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#ifndef SetChiMobility_H_
#define SetChiMobility_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) 2006-7 Stanford University and the Authors. *
* Authors: Samuel Flores *
* 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. *
* -------------------------------------------------------------------------- */
//using std::cout;
//using std::endl;
class SetChiMobility : public Biopolymer { public:
SetChiMobility ( //this polymorphism, with one less parameter, sets up welds to rigidify the chi bond without losing the body frames of the glycosidic nitrogens.
Biopolymer & myChain,
int residueNumber,
LeontisWesthofClass & myLeontisWesthofClass ,
SimbodyMatterSubsystem & matter,
State& state,
Constraint myWeld1,
Constraint myWeld2,
Constraint myWeld3
//BondMobility::Mobility mobility = BondMobility::Torsion
)
{
BondMobility::Mobility mobility = BondMobility::Torsion;
String myPdbResidueName1 = (myChain.updResidue(ResidueInfo::Index(residueNumber))).getPdbResidueName();
LeontisWesthofBondRow myLeontisWesthofBondRow2 = myLeontisWesthofClass.getLeontisWesthofBondRow((myChain.updResidue(ResidueInfo::Index(residueNumber))).getPdbResidueNumber(), (myChain.updResidue(ResidueInfo::Index(residueNumber))).getPdbResidueNumber() , myPdbResidueName1,"ChiBond","","","",0);
stringstream ss3;
ss3<<residueNumber<<"/"<<"C1*";
stringstream ss4;
ss4<<residueNumber<<"/"<<(myLeontisWesthofBondRow2.residue1Atom[1]);
myChain.setBondMobility(mobility,ss3.str(),ss4.str());
stringstream ss5;
ss5<<residueNumber<<"/"<<"O4*";
myChain.setBondMobility(BondMobility::Torsion,ss3.str(),ss5.str());
stringstream ss6;
ss6<<residueNumber<<"/"<<"C2*";
//C1* //C2*
myChain.setBondMobility(BondMobility::Torsion,ss3.str(),ss6.str());
const SimTK::Transform& mytransform1 = (matter.updMobilizedBody(myChain.getAtomMobilizedBodyIndex(myChain.getAtomIndex(ss3.str())))).findBodyTransformInAnotherBody(state,(matter.updMobilizedBody(myChain.getAtomMobilizedBodyIndex(myChain.getAtomIndex(ss4.str())))));
myWeld1 = Constraint::Weld (
matter.updMobilizedBody(myChain.getAtomMobilizedBodyIndex(myChain.getAtomIndex(ss3.str()))),
Transform(Vec3(0)),
(matter.updMobilizedBody(myChain.getAtomMobilizedBodyIndex(myChain.getAtomIndex(ss4.str())))),
mytransform1
);
const SimTK::Transform& mytransform2 = (matter.updMobilizedBody(myChain.getAtomMobilizedBodyIndex(myChain.getAtomIndex(ss3.str())))).findBodyTransformInAnotherBody(state,(matter.updMobilizedBody(myChain.getAtomMobilizedBodyIndex(myChain.getAtomIndex(ss5.str())))));
myWeld2 = Constraint::Weld (
(matter.updMobilizedBody(myChain.getAtomMobilizedBodyIndex(myChain.getAtomIndex(ss3.str())))),
Transform(Vec3(0)),
(matter.updMobilizedBody(myChain.getAtomMobilizedBodyIndex(myChain.getAtomIndex(ss5.str())))),
mytransform2
);
const SimTK::Transform& mytransform3 = (matter.updMobilizedBody(myChain.getAtomMobilizedBodyIndex(myChain.getAtomIndex(ss3.str())))).findBodyTransformInAnotherBody(state,(matter.updMobilizedBody(myChain.getAtomMobilizedBodyIndex(myChain.getAtomIndex(ss6.str())))));
myWeld3 = Constraint::Weld (
(matter.updMobilizedBody(myChain.getAtomMobilizedBodyIndex(myChain.getAtomIndex(ss3.str())))),
Transform(Vec3(0)),
(matter.updMobilizedBody(myChain.getAtomMobilizedBodyIndex(myChain.getAtomIndex(ss6.str())))),
mytransform3
);
}
SetChiMobility (
Biopolymer & myChain,
int residueNumber,
LeontisWesthofClass & myLeontisWesthofClass ,
BondMobility::Mobility mobility = BondMobility::Free
)
{
//std::cout<<"[SetChiMobility.h] mobility ="<<mobility<<std::endl;
String myPdbResidueName1 = (myChain.updResidue(ResidueInfo::Index(residueNumber))).getPdbResidueName();
LeontisWesthofBondRow myLeontisWesthofBondRow2 = myLeontisWesthofClass.getLeontisWesthofBondRow((myChain.updResidue(ResidueInfo::Index(residueNumber))).getPdbResidueNumber(), (myChain.updResidue(ResidueInfo::Index(residueNumber))).getPdbResidueNumber(),myPdbResidueName1,"ChiBond","","","",0);
stringstream ss3;
ss3<<residueNumber<<"/"<<"C1*";
stringstream ss4;
ss4<<residueNumber<<"/"<<(myLeontisWesthofBondRow2.residue1Atom[1]);
myChain.setBondMobility(mobility,ss3.str(),ss4.str());
stringstream ss5;
ss5<<residueNumber<<"/"<<"O4*";
myChain.setBondMobility(BondMobility::Torsion,ss3.str(),ss5.str());
stringstream ss6;
ss6<<residueNumber<<"/"<<"C2*";
myChain.setBondMobility(BondMobility::Torsion,ss3.str(),ss6.str());
}
};
#endif
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