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protocols::cartesian::MolecularDynamics Class Reference

#include <md.hh>

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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 name1, std::string name2, std::string name3, std::string 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 name1, std::string name2, std::string name3, std::string 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 (double tgtTemp)
 
void calcKineticEnergy (float &ekin, float &Temp)
 
void applyForces_BeeMan (float &kin, float &temp)
 
void applyForces_LangevinIntegration (double 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< CartesianAtom > cartom
 
utility::vector1< MD_Bond > bondlist
 
utility::vector1< MD_Angle > anglelist
 
utility::vector1
< MD_HarmonicDihedral > 		dihedrallist
 
core::kinematics::MoveMap mm
 
core::optimization::MinimizerMap min_map
 
core::kinematics::DomainMap domain_map
 
core::pose::PoseOP pose
 

Detailed Description

Definition at line 93 of file md.hh.

Constructor & Destructor Documentation

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

Definition at line 77 of file md.cc.

References createAngleList(), createBondList(), createCartesianArray(), createDihedralList(), core::optimization::MinimizerMap::domain_map(), min_map, mm, pose, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), setDihedralDerivatives(), core::optimization::MinimizerMap::setup(), and core::scoring::ScoreFunction::setup_for_minimizing().

Member Function Documentation

void protocols::cartesian::MolecularDynamics::applyForces_BeeMan ( float &  kin,
float &  temp 
)
private

Definition at line 1336 of file md.cc.

References calcKineticEnergy(), cartom, protocols::comparative_modeling::features::E, and core::scoring::hbonds::t().

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

Definition at line 1540 of file md.cc.

References cartom.

Referenced by doMinimising().

void protocols::cartesian::MolecularDynamics::applyForces_LangevinIntegration ( double  T,
float &  kin,
float &  temp 
)
private

Definition at line 1401 of file md.cc.

References calcKineticEnergy(), cartom, protocols::comparative_modeling::features::E, protocols::cartesian::sqr(), and core::scoring::hbonds::t().

Referenced by doMD().

void protocols::cartesian::MolecularDynamics::calcKineticEnergy ( float &  ekin,
float &  Temp 
)
private

Definition at line 1317 of file md.cc.

References cartom.

Referenced by applyForces_BeeMan(), and applyForces_LangevinIntegration().

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

Definition at line 548 of file md.cc.

References anglelist, protocols::cartesian::MD_Angle::atom_id_1, protocols::cartesian::MD_Angle::atom_id_2, protocols::cartesian::MD_Angle::atom_id_3, bondlist, cartom, protocols::cartesian::MD_Angle::index1, protocols::cartesian::MD_Angle::index2, protocols::cartesian::MD_Angle::index3, protocols::cartesian::MD_Angle::length, and pose.

Referenced by MolecularDynamics().

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

Definition at line 469 of file md.cc.

References protocols::cartesian::MD_Bond::atom_id_1, protocols::cartesian::MD_Bond::atom_id_2, core::conformation::Residue::bonded_neighbor(), bondlist, cartom, core::conformation::Residue::connect_atom(), protocols::cartesian::MD_Bond::index1, protocols::cartesian::MD_Bond::index2, and pose.

Referenced by MolecularDynamics().

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

Definition at line 121 of file md.cc.

References protocols::cartesian::CartesianAtom::atom_id, cartom, protocols::cartesian::CartesianAtom::force, protocols::cartesian::CartesianAtom::index, protocols::cartesian::CartesianAtom::mass, protocols::cartesian::CartesianAtom::old_force, protocols::cartesian::CartesianAtom::old_position, protocols::cartesian::CartesianAtom::old_velocity, pose, protocols::cartesian::CartesianAtom::position, protocols::cartesian::CartesianAtom::res, and protocols::cartesian::CartesianAtom::velocity.

Referenced by MolecularDynamics(), and testCartesianDerivatives().

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

Definition at line 1261 of file md.cc.

References protocols::cartesian::CartesianAtom::atom_id, cartom, core::optimization::MinimizerMap::domain_map(), core::scoring::ScoreFunction::eval_npd_atom_derivative(), protocols::cartesian::CartesianAtom::force, protocols::cartesian::CartesianAtom::index, min_map, protocols::cartesian::CartesianAtom::old_force, protocols::cartesian::CartesianAtom::old_position, protocols::cartesian::CartesianAtom::old_velocity, pose, protocols::cartesian::CartesianAtom::res, and core::scoring::ScoreFunction::setup_for_derivatives().

MD_HarmonicDihedral protocols::cartesian::MolecularDynamics::createDihedral ( const core::conformation::Residue &  rsd,
std::string  name1,
std::string  name2,
std::string  name3,
std::string  name4 
)
private

Definition at line 666 of file md.cc.

References protocols::cartesian::MD_HarmonicDihedral::atom_id_1, core::conformation::Residue::atom_index(), findCartomAtom(), and core::conformation::Residue::seqpos().

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  name1,
std::string  name2,
std::string  name3,
std::string  name4 
)
private

Definition at line 610 of file md.cc.

References protocols::cartesian::MD_HarmonicDihedral::atom_id_1, core::conformation::Residue::atom_index(), findCartomAtom(), and core::conformation::Residue::seqpos().

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

Yes i know this is hard coded stuff. Read warning at the top of this file.

Definition at line 717 of file md.cc.

References core::conformation::Residue::aa(), core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_his, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_trp, core::chemical::aa_tyr, createDihedral(), dihedrallist, core::conformation::Residue::has(), and pose.

Referenced by MolecularDynamics().

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

Definition at line 1059 of file md.cc.

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

Referenced by doMD(), and doMinimising().

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

Definition at line 1035 of file md.cc.

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

Referenced by doMD(), and doMinimising().

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

Definition at line 1083 of file md.cc.

References cartom, dihedrallist, protocols::swa::phi(), 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 
)

Definition at line 1695 of file md.cc.

References applyForces_LangevinIntegration(), doAngleDerivatives(), doBondDerivatives(), doDihedralDerivatives(), protocols::abinitio::filename(), getCartesianDerivatives(), pose, setInitialSpeeds(), and setPosePositionsFromCartesian().

void protocols::cartesian::MolecularDynamics::doMinimising ( core::scoring::ScoreFunction const &  scorefxn)

Definition at line 1633 of file md.cc.

References applyForces_ConjugateGradient(), doAngleDerivatives(), doBondDerivatives(), doDihedralDerivatives(), protocols::abinitio::filename(), getCartesianDerivatives(), pose, setPosePositionsFromCartesian(), and zeroForces().

int protocols::cartesian::MolecularDynamics::findCartomAtom ( const core::id::AtomID &  id1)
private

Definition at line 181 of file md.cc.

References core::id::AtomID::atomno(), cartom, and core::id::AtomID::rsd().

Referenced by createDihedral(), and getCartesianDerivatives().

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

Definition at line 197 of file md.cc.

References core::optimization::MinimizerMap::begin(), cartom, core::optimization::DOF_Node::dof_id(), core::optimization::MinimizerMap::domain_map(), core::optimization::MinimizerMap::end(), core::scoring::ScoreFunction::eval_dof_derivative(), core::scoring::ScoreFunction::eval_npd_atom_derivative(), findCartomAtom(), min_map, pose, core::scoring::ScoreFunction::setup_for_derivatives(), protocols::cartesian::sqr(), and core::optimization::DOF_Node::torsion_id().

Referenced by doMD(), doMinimising(), and testCartesianDerivatives().

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

Definition at line 151 of file md.cc.

References cartom, and pose.

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

Definition at line 966 of file md.cc.

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

Referenced by MolecularDynamics().

void protocols::cartesian::MolecularDynamics::setInitialSpeeds ( double  tgtTemp)
private

Definition at line 1301 of file md.cc.

References cartom, and protocols::comparative_modeling::features::E.

Referenced by doMD().

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

Definition at line 162 of file md.cc.

References cartom, and pose.

Referenced by doMD(), and doMinimising().

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

Definition at line 1778 of file md.cc.

References cartom, createCartesianArray(), getCartesianDerivatives(), pose, and core::scoring::ScoreFunction::show().

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

Definition at line 172 of file md.cc.

References cartom.

Referenced by doMinimising().

Member Data Documentation

utility::vector1< MD_Angle > protocols::cartesian::MolecularDynamics::anglelist
private

Definition at line 196 of file md.hh.

Referenced by createAngleList(), and doAngleDerivatives().

utility::vector1< MD_Bond > protocols::cartesian::MolecularDynamics::bondlist
private

Definition at line 195 of file md.hh.

Referenced by createAngleList(), createBondList(), and doBondDerivatives().

utility::vector1< CartesianAtom > protocols::cartesian::MolecularDynamics::cartom
private

Definition at line 194 of file md.hh.

Referenced by applyForces_BeeMan(), applyForces_ConjugateGradient(), applyForces_LangevinIntegration(), calcKineticEnergy(), createAngleList(), createBondList(), createCartesianArray(), createCartesianDerivatives(), doAngleDerivatives(), doBondDerivatives(), doDihedralDerivatives(), findCartomAtom(), getCartesianDerivatives(), setCartesianPositionsFromPose(), setDihedralDerivatives(), setInitialSpeeds(), setPosePositionsFromCartesian(), testCartesianDerivatives(), and zeroForces().

utility::vector1< MD_HarmonicDihedral > protocols::cartesian::MolecularDynamics::dihedrallist
private

Definition at line 197 of file md.hh.

Referenced by createDihedralList(), doDihedralDerivatives(), and setDihedralDerivatives().

core::kinematics::DomainMap protocols::cartesian::MolecularDynamics::domain_map
private

Definition at line 201 of file md.hh.

core::optimization::MinimizerMap protocols::cartesian::MolecularDynamics::min_map
private

Definition at line 200 of file md.hh.

Referenced by createCartesianDerivatives(), getCartesianDerivatives(), and MolecularDynamics().

core::kinematics::MoveMap protocols::cartesian::MolecularDynamics::mm
private

Definition at line 199 of file md.hh.

Referenced by MolecularDynamics().

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

Definition at line 203 of file md.hh.

Referenced by createAngleList(), createBondList(), createCartesianArray(), createCartesianDerivatives(), createDihedralList(), doAngleDerivatives(), doBondDerivatives(), doMD(), doMinimising(), getCartesianDerivatives(), MolecularDynamics(), setCartesianPositionsFromPose(), setPosePositionsFromCartesian(), and testCartesianDerivatives().

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