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protocols::cartesian::MolecularDynamics Class Reference

#include <md.hh>

Public Member Functions

 MolecularDynamics (core::pose::PoseOP &inputpose, core::scoring::ScoreFunction const &scorefxn)
 
void doMinimising (core::scoring::ScoreFunction const &scorefxn)
 
void doMD (core::scoring::ScoreFunction const &scorefxn, int Steps, float startTemp, float endTemp)
 
void testCartesianDerivatives (core::scoring::ScoreFunction const &scorefxn)
 

Private Member Functions

void createCartesianArray ()
 
void setCartesianPositionsFromPose ()
 
void setPosePositionsFromCartesian ()
 
void zeroForces ()
 
int findCartomAtom (const core::id::AtomID &id1)
 
void getCartesianDerivatives (core::scoring::ScoreFunction const &scorefxn)
 
void createBondList ()
 
void createAngleList ()
 
void createDihedralList ()
 Yes i know this is hard coded stuff. Read warning at the top of this file. More...
 
MD_HarmonicDihedral createDihedral (const core::conformation::Residue &rsd, std::string const &name1, std::string const &name2, std::string const &name3, std::string const &name4)
 
MD_HarmonicDihedral createDihedral (const core::conformation::Residue &rsd1, const core::conformation::Residue &rsd2, const core::conformation::Residue &rsd3, const core::conformation::Residue &rsd4, std::string const &name1, std::string const &name2, std::string const &name3, std::string const &name4)
 
void setDihedralDerivatives ()
 
void doBondDerivatives (float &totalepot)
 
void doAngleDerivatives (float &totalepot)
 
void doDihedralDerivatives (float &totalepot)
 
void createCartesianDerivatives (core::pose::Pose &pose, core::scoring::ScoreFunction const &scorefxn)
 
void setInitialSpeeds (core::Real tgtTemp)
 
void calcKineticEnergy (float &ekin, float &Temp)
 
void applyForces_BeeMan (float &kin, float &temp)
 
void applyForces_LangevinIntegration (core::Real T, float &kin, float &temp)
 
void applyForces_ConjugateGradient (int Step, float &current_energy, float &m_OldEnergy)
 
void createCartesianDerivatives (core::scoring::ScoreFunction const &scorefxn)
 

Private Attributes

utility::vector1< CartesianAtomcartom
 
utility::vector1< MD_Bondbondlist
 
utility::vector1< MD_Angleanglelist
 
utility::vector1
< MD_HarmonicDihedral
dihedrallist
 
core::kinematics::MoveMap mm
 
core::optimization::MinimizerMap min_map
 
core::kinematics::DomainMap domain_map
 
core::pose::PoseOP pose
 

Constructor & Destructor Documentation

protocols::cartesian::MolecularDynamics::MolecularDynamics ( core::pose::PoseOP inputpose,
core::scoring::ScoreFunction const &  scorefxn 
)

Member Function Documentation

void protocols::cartesian::MolecularDynamics::applyForces_BeeMan ( float &  kin,
float &  temp 
)
private
void protocols::cartesian::MolecularDynamics::applyForces_ConjugateGradient ( int  Step,
float &  current_energy,
float &  m_OldEnergy 
)
private

References cartom.

Referenced by doMinimising().

void protocols::cartesian::MolecularDynamics::applyForces_LangevinIntegration ( core::Real  T,
float &  kin,
float &  temp 
)
private
void protocols::cartesian::MolecularDynamics::calcKineticEnergy ( float &  ekin,
float &  Temp 
)
private
void protocols::cartesian::MolecularDynamics::createAngleList ( )
private
void protocols::cartesian::MolecularDynamics::createBondList ( )
private
void protocols::cartesian::MolecularDynamics::createCartesianArray ( )
private
void protocols::cartesian::MolecularDynamics::createCartesianDerivatives ( core::pose::Pose pose,
core::scoring::ScoreFunction const &  scorefxn 
)
private
void protocols::cartesian::MolecularDynamics::createCartesianDerivatives ( core::scoring::ScoreFunction const &  scorefxn)
private
MD_HarmonicDihedral protocols::cartesian::MolecularDynamics::createDihedral ( const core::conformation::Residue rsd,
std::string const &  name1,
std::string const &  name2,
std::string const &  name3,
std::string const &  name4 
)
private

Referenced by createDihedralList().

MD_HarmonicDihedral protocols::cartesian::MolecularDynamics::createDihedral ( const core::conformation::Residue rsd1,
const core::conformation::Residue rsd2,
const core::conformation::Residue rsd3,
const core::conformation::Residue rsd4,
std::string const &  name1,
std::string const &  name2,
std::string const &  name3,
std::string const &  name4 
)
private
void protocols::cartesian::MolecularDynamics::createDihedralList ( )
private
void protocols::cartesian::MolecularDynamics::doAngleDerivatives ( float &  totalepot)
private

References anglelist, cartom, pose, and protocols::cartesian::sqr().

Referenced by doMD(), and doMinimising().

void protocols::cartesian::MolecularDynamics::doBondDerivatives ( float &  totalepot)
private

References bondlist, cartom, pose, and protocols::cartesian::sqr().

Referenced by doMD(), and doMinimising().

void protocols::cartesian::MolecularDynamics::doDihedralDerivatives ( float &  totalepot)
private

References cartom, dihedrallist, and protocols::cartesian::sqr().

Referenced by doMD(), and doMinimising().

void protocols::cartesian::MolecularDynamics::doMD ( core::scoring::ScoreFunction const &  scorefxn,
int  Steps,
float  startTemp,
float  endTemp 
)
void protocols::cartesian::MolecularDynamics::doMinimising ( core::scoring::ScoreFunction const &  scorefxn)
int protocols::cartesian::MolecularDynamics::findCartomAtom ( const core::id::AtomID id1)
private
void protocols::cartesian::MolecularDynamics::getCartesianDerivatives ( core::scoring::ScoreFunction const &  scorefxn)
private
void protocols::cartesian::MolecularDynamics::setCartesianPositionsFromPose ( )
private

References cartom, and pose.

void protocols::cartesian::MolecularDynamics::setDihedralDerivatives ( )
private
void protocols::cartesian::MolecularDynamics::setInitialSpeeds ( core::Real  tgtTemp)
private

References cartom, and core::pose::mass().

Referenced by doMD().

void protocols::cartesian::MolecularDynamics::setPosePositionsFromCartesian ( )
private

References cartom, and pose.

Referenced by doMD(), and doMinimising().

void protocols::cartesian::MolecularDynamics::testCartesianDerivatives ( core::scoring::ScoreFunction const &  scorefxn)
void protocols::cartesian::MolecularDynamics::zeroForces ( )
private

References cartom.

Referenced by doMinimising().

Member Data Documentation

utility::vector1< MD_Angle > protocols::cartesian::MolecularDynamics::anglelist
private
utility::vector1< MD_Bond > protocols::cartesian::MolecularDynamics::bondlist
private
utility::vector1< CartesianAtom > protocols::cartesian::MolecularDynamics::cartom
private
utility::vector1< MD_HarmonicDihedral > protocols::cartesian::MolecularDynamics::dihedrallist
private
core::kinematics::DomainMap protocols::cartesian::MolecularDynamics::domain_map
private
core::optimization::MinimizerMap protocols::cartesian::MolecularDynamics::min_map
private
core::kinematics::MoveMap protocols::cartesian::MolecularDynamics::mm
private

Referenced by MolecularDynamics().

core::pose::PoseOP protocols::cartesian::MolecularDynamics::pose
private

The documentation for this class was generated from the following files: