom( TrivalentAtom("ND1", Element::Nitrogen(), ringAngle, outerRingAngle), "CG/bond2", CG_NDdistance, 180*Deg2Rad);
        // optional proton depends upon protonation state
        bondAtom( UnivalentAtom("HD1", Element::Hydrogen()), "ND1/bond3", H_Ndistance);

        bondAtom( TrivalentAtom("CE1", Element::Carbon(), ringAngle, outerRingAngle), "ND1/bond2", N_CEdistance, 0*Deg2Rad);
        bondAtom( UnivalentAtom("HE1", Element::Hydrogen()), "CE1/bond3", H_Cdistance);

        bondAtom( TrivalentAtom("NE2", Element::Nitrogen(), ringAngle, outerRingAngle), "CE1/bond2", CG_NDdistance, 0*Deg2Rad);
        // optional proton depends upon protonation state
        bondAtom( UnivalentAtom("HE2", Element::Hydrogen()), "NE2/bond3", H_Ndistance);

        bondAtom( TrivalentAtom("CD2", Element::Carbon(), ringAngle, outerRingAngle), "NE2/bond2", N_CEdistance, 0*Deg2Rad);
        bondAtom( UnivalentAtom("HD2", Element::Hydrogen()), "CD2/bond3", H_Cdistance);

        addRingClosingBond("CD2/bond2", "CG/bond3", CD_CGdistance, 0*Deg2Rad);

        defineDihedralAngle("chi2", "ND1", "CG", "CB", "CA");

        setDefaultDihedralAngle("chi2", 90*Deg2Rad); // from Dunbrack site

        // Biotypes for histidine are tricky
        // Since both acidic protons are added above, this residue defaults to positive charge
        // There is more work to do to handle HIS protonation properly TODO

        // Synonym hints to help resolve biotypes from tinker files
        // eventually, these biotypes will be pre-defined and hard coded
        addCompoundSynonym("histidine (+)");

        // Make ring rigid for internal coordinate simulation
        setBondMobility(BondMobility::Rigid, "CG", "ND1");
        setBondMobility(BondMobility::Rigid, "ND1", "CE1");
        setBondMobility(BondMobility::Rigid, "CE1", "NE2");
        setBondMobility(BondMobility::Rigid, "NE2", "CD2");
        setBondMobility(BondMobility::Rigid, "CD2", "CG");
    }
};


// Unlike the case with Threonine, the chirality of Isoleucine comes out
// correctly when built up from BetaBranchedAminoAcidResidue
class  AminoAcidResidue::Isoleucine : public AminoAcidResidue::BetaBranchedAminoAcidResidue {
public:
    Isoleucine()
        : AminoAcidResidue::BetaBranchedAminoAcidResidue("isoleucine", "Ile", 'I')
    {
        bondCompound("gamma methylene", MethyleneGroup(), "bondCB1");
        nameAtom("CG1", "gamma methylene/C");
        nameAtom("1HG1", "gamma methylene/H1");
        nameAtom("2HG1", "gamma methylene/H2");

        bondCompound("delta methyl", MethylGroup(), "gamma methylene/bond2");
        nameAtom("CD", "delta methyl/C");
        nameAtom("1HD", "delta methyl/H1");
        nameAtom("2HD", "delta methyl/H2");
        nameAtom("3HD", "delta methyl/H3");

        bondCompound("gamma methyl", MethylGroup(), "bondCB2");
        nameAtom("CG2", "gamma methyl/C");
        nameAtom("1HG2", "gamma methyl/H1");
        nameAtom("2HG2", "gamma methyl/H2");
        nameAtom("3HG2", "gamma methyl/H3");

        defineDihedralAngle("chi2", "CD", "CG1", "CB", "CA");

        setDefaultDihedralAngle("chi1", -70*Deg2Rad);
        setDefaultDihedralAngle("chi2", 170*Deg2Rad);
    }
};


class  AminoAcidResidue::Lysine : public AminoAcidResidue::BetaUnbranchedAminoAcidResidue {
public:
    Lysine()
        : AminoAcidResidue::BetaUnbranchedAminoAcidResidue("lysine", "Lys", 'K') 
    {
        bondAtom(AliphaticCarbon("CG"), "bondCB");
        bondAtom(AliphaticHydrogen("1HG"), "CG/bond3");
        bondAtom(AliphaticHydrogen("2HG"), "CG/bond4");

        bondAtom(AliphaticCarbon("CD"), "CG/bond2");
        bondAtom(AliphaticHydrogen("1HD"), "CD/bond3");
        bondAtom(AliphaticHydrogen("2HD"), "CD/bond4");

        bondAtom(AliphaticCarbon("CE"), "CD/bond2");
        bondAtom(AliphaticHydrogen("1HE"), "CE/bond3");
        bondAtom(AliphaticHydrogen("2HE"), "CE/bond4");

        bondCompound("zeta amine", PrimaryAmineGroup(), "CE/bond2");
        nameAtom("NZ", "zeta amine/N");
        nameAtom("1HZ", "zeta amine/H1");
        nameAtom("2HZ", "zeta amine/H2");
        nameAtom("3HZ", "zeta amine/H3");

        defineDihedralAngle("chi2", "CD", "CG", "CB", "CA");
        defineDihedralAngle("chi3", "CE", "CD", "CG", "CB");
        defineDihedralAngle("chi4", "NZ", "CE", "CD", "CG");
        defineDihedralAngle("chi5", "1HZ", "NZ", "CE", "CD");
    }
};

    
class  AminoAcidResidue::Leucine : public AminoAcidResidue::BetaUnbranchedAminoAcidResidue {
public:
    Leucine()
        : AminoAcidResidue::BetaUnbranchedAminoAcidResidue("leucine", "Leu", 'L')
    {
        bondAtom(AliphaticCarbon("CG"), "bondCB");
        bondAtom(AliphaticHydrogen("HG"), "CG/bond4");

        // It actually takes more lines of code to add a MethylGroup and rename the 
        // atoms, than it does to add the atoms individually

        // First delta methyl group
        bondAtom(AliphaticCarbon("CD1"), "CG/bond2");
        bondAtom(AliphaticHydrogen("1HD1"), "CD1/bond2");
        bondAtom(AliphaticHydrogen("2HD1"), "CD1/bond3");
        bondAtom(AliphaticHydrogen("3HD1"), "CD1/bond4");

        // Second delta methyl group
        bondAtom(AliphaticCarbon("CD2"), "CG/bond3");
        bondAtom(AliphaticHydrogen("1HD2"), "CD2/bond2");
        bondAtom(AliphaticHydrogen("2HD2"), "CD2/bond3");
        bondAtom(AliphaticHydrogen("3HD2"), "CD2/bond4");

        defineDihedralAngle("chi2", "CD1", "CG", "CB", "CA");

        setDefaultDihedralAngle("chi1", -70*Deg2Rad);
        setDefaultDihedralAngle("chi2", 170*Deg2Rad);
    }
};


class  AminoAcidResidue::Methionine : public AminoAcidResidue::BetaUnbranchedAminoAcidResidue {
public:
    Methionine()
        : AminoAcidResidue::BetaUnbranchedAminoAcidResidue("methionine", "Met", 'M') 
    {
        bondAtom(AliphaticCarbon("CG"), "bondCB");
        bondAtom(AliphaticHydrogen("1HG"), "CG/bond3");
        bondAtom(AliphaticHydrogen("2HG"), "CG/bond4");

        bondAtom( BivalentAtom("SD", Element::Sulfur(), 98.90*Deg2Rad), "CG/bond2", 0.1810, 180*Deg2Rad);

        bondAtom(AliphaticCarbon("CE"), "SD/bond2", 0.1810, 180*Deg2Rad);
        bondAtom(AliphaticHydrogen("1HE"), "CE/bond2");
        bondAtom(AliphaticHydrogen("2HE"), "CE/bond3");
        bondAtom(AliphaticHydrogen("3HE"), "CE/bond4");

        defineDihedralAngle("chi2", "SD", "CG", "CB", "CA");
        defineDihedralAngle("chi3", "CE", "SD", "CG", "CB");
        defineDihedralAngle("chi4", "1HE", "CE", "SD", "CG");
    }
};

    
class  AminoAcidResidue::Asparagine : public AminoAcidResidue::BetaUnbranchedAminoAcidResidue {
public:
    Asparagine() 
        : AminoAcidResidue::BetaUnbranchedAminoAcidResidue("asparagine", "Asn", 'N')
    {
        bondAtom(TrivalentAtom("CG", Element::Carbon(), 120.4*Deg2Rad, 116.6*Deg2Rad), "bondCB", 0.15220);

        bondAtom(UnivalentAtom("OD1", Element::Oxygen()), "CG/bond2", 0.12290);

        bondAtom(TrivalentAtom("ND2", Element::Nitrogen()), "CG/bond3", 0.13350);
        bondAtom(UnivalentAtom("1HD2", Element::Hydrogen()), "ND2/bond2", 0.1010);
        bondAtom(UnivalentAtom("2HD2", Element::Hydrogen()), "ND2/bond3", 0.1010);

        defineDihedralAngle("chi2", "OD1", "CG", "CB", "CA");

        // From Roland Dunbrack's side chain rotamer statistics
        // http://dunbrack.fccc.edu/bbdep/confanalysis.php
        setDefaultDihedralAngle("chi2", -20*Deg2Rad);

        // For internal coordinate simulation, make amide group rigid
        setBondMobility(BondMobility::Rigid, "CG", "ND2");
    }
};


class  AminoAcidResidue::Proline : public AminoAcidResidue {
public:
    Proline() 
        : AminoAcidResidue("proline", "Pro", 'P')
    {
        // TODO check chirality of all these hydrogen names (in all residues)

        // beta methylene
        bondAtom(AliphaticCarbon("CB"), "bondCA");
        bondAtom(AliphaticHydrogen("1HB"), "CB/bond3");
        bondAtom(AliphaticHydrogen("2HB"), "CB/bond4");

        // gamma methylene
        bondAtom(AliphaticCarbon("CG"), "CB/bond2");
        bondAtom(AliphaticHydrogen("1HG"), "CG/bond3");
        bondAtom(AliphaticHydrogen("2HG"), "CG/bond4");

        // delta methylene
        bondAtom(AliphaticCarbon("CD"), "CG/bond2");
        bondAtom(AliphaticHydrogen("1HD"), "CD/bond3");
        bondAtom(AliphaticHydrogen("2HD"), "CD/bond4");

        addRingClosingBond("CD/bond2", "N/bond3", 0.14490);

        // defineDihedralAngle("phi", "CD", "N", "CA", "C", 180*Deg2Rad);

        defineDihedralAngle("chi1", "CG", "CB", "CA", "N");
        defineDihedralAngle("chi2", "CD", "CG", "CB", "CA");
        defineDihedralAngle("chi3", "N", "CD", "CG", "CB");
        defineDihedralAngle("chi4", "CA", "N", "CD", "CG"); // ring closing bond...

        // Ring strain decreases bond angles in the side chain
        // 102.9 chosen to match bond distance N-CD in beta down configuration
        // cmbruns
        setDefaultBondAngle(102.9*Deg2Rad, "N", "CA", "CB");
        setDefaultBondAngle(102.9*Deg2Rad, "CA", "CB", "CG");
        setDefaultBondAngle(102.9*Deg2Rad, "CB", "CG", "CD");
        setDefaultBondAngle(102.9*Deg2Rad, "CG", "CD", "N");

        setDefaultDownPucker();
        setDefaultPhiAngle(-70*Deg2Rad);

        // Fix phi angle for internal coordinate simulation
        setBondMobility(BondMobility::Rigid, "N", "CA");
    }

    // Up and down configurations are about equally abundant,
    // except in cis-proline, where down is preferred.
    // 
    // Ho, B.K.; Coutsias, E.A.; Seok, C.; & Dill, K.A. (2005) 
    // "The flexibility in the proline ring couples to the protein
    // backbone"  Protein Science: 14:1011-1018

    Proline& setDefaultUpPucker() { // red
        // Angles are estimated from figures in Ho et al
        // TODO get more accurate angles
        setDefaultDihedralAngle("chi1", -25*Deg2Rad);
        setDefaultDihedralAngle("chi2", 42*Deg2Rad);
        setDefaultDihedralAngle("chi3", -38*Deg2Rad);
        setDefaultDihedralAngle("chi4", 20*Deg2Rad);

        return *this;
    }

    Proline& setDefaultDownPucker() { // yellow, CG-endo
        // Angles from gaussian03 6-31G** restricted Hartree-Fock
        // minimization in beta main chain configuration
        setDefaultDihedralAngle("chi1", 32.8*Deg2Rad);
        setDefaultDihedralAngle("chi2", -35.9*Deg2Rad);
        setDefaultDihedralAngle("chi3", 25.0*Deg2Rad);
        setDefaultDihedralAngle("chi4", -16.9*Deg2Rad);

        // Angles are estimated from figures in Ho et al
        //setDefaultDihedralAngle("chi1", 30*Deg2Rad);
        //setDefaultDihedralAngle("chi2", -42*Deg2Rad);
        //setDefaultDihedralAngle("chi3", 38*Deg2Rad);
        //setDefaultDihedralAngle("chi4", -20*Deg2Rad);

        return *this;
    }

};


class  AminoAcidResidue::Glutamine : public AminoAcidResidue::BetaUnbranchedAminoAcidResidue {
public:
    Glutamine() 
        : AminoAcidResidue::BetaUnbranchedAminoAcidResidue("glutamine", "Gln", 'Q')
    {
        bondAtom( AliphaticCarbon("CG"), "bondCB" );
        bondAtom( AliphaticHydrogen("1HG"), "CG/bond3" ); 
        bondAtom( AliphaticHydrogen("2HG"), "CG/bond4" ); 

        bondAtom(TrivalentAtom("CD", Element::Carbon(), 120.4*Deg2Rad, 116.6*Deg2Rad), "CG/bond2", 0.15220);

        bondAtom(UnivalentAtom("OE1", Element::Oxygen()), "CD/bond2", 0.12290);

        bondAtom(TrivalentAtom("NE2", Element::Nitrogen()), "CD/bond3", 0.13350);
        bondAtom(UnivalentAtom("1HE2", Element::Hydrogen()), "NE2/bond2", 0.1010);
        bondAtom(UnivalentAtom("2HE2", Element::Hydrogen()), "NE2/bond3", 0.1010);

        defineDihedralAngle("chi2", "CD", "CG", "CB", "CA");
        defineDihedralAngle("chi3", "OE1", "CD", "CG", "CB");

        setDefaultDihedralAngle("chi3", -20*Deg2Rad);

        // For internal coordinate simulation, make amide group rigid
        setBondMobility(BondMobility::Rigid, "CD", "NE2");

    }
};


class  AminoAcidResidue::Arginine : public AminoAcidResidue::BetaUnbranchedAminoAcidResidue {
public:
    Arginine()
        : AminoAcidResidue::BetaUnbranchedAminoAcidResidue("arginine", "Arg", 'R') 
    {
        bondAtom(AliphaticCarbon("CG"), "bondCB");
        bondAtom(AliphaticHydrogen("1HG"), "CG/bond3");
        bondAtom(AliphaticHydrogen("2HG"), "CG/bond4");

        bondAtom(AliphaticCarbon("CD"), "CG/bond2");
        bondAtom(AliphaticHydrogen("1HD"), "CD/bond3");
        bondAtom(AliphaticHydrogen("2HD"), "CD/bond4");

        // TODO - set bond angle CB/CD/NE to 111.2

        bondAtom(TrivalentAtom("NE", Element::Nitrogen(), 123.2*Deg2Rad, 118.4*Deg2Rad), "CD/bond2", 0.1436, 180*Deg2Rad);
        bondAtom(UnivalentAtom("HE", Element::Hydrogen()), "NE/bond3", 0.1010);

        bondAtom(TrivalentAtom("CZ", Element::Carbon()), "NE/bond2", 0.1340, 180*Deg2Rad);

        bondAtom(TrivalentAtom("NH1", Element::Nitrogen()), "CZ/bond2", 0.1340, 180*Deg2Rad);
        bondAtom(UnivalentAtom("1HH1", Element::Hydrogen()), "NH1/bond2", 0.1010);
        bondAtom(UnivalentAtom("2HH1", Element::Hydrogen()), "NH1/bond3", 0.1010);

        bondAtom(TrivalentAtom("NH2", Element::Nitrogen()), "CZ/bond3", 0.1340, 180*Deg2Rad);
        bondAtom(UnivalentAtom("1HH2", Element::Hydrogen()), "NH2/bond2", 0.1010);
        bondAtom(UnivalentAtom("2HH2", Element::Hydrogen()), "NH2/bond3", 0.1010);

        defineDihedralAngle("chi2", "CD", "CG", "CB", "CA");
        defineDihedralAngle("chi3", "NE", "CD", "CG", "CB");
        defineDihedralAngle("chi4", "CZ", "NE", "CD", "CG");
        defineDihedralAngle("chi5", "NH1", "CZ", "NE", "CD");

        // TODO research default dihedral for chi4

        // Make guanidinium group rigid for internal coordinate simulation (resonance)
        setBondMobility(BondMobility::Rigid, "CZ", "NH1");
        setBondMobility(BondMobility::Rigid, "CZ", "NH2");
        setBondMobility(BondMobility::Rigid, "NE", "CZ");
    }
};

    
class  AminoAcidResidue::Serine : public AminoAcidResidue::BetaUnbranchedAminoAcidResidue {
public:
    Serine() 
        : AminoAcidResidue::BetaUnbranchedAminoAcidResidue("serine", "Ser", 'S')
    {
        // side chain hydroxyl group
        bondCompound("oh", AlcoholOHGroup(), "bondCB");
        nameAtom("OG", "oh/O", Biotype::SerineOG().getIndex() );
        nameAtom("HG", "oh/H", Biotype::SerineHG().getIndex() );

        defineDihedralAngle("chi2", "HG", "OG", "CB", "CA");

        // Set atom biotypes
        setBiotypeIndex("N", Biotype::SerineN().getIndex() );
        setBiotypeIndex("HN", Biotype::SerineHN().getIndex() );
        setBiotypeIndex("CA", Biotype::SerineCA().getIndex() );
        setBiotypeIndex("HA", Biotype::SerineHA().getIndex() );
        setBiotypeIndex("C", Biotype::SerineC().getIndex() );
        setBiotypeIndex("O", Biotype::SerineO().getIndex() );
    }
};

// Threonine has a chirality about the beta carbon, so care
// must be observed when placing groups
// Thus derive from AminoAcidResidue instead of from BetaBranchedAminoAcidResidue
class  AminoAcidResidue::Threonine : public AminoAcidResidue::BetaBranchedAminoAcidResidue {
public:
    Threonine()
        : AminoAcidResidue::BetaBranchedAminoAcidResidue("threonine", "Thr", 'T')
    {
        // hydroxyl has precedence over methyl and hydrogen
        // w.r.t. dihedral definition
        bondCompound("gamma hydroxyl", AlcoholOHGroup(), "bondCB1");
        nameAtom("OG1", "gamma hydroxyl/O");
        nameAtom("HG1", "gamma hydroxyl/H");

        // place methyl and hydrogen so as to get correct chirality
        // i.e. clockwise rotation of OG/H/CG when viewed down CA/CB bond

        bondCompound("gamma methyl", MethylGroup(), "bondCB2");
        nameAtom("CG2", "gamma methyl/C");
        nameAtom("1HG2", "gamma methyl/H1");
        nameAtom("2HG2", "gamma methyl/H2");
        nameAtom("3HG2", "gamma methyl/H3");
    }
};


// To get atom precedence correct, build custom side chain,
// rather than deriving from BetaBranchedAminoAcidResidue
class  AminoAcidResidue::Valine : public AminoAcidResidue::HNAminoAcidResidue {
public:
    Valine()
        : AminoAcidResidue::HNAminoAcidResidue("valine", "Val", 'V')
    {
        bondAtom(AliphaticCarbon("CB"), "bondCA");
        bondAtom(AliphaticHydrogen("HB"), "CB/bond4");

        bondCompound("gamma methyl 1", MethylGroup(), "CB/bond2");
        nameAtom("CG1", "gamma methyl 1/C");
        nameAtom("1HG1", "gamma methyl 1/H1");
        nameAtom("2HG1", "gamma methyl 1/H2");
        nameAtom("3HG1", "gamma methyl 1/H3");

        bondCompound("gamma methyl 2", MethylGroup(), "CB/bond3");
        nameAtom("CG2", "gamma methyl 2/C");
        nameAtom("1HG2", "gamma methyl 2/H1");
        nameAtom("2HG2", "gamma methyl 2/H2");
        nameAtom("3HG2", "gamma methyl 2/H3");

        defineDihedralAngle("chi1", "CG1", "CB", "CA", "N");

        // definition of CG1 vs. CG2 makes preferred chi1 180 instead of -60 for valine
        setDefaultDihedralAngle("chi1", 180*Deg2Rad);
    }
};


class  AminoAcidResidue::Tryptophan : public AminoAcidResidue::BetaUnbranchedAminoAcidResidue {
public:
    Tryptophan()
        : AminoAcidResidue::BetaUnbranchedAminoAcidResidue("tryptophan", "Trp", 'W')
    {
        bondAtom( TrivalentAtom("CG", Element::Carbon(), 125.0*Deg2Rad, 128.6*Deg2Rad), "bondCB", 0.14950);

        // 125.65 angle computed to place hydrogen symmetrically
        bondAtom( TrivalentAtom("CD1", Element::Carbon(), 108.7*Deg2Rad, 125.65*Deg2Rad), "CG/bond2", 0.13520, 180*Deg2Rad);
        bondAtom( UnivalentAtom("HD1", Element::Hydrogen()), "CD1/bond3", 0.1080);

        // 124.25 computed to center hydrogen
        bondAtom( TrivalentAtom("NE1", Element::Nitrogen(), 111.50*Deg2Rad, 124.25*Deg2Rad), "CD1/bond2", 0.13810, 0*Deg2Rad);
        bondAtom( UnivalentAtom("HE1", Element::Hydrogen()), "NE1/bond3", 0.1010);

        bondAtom( TrivalentAtom("CE2", Element::Carbon(), 104.4*Deg2Rad, 132.80*Deg2Rad), "NE1/bond2", 0.1380, 0*Deg2Rad);

        // 180 degrees to bulge back out for the six-membered ring
        bondAtom( TrivalentAtom("CZ2", Element::Carbon()), "CE2/bond3", 0.1400, 180*Deg2Rad);
        bondAtom( UnivalentAtom("HZ2", Element::Hydrogen()), "CZ2/bond3", 0.1080);

        bondAtom( TrivalentAtom("CH2", Element::Carbon()), "CZ2/bond2", 0.1400, 0*Deg2Rad);
        bondAtom( UnivalentAtom("HH2", Element::Hydrogen()), "CH2/bond3", 0.1080);



        bondAtom( TrivalentAtom("CD2", Element::Carbon(), 108.8*Deg2Rad, 122.7*Deg2Rad), "CE2/bond2", 0.1419, 0*Deg2Rad);
        addRingClosingBond("CD2/bond2", "CG/bond3", 0.1459);

        bondAtom( TrivalentAtom("CE3", Element::Carbon()), "CD2/bond3", 0.1404, 0*Deg2Rad);
        bondAtom( UnivalentAtom("HE3", Element::Hydrogen()), "CE3/bond3", 0.1080);

        bondAtom( TrivalentAtom("CZ3", Element::Carbon()), "CE3/bond2", 0.1400, 0*Deg2Rad);
        bondAtom( UnivalentAtom("HZ3", Element::Hydrogen()), "CZ3/bond3", 0.1080);

        addRingClosingBond("CZ3/bond2", "CH2/bond2", 0.1400);

        defineDihedralAngle("chi2", "CD1", "CG", "CB", "CA");

        setDefaultDihedralAngle("chi2", 90*Deg2Rad);

        setBondMobility(BondMobility::Rigid, "CG", "CD1");
        setBondMobility(BondMobility::Rigid, "CD1", "NE1");
        setBondMobility(BondMobility::Rigid, "NE1", "CE2");
        setBondMobility(BondMobility::Rigid, "CZ2", "CE2");
        setBondMobility(BondMobility::Rigid, "CH2", "CZ2");
        setBondMobility(BondMobility::Rigid, "CD2", "CE3");
        setBondMobility(BondMobility::Rigid, "CZ3", "CE3");
        setBondMobility(BondMobility::Rigid, "CZ3", "CH2");
    }
};


class  AminoAcidResidue::Tyrosine : public AminoAcidResidue::BetaUnbranchedAminoAcidResidue {
public:
    Tyrosine()
        : AminoAcidResidue::BetaUnbranchedAminoAcidResidue("tyrosine", "Tyr", 'Y')
    {
        static const mdunits::Length CB_CGdistance = 0.1510;
        static const mdunits::Length C_Hdistance = 0.1080; // from tinker amber99.dat
        static const mdunits::Length C_Cdistance = 0.1400; // from tinker amber99.dat
        static const mdunits::Length CZ_Odistance = 0.1364; // from tinker amber99.dat

        // default angle for TrivalentAtom is 120 degrees, which is what we want
        // for a six-membered ring
        bondAtom( TrivalentAtom("CG", Element::Carbon()), "bondCB", CB_CGdistance, 180*Deg2Rad);

        bondAtom( TrivalentAtom("CD1", Element::Carbon()), "CG/bond2", C_Cdistance, 180*Deg2Rad );
        bondAtom( UnivalentAtom("HD1", Element::Hydrogen()), "CD1/bond3", C_Hdistance );

        // Start using hidedral of zero, to loop ring back to beginning
        bondAtom( TrivalentAtom("CE1", Element::Carbon()), "CD1/bond2", C_Cdistance, 0*Deg2Rad );
        bondAtom( UnivalentAtom("HE1", Element::Hydrogen()), "CE1/bond3", C_Hdistance );

        bondAtom( TrivalentAtom("CZ", Element::Carbon()), "CE1/bond2", C_Cdistance, 180*Deg2Rad );
        bondCompound( "oh", AlcoholOHGroup(), "CZ/bond2", CZ_Odistance );
        nameAtom("OH", "oh/O");
        nameAtom("HH", "oh/H");

        bondAtom( TrivalentAtom("CE2", Element::Carbon()), "CZ/bond3", C_Cdistance, 0*Deg2Rad );
        bondAtom( UnivalentAtom("HE2", Element::Hydrogen()), "CE2/bond3", C_Hdistance );

        bondAtom( TrivalentAtom("CD2", Element::Carbon()), "CE2/bond2", C_Cdistance, 0*Deg2Rad );
        bondAtom( UnivalentAtom("HD2", Element::Hydrogen()), "CD2/bond3", C_Hdistance );

        addRingClosingBond("CD2/bond2", "CG/bond3", 0.1459);

        defineDihedralAngle("chi2", "CD1", "CG", "CB", "CA");

        setDefaultDihedralAngle("chi2", 90*Deg2Rad); // from Dunbrack site

        setBondMobility(BondMobility::Rigid, "CG", "CD1");
        setBondMobility(BondMobility::Rigid, "CD1", "CE1");
        setBondMobility(BondMobility::Rigid, "CE1", "CZ");
        setBondMobility(BondMobility::Rigid, "CZ", "CE2");
        setBondMobility(BondMobility::Rigid, "CE2", "CD2");
        setBondMobility(BondMobility::Rigid, "CD2", "CG");
    }
};


class SimTK_MOLMODEL_EXPORT Protein : public Biopolymer {
public:

    void loadFromPdbStructure(const PdbStructure& pdbStructure, SimTK::Real targetRms)
    {
        const PdbChain& pdbChain = pdbStructure.getModel(Pdb::ModelIndex(0)).getChain(Pdb::ChainIndex(0));
        loadFromPdbChain(pdbChain, targetRms);
    }
    
    void loadFromPdbChain(const PdbChain& pdbChain, SimTK::Real targetRms);
    
    explicit Protein(std::istream& pdbStream, SimTK::Real targetRms = 0.02)
    {
        PdbStructure pdbStructure(pdbStream);
        loadFromPdbStructure(pdbStructure, targetRms);
    }
    
    explicit Protein(const PdbStructure& pdbStructure, SimTK::Real targetRms = 0.02)
    {
        loadFromPdbStructure(pdbStructure, targetRms);
    }
    
    explicit Protein(const PdbChain& pdbChain, SimTK::Real targetRms)
    {
        loadFromPdbChain(pdbChain, targetRms);
    }
    
    explicit Protein(const Sequence& seq, const BondMobility::Mobility mobility= BondMobility::Rigid, bool addEndCaps = true  ) 
    {
        initialize(seq, mobility, addEndCaps);
    }
    
    explicit Protein( const Sequence& seq, CompoundSystem& system, Transform transform = Transform() ) 
    {
        initialize(seq, BondMobility::Rigid);
        system.adoptCompound(*this, transform);
    }
    
protected:
    void initialize( const Sequence& seq, const BondMobility::Mobility mobility , bool addEndCaps = true) 
    {
        Biotype::initializePopularBiotypes();
        
        // TODO - provide alternatives for end caps
        String previousResidueName = "acetyl0";
        if (addEndCaps) appendResidue(previousResidueName, AcetylResidue());

        for (int resi = 0; resi < (int)seq.size(); ++resi)
        {
            AminoAcidResidue residue = AminoAcidResidue::create(seq[resi]);
            residue.setPdbResidueNumber(resi + 1);
            residue.assignBiotypes();

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

            // Rigidify peptide bond 
            if (getNumResidues() > 1) // First residue lacks a preceding peptide bond
            {
                String omegaAngleName = String("omega") + String(resi);

                defineDihedralAngle(
                    omegaAngleName, 
                    previousResidueName+"/C/bond1", 
                    residueName+"/N/bond2");
                setDefaultDihedralAngle(omegaAngleName, 180*Deg2Rad);

                // Make omega torsion rigid
                String cAtomName = previousResidueName + "/" + "C";
                String nAtomName = residueName + "/" + "N";
                setBondMobility(mobility, cAtomName, nAtomName);
            }

            previousResidueName = residueName;
        }

        // TODO - create C-terminal end cap, if we are producing end caps
        String cCapName = String("nme") + String((int)seq.size());
        if (addEndCaps) appendResidue(cCapName, NMethylAmideResidue());
        // Rigidify final omega angle
        String omegaAngleName = String("omega") + String(cCapName);
        defineDihedralAngle(
            omegaAngleName, 
            previousResidueName+"/C/bond1", 
            cCapName+"/N/bond2");
        setDefaultDihedralAngle(omegaAngleName, 180*Deg2Rad);

        // Make omega torsion rigid
        String cAtomName = previousResidueName + "/" + "C";
        String nAtomName = cCapName + "/" + "N";
        setBondMobility(BondMobility::Rigid, cAtomName, nAtomName);
    }
};


} // namespace SimTK

#endif // SimTK_MOLMODEL_PROTEIN_H_