#include <BranchAngleOptimizer.hh>

Public Member Functions
	BranchAngleOptimizer (core::scoring::mm::MMBondAngleLibrary const &mm_bondangle_library)

	BranchAngleOptimizer ()

	BranchAngleOptimizer (BranchAngleOptimizer const &src)

core::Real	tolerance () const

void	tolerance (core::Real tolerance)

virtual	~BranchAngleOptimizer ()

core::scoring::mm::MMBondAngleResidueTypeParamSetOP	bond_angle_residue_type_param_set ()

core::scoring::mm::MMBondAngleResidueTypeParamSetCOP	bond_angle_residue_type_param_set () const

void	bond_angle_residue_type_param_set (core::scoring::mm::MMBondAngleResidueTypeParamSetOP param_set)
	set input MMBondAngleResidueTypeParamSet, sharing with the input More...

void	bond_angle_residue_type_param_set (core::scoring::mm::MMBondAngleResidueTypeParamSetCOP param_set)
	set input MMBondAngleResidueTypeParamSet, making a copy More...

bool	initialized () const

core::Size	optimize_angles (core::pose::Pose &pose, core::id::AtomID main_atomid1, core::id::AtomID center_atomid, core::id::AtomID main_atomid2, bool optimize_for_minimum=false)
	optimize angles branching off the defined mainchain More...

core::Size	overall_params (core::pose::Pose const &pose, core::id::AtomID main_atomid1, core::id::AtomID center_atomid, core::id::AtomID main_atomid2, core::Real &Ktheta, core::Real &theta0, core::Real &energy0)
	get overall bond angle parameters for the defined mainchian More...

BranchParam1	param1 (core::pose::Pose const &pose, core::id::AtomID const &main_atomid1, core::id::AtomID const &center_atomid, core::id::AtomID const &main_atomid2, core::id::AtomID const &branch_atomid1) const
	get single branching atom bond angle parameters More...

BranchParam2	param2 (core::pose::Pose const &pose, core::id::AtomID const &main_atomid1, core::id::AtomID const &center_atomid, core::id::AtomID const &main_atomid2, core::id::AtomID const &branch_atomid1, core::id::AtomID const &branch_atomid2) const
	get double branching atom bond angle parameters More...

core::Size	num_coef1 () const
	get number of single branching atom coefficients More...

core::Size	num_coef2 () const
	get number of double branching atom coefficients More...

core::Size	num_undefined_coef1 () const
	get number of undefined single branching atom coefficients More...

core::Size	num_undefined_coef2 () const
	get number of undefined double branching atom coefficients More...

void	read_database ()
	read known parameters from the database More...

void	write_database () const
	write undefined parameters to the database More...

void	read_coef1 (std::istream &in)
	read single branching atom coefficients from an input stream More...

bool	read_coef1 (std::string const &filename)
	read single branching atom coefficients from a file More...

void	read_coef1_default ()
	read single branching atom coefficients from default database file More...

bool	read_coef1_user ()
	read single branching atom coefficients from user database file More...

void	read_coef2 (std::istream &in)
	read single branching atom coefficients More...

bool	read_coef2 (std::string const &filename)
	read double branching atom coefficients from a file More...

void	read_coef2_default ()
	read double branching atom coefficients from default database file More...

bool	read_coef2_user ()
	read double branching atom coefficients from user database file More...

void	read_undefined_coef1 (std::istream &in)
	read parameters for undefined single branching atom coefficients More...

bool	read_undefined_coef1 (std::string const &filename)
	read parameters for undefined single branching atom coefficients from a file More...

bool	read_undefined_coef1 ()
	read single branching atom undefined coefficients from the database file More...

void	write_undefined_coef1 (std::ostream &out) const
	write out parameters for undefined single branching atom coefficients More...

bool	write_undefined_coef1 (std::string const &filename) const
	write parameters for undefined single branching atom coefficients to a file More...

bool	write_undefined_coef1 () const
	write single branching atom undefined coefficients to the database file More...

void	read_undefined_coef2 (std::istream &in)
	read parameters for undefined double branching atom coefficients More...

bool	read_undefined_coef2 (std::string const &filename)
	read parameters for undefined double branching atom coefficients from a file More...

bool	read_undefined_coef2 ()
	read double branching atom undefined coefficients from the database file More...

void	write_undefined_coef2 (std::ostream &out) const
	write out parameters for undefined double branching atom coefficients More...

bool	write_undefined_coef2 (std::string const &filename) const
	write parameters for undefined double branching atom coefficients to a file More...

bool	write_undefined_coef2 () const
	write double branching atom undefined coefficients to the database file More...

Private Member Functions
BranchAngleOptimizer const &	operator= (BranchAngleOptimizer const &src)=delete

Private Attributes
core::scoring::mm::MMBondAngleLibrary const &	mm_bondangle_library_

core::scoring::mm::MMBondAngleResidueTypeParamSetOP	bond_angle_residue_type_param_set_

utility::vector1< BranchCoef1 >	coef1_

utility::vector1< BranchCoef2 >	coef2_

std::map< BranchParam1, core::Size >	coef_map1_

std::map< BranchParam2, core::Size >	coef_map2_

std::set< BranchParam1 >	undefined_coef1_

std::set< BranchParam2 >	undefined_coef2_

core::Real	tolerance_

bool	initialized_

Constructor & Destructor Documentation

◆ BranchAngleOptimizer() [1/3]

protocols::branch_angle::BranchAngleOptimizer::BranchAngleOptimizer ( core::scoring::mm::MMBondAngleLibrary const & mm_bondangle_library )

◆ BranchAngleOptimizer() [2/3]

protocols::branch_angle::BranchAngleOptimizer::BranchAngleOptimizer ( )

◆ BranchAngleOptimizer() [3/3]

protocols::branch_angle::BranchAngleOptimizer::BranchAngleOptimizer ( BranchAngleOptimizer const & src )

default

◆ ~BranchAngleOptimizer()

protocols::branch_angle::BranchAngleOptimizer::~BranchAngleOptimizer ( )

virtualdefault

Member Function Documentation

◆ bond_angle_residue_type_param_set() [1/4]

core::scoring::mm::MMBondAngleResidueTypeParamSetOP protocols::branch_angle::BranchAngleOptimizer::bond_angle_residue_type_param_set ( )

References bond_angle_residue_type_param_set_.

◆ bond_angle_residue_type_param_set() [2/4]

core::scoring::mm::MMBondAngleResidueTypeParamSetCOP protocols::branch_angle::BranchAngleOptimizer::bond_angle_residue_type_param_set ( ) const

References bond_angle_residue_type_param_set_.

◆ bond_angle_residue_type_param_set() [3/4]

void protocols::branch_angle::BranchAngleOptimizer::bond_angle_residue_type_param_set ( core::scoring::mm::MMBondAngleResidueTypeParamSetCOP param_set )

set input MMBondAngleResidueTypeParamSet, making a copy

References bond_angle_residue_type_param_set_.

◆ bond_angle_residue_type_param_set() [4/4]

void protocols::branch_angle::BranchAngleOptimizer::bond_angle_residue_type_param_set ( core::scoring::mm::MMBondAngleResidueTypeParamSetOP param_set )

set input MMBondAngleResidueTypeParamSet, sharing with the input

References bond_angle_residue_type_param_set_.

◆ initialized()

bool protocols::branch_angle::BranchAngleOptimizer::initialized ( ) const

inline

References initialized_.

◆ num_coef1()

core::Size protocols::branch_angle::BranchAngleOptimizer::num_coef1 ( ) const

get number of single branching atom coefficients

References coef1_.

◆ num_coef2()

core::Size protocols::branch_angle::BranchAngleOptimizer::num_coef2 ( ) const

get number of double branching atom coefficients

References coef2_.

◆ num_undefined_coef1()

core::Size protocols::branch_angle::BranchAngleOptimizer::num_undefined_coef1 ( ) const

get number of undefined single branching atom coefficients

References undefined_coef1_.

◆ num_undefined_coef2()

core::Size protocols::branch_angle::BranchAngleOptimizer::num_undefined_coef2 ( ) const

get number of undefined double branching atom coefficients

References undefined_coef2_.

◆ operator=()

BranchAngleOptimizer const& protocols::branch_angle::BranchAngleOptimizer::operator= ( BranchAngleOptimizer const & src )

privatedelete

◆ optimize_angles()

Size protocols::branch_angle::BranchAngleOptimizer::optimize_angles	(	core::pose::Pose &	pose,
		core::id::AtomID	main_atomid1,
		core::id::AtomID	center_atomid,
		core::id::AtomID	main_atomid2,
		bool	optimize_for_minimum = `false`
	)

optimize angles branching off the defined mainchain

Add a branch point to the object, if optimization parameters were found, returns an index to them, otherwise returns 0. If other failure conditions are met, a warning is output and the function returns 0.

References core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), core::id::AtomID::atomno(), protocols::branch_angle::branching_atomid1(), protocols::branch_angle::branching_atomids2(), coef1_, coef2_, coef_map1_, coef_map2_, core::kinematics::tree::Atom::get_self_ptr(), core::conformation::Residue::has_incomplete_connection(), core::conformation::Residue::n_bonded_neighbor_all_res(), param1(), param2(), core::chemical::rings::PHI, core::pose::Pose::residue(), core::id::AtomID::rsd(), core::pose::Pose::set_dof(), core::chemical::rings::THETA, protocols::TR(), undefined_coef1_, undefined_coef2_, and core::pose::Pose::xyz().

◆ overall_params()

core::Size protocols::branch_angle::BranchAngleOptimizer::overall_params	(	core::pose::Pose const &	pose,
		core::id::AtomID	main_atomid1,
		core::id::AtomID	center_atomid,
		core::id::AtomID	main_atomid2,
		core::Real &	Ktheta,
		core::Real &	theta0,
		core::Real &	energy0
	)

get overall bond angle parameters for the defined mainchian

if overall parameters are not available, single bond parameters will be returned

References core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), core::id::AtomID::atomno(), protocols::branch_angle::branching_atomid1(), protocols::branch_angle::branching_atomids2(), coef1_, coef2_, coef_map1_, coef_map2_, core::kinematics::tree::Atom::get_self_ptr(), core::conformation::Residue::has_incomplete_connection(), protocols::branch_angle::BranchParam1::m1_m2_Ktheta(), protocols::branch_angle::BranchParam1::m1_m2_theta0(), core::conformation::Residue::n_bonded_neighbor_all_res(), param1(), param2(), core::pose::Pose::residue(), core::id::AtomID::rsd(), protocols::TR(), undefined_coef1_, and undefined_coef2_.

◆ param1()

BranchParam1 protocols::branch_angle::BranchAngleOptimizer::param1	(	core::pose::Pose const &	pose,
		core::id::AtomID const &	main_atomid1,
		core::id::AtomID const &	center_atomid,
		core::id::AtomID const &	main_atomid2,
		core::id::AtomID const &	branch_atomid1
	)		const

get single branching atom bond angle parameters

use the MMBondAngleLibrary referenced by this object

References core::id::AtomID::atomno(), bond_angle_residue_type_param_set_, core::pose::Pose::conformation(), core::scoring::mm::MMBondAngleLibrary::lookup(), core::chemical::ResidueType::mm_atom_type_index(), mm_bondangle_library_, core::pose::Pose::residue_type(), core::id::AtomID::rsd(), and tolerance_.

Referenced by optimize_angles(), and overall_params().

◆ param2()

BranchParam2 protocols::branch_angle::BranchAngleOptimizer::param2	(	core::pose::Pose const &	pose,
		core::id::AtomID const &	main_atomid1,
		core::id::AtomID const &	center_atomid,
		core::id::AtomID const &	main_atomid2,
		core::id::AtomID const &	branch_atomid1,
		core::id::AtomID const &	branch_atomid2
	)		const

get double branching atom bond angle parameters

use the MMBondAngleLibrary referenced by this object

References core::id::AtomID::atomno(), bond_angle_residue_type_param_set_, core::pose::Pose::conformation(), core::scoring::mm::MMBondAngleLibrary::lookup(), core::chemical::ResidueType::mm_atom_type_index(), mm_bondangle_library_, core::pose::Pose::residue_type(), core::id::AtomID::rsd(), and tolerance_.

Referenced by optimize_angles(), and overall_params().

◆ read_coef1() [1/2]

void protocols::branch_angle::BranchAngleOptimizer::read_coef1 ( std::istream & in )

read single branching atom coefficients from an input stream

reads records of the format:

m1_m2_Ktheta(kcal/radians^2) m1_m2_theta0(degrees) m1_b1_Ktheta(kcal/radians^2) m1_b1_theta0(degrees) m2_b1_Ktheta(kcal/radians^2) m2_b1_theta0(degrees)

overall_Ktheta(kcal/radians^2) overall_theta0(degrees) overall_energy0(kcal/mol)

b1_torsion_offset_A(radians) b1_torsion_offset_B(unitless) b1_torsion_offset_C(radians^-1) b1_bond_angle_A(radians) b1_bond_angle_B(unitless) b1_bond_angle_C(radians^-1)

References coef1_, coef_map1_, core::conformation::membrane::in, and tolerance_.

Referenced by read_coef1(), read_coef1_default(), and read_coef1_user().

◆ read_coef1() [2/2]

bool protocols::branch_angle::BranchAngleOptimizer::read_coef1 ( std::string const & filename )

read single branching atom coefficients from a file

read from an uncompressed or gzip-compressed file, returns false on failure

References protocols::abinitio::filename(), and read_coef1().

◆ read_coef1_default()

void protocols::branch_angle::BranchAngleOptimizer::read_coef1_default ( )

read single branching atom coefficients from default database file

read from sampling/branch_angle/branch_angle_1.txt

References read_coef1().

Referenced by read_database().

◆ read_coef1_user()

bool protocols::branch_angle::BranchAngleOptimizer::read_coef1_user ( )

read single branching atom coefficients from user database file

read from branch_angle/branch_angle_1_user.txt

References read_coef1().

Referenced by read_database().

◆ read_coef2() [1/2]

void protocols::branch_angle::BranchAngleOptimizer::read_coef2 ( std::istream & in )

read single branching atom coefficients

reads records of the format:

m1_m2_Ktheta(kcal/radians^2) m1_m2_theta0(degrees) m1_b1_Ktheta(kcal/radians^2) m1_b1_theta0(degrees) m2_b1_Ktheta(kcal/radians^2) m2_b1_theta0(degrees) m1_b2_Ktheta(kcal/radians^2) m1_b2_theta0(degrees) m2_b2_Ktheta(kcal/radians^2) m2_b2_theta0(degrees) b1_b2_Ktheta(kcal/radians^2) b1_b2_theta0(degrees)

overall_Ktheta(kcal/radians^2) overall_theta0(degrees) overall_energy0(kcal/mol)

b1_torsion_offset_A(radians) b1_torsion_offset_B(unitless) b1_torsion_offset_C(radians^-1) b1_bond_angle_A(radians) b1_bond_angle_B(unitless) b1_bond_angle_C(radians^-1) b2_torsion_offset_A(radians) b2_torsion_offset_B(unitless) b2_torsion_offset_C(radians^-1) b2_bond_angle_A(radians) b2_bond_angle_B(unitless) b2_bond_angle_C(radians^-1)

References coef2_, coef_map2_, core::conformation::membrane::in, and tolerance_.

Referenced by read_coef2(), read_coef2_default(), and read_coef2_user().

◆ read_coef2() [2/2]

bool protocols::branch_angle::BranchAngleOptimizer::read_coef2 ( std::string const & filename )

read double branching atom coefficients from a file

read from an uncompressed or gzip-compressed file, returns false on failure

References protocols::abinitio::filename(), and read_coef2().

◆ read_coef2_default()

void protocols::branch_angle::BranchAngleOptimizer::read_coef2_default ( )

read double branching atom coefficients from default database file

read from sampling/branch_angle/branch_angle_2.txt, fails hard

References read_coef2().

Referenced by read_database().

◆ read_coef2_user()

bool protocols::branch_angle::BranchAngleOptimizer::read_coef2_user ( )

read double branching atom coefficients from user database file

read from branch_angle/branch_angle_2_user.txt

References read_coef2().

Referenced by read_database().

◆ read_database()

void protocols::branch_angle::BranchAngleOptimizer::read_database ( )

read known parameters from the database

References initialized_, read_coef1_default(), read_coef1_user(), read_coef2_default(), and read_coef2_user().

Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), and protocols::dna::DesignProteinBackboneAroundDNA::backrub().

◆ read_undefined_coef1() [1/3]

bool protocols::branch_angle::BranchAngleOptimizer::read_undefined_coef1 ( )

read single branching atom undefined coefficients from the database file

read from branch_angle/branch_angle_1_undefined.txt

Referenced by read_undefined_coef1().

◆ read_undefined_coef1() [2/3]

void protocols::branch_angle::BranchAngleOptimizer::read_undefined_coef1 ( std::istream & in )

read parameters for undefined single branching atom coefficients

reads records of the format:

m1_m2_Ktheta(kcal/radians^2) m1_m2_theta0(degrees) m1_b1_Ktheta(kcal/radians^2) m1_b1_theta0(degrees) m2_b1_Ktheta(kcal/radians^2) m2_b1_theta0(degrees)

References core::conformation::membrane::in, tolerance_, and undefined_coef1_.

◆ read_undefined_coef1() [3/3]

bool protocols::branch_angle::BranchAngleOptimizer::read_undefined_coef1 ( std::string const & filename )

read parameters for undefined single branching atom coefficients from a file

read from an uncompressed or gzip-compressed file, returns false on failure

References protocols::abinitio::filename(), and read_undefined_coef1().

◆ read_undefined_coef2() [1/3]

bool protocols::branch_angle::BranchAngleOptimizer::read_undefined_coef2 ( )

read double branching atom undefined coefficients from the database file

read from branch_angle/branch_angle_2_undefined.txt

Referenced by read_undefined_coef2().

◆ read_undefined_coef2() [2/3]

void protocols::branch_angle::BranchAngleOptimizer::read_undefined_coef2 ( std::istream & in )

read parameters for undefined double branching atom coefficients

reads records of the format:

m1_m2_Ktheta(kcal/radians^2) m1_m2_theta0(degrees) m1_b1_Ktheta(kcal/radians^2) m1_b1_theta0(degrees) m2_b1_Ktheta(kcal/radians^2) m2_b1_theta0(degrees) m1_b2_Ktheta(kcal/radians^2) m1_b2_theta0(degrees) m2_b2_Ktheta(kcal/radians^2) m2_b2_theta0(degrees) b1_b2_Ktheta(kcal/radians^2) b1_b2_theta0(degrees)

References core::conformation::membrane::in, tolerance_, and undefined_coef2_.

◆ read_undefined_coef2() [3/3]

bool protocols::branch_angle::BranchAngleOptimizer::read_undefined_coef2 ( std::string const & filename )

read parameters for undefined double branching atom coefficients from a file

read from an uncompressed or gzip-compressed file, returns false on failure

References protocols::abinitio::filename(), and read_undefined_coef2().

◆ tolerance() [1/2]

core::Real protocols::branch_angle::BranchAngleOptimizer::tolerance ( ) const

inline

References tolerance_.

Referenced by tolerance().

◆ tolerance() [2/2]

void protocols::branch_angle::BranchAngleOptimizer::tolerance ( core::Real tolerance )

inline

References tolerance(), and tolerance_.

◆ write_database()

void protocols::branch_angle::BranchAngleOptimizer::write_database ( ) const

write undefined parameters to the database

References protocols::TR(), undefined_coef1_, undefined_coef2_, write_undefined_coef1(), and write_undefined_coef2().

Referenced by protocols::protein_interface_design::movers::BackrubDDMover::apply().

◆ write_undefined_coef1() [1/3]

bool protocols::branch_angle::BranchAngleOptimizer::write_undefined_coef1 ( ) const

write single branching atom undefined coefficients to the database file

overwrite branch_angle/branch_angle_1_undefined.txt if undefined parameters exist

References undefined_coef1_.

Referenced by write_database(), and write_undefined_coef1().

◆ write_undefined_coef1() [2/3]

void protocols::branch_angle::BranchAngleOptimizer::write_undefined_coef1 ( std::ostream & out ) const

write out parameters for undefined single branching atom coefficients

for every set of parameters, dump out three lines in the format:

m1_m2_Ktheta(kcal/radians^2) m1_m2_theta0(degrees) m1_b1_Ktheta(kcal/radians^2) m1_b1_theta0(degrees) m2_b1_Ktheta(kcal/radians^2) m2_b1_theta0(degrees)

each set of parameters will be followed by a blank line

References core::conformation::membrane::out, and undefined_coef1_.

◆ write_undefined_coef1() [3/3]

bool protocols::branch_angle::BranchAngleOptimizer::write_undefined_coef1 ( std::string const & filename ) const

write parameters for undefined single branching atom coefficients to a file

write to an uncompressed or gzip-compressed file, returns false on failure

References protocols::abinitio::filename(), and write_undefined_coef1().

◆ write_undefined_coef2() [1/3]

bool protocols::branch_angle::BranchAngleOptimizer::write_undefined_coef2 ( ) const

write double branching atom undefined coefficients to the database file

overwrite branch_angle/branch_angle_2_undefined.txt if undefined parameters exist

References undefined_coef2_.

Referenced by write_database(), and write_undefined_coef2().

◆ write_undefined_coef2() [2/3]

void protocols::branch_angle::BranchAngleOptimizer::write_undefined_coef2 ( std::ostream & out ) const

write out parameters for undefined double branching atom coefficients

for every set of parameters, dump out three lines in the format:

m1_m2_Ktheta(kcal/radians^2) m1_m2_theta0(degrees) m1_b1_Ktheta(kcal/radians^2) m1_b1_theta0(degrees) m2_b1_Ktheta(kcal/radians^2) m2_b1_theta0(degrees) m1_b2_Ktheta(kcal/radians^2) m1_b2_theta0(degrees) m2_b2_Ktheta(kcal/radians^2) m2_b2_theta0(degrees) b1_b2_Ktheta(kcal/radians^2) b1_b2_theta0(degrees)

each set of parameters will be followed by a blank line

References core::conformation::membrane::out, and undefined_coef2_.

◆ write_undefined_coef2() [3/3]

bool protocols::branch_angle::BranchAngleOptimizer::write_undefined_coef2 ( std::string const & filename ) const

write parameters for undefined double branching atom coefficients to a file

write to an uncompressed or gzip-compressed file, returns false on failure

References protocols::abinitio::filename(), and write_undefined_coef2().

Member Data Documentation

◆ bond_angle_residue_type_param_set_

core::scoring::mm::MMBondAngleResidueTypeParamSetOP protocols::branch_angle::BranchAngleOptimizer::bond_angle_residue_type_param_set_

private

Referenced by bond_angle_residue_type_param_set(), param1(), and param2().

◆ coef1_

utility::vector1<BranchCoef1> protocols::branch_angle::BranchAngleOptimizer::coef1_

private

Referenced by num_coef1(), optimize_angles(), overall_params(), and read_coef1().

◆ coef2_

utility::vector1<BranchCoef2> protocols::branch_angle::BranchAngleOptimizer::coef2_

private

Referenced by num_coef2(), optimize_angles(), overall_params(), and read_coef2().

◆ coef_map1_

std::map<BranchParam1, core::Size> protocols::branch_angle::BranchAngleOptimizer::coef_map1_

private

Referenced by optimize_angles(), overall_params(), and read_coef1().

◆ coef_map2_

std::map<BranchParam2, core::Size> protocols::branch_angle::BranchAngleOptimizer::coef_map2_

private

Referenced by optimize_angles(), overall_params(), and read_coef2().

◆ initialized_

bool protocols::branch_angle::BranchAngleOptimizer::initialized_

private

Referenced by initialized(), and read_database().

◆ mm_bondangle_library_

core::scoring::mm::MMBondAngleLibrary const& protocols::branch_angle::BranchAngleOptimizer::mm_bondangle_library_

private

Referenced by param1(), and param2().

◆ tolerance_

core::Real protocols::branch_angle::BranchAngleOptimizer::tolerance_

private

Referenced by param1(), param2(), read_coef1(), read_coef2(), read_undefined_coef1(), read_undefined_coef2(), and tolerance().

◆ undefined_coef1_

std::set<BranchParam1> protocols::branch_angle::BranchAngleOptimizer::undefined_coef1_

private

Referenced by num_undefined_coef1(), optimize_angles(), overall_params(), read_undefined_coef1(), write_database(), and write_undefined_coef1().

◆ undefined_coef2_

std::set<BranchParam2> protocols::branch_angle::BranchAngleOptimizer::undefined_coef2_

private

Referenced by num_undefined_coef2(), optimize_angles(), overall_params(), read_undefined_coef2(), write_database(), and write_undefined_coef2().

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

src/protocols/branch_angle/BranchAngleOptimizer.hh
src/protocols/branch_angle/BranchAngleOptimizer.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ BranchAngleOptimizer() [1/3]

◆ BranchAngleOptimizer() [2/3]

◆ BranchAngleOptimizer() [3/3]

◆ ~BranchAngleOptimizer()

Member Function Documentation

◆ bond_angle_residue_type_param_set() [1/4]

◆ bond_angle_residue_type_param_set() [2/4]

◆ bond_angle_residue_type_param_set() [3/4]

◆ bond_angle_residue_type_param_set() [4/4]

◆ initialized()

◆ num_coef1()

◆ num_coef2()

◆ num_undefined_coef1()

◆ num_undefined_coef2()

◆ operator=()

◆ optimize_angles()

◆ overall_params()

◆ param1()

◆ param2()

◆ read_coef1() [1/2]

◆ read_coef1() [2/2]

◆ read_coef1_default()

◆ read_coef1_user()

◆ read_coef2() [1/2]

◆ read_coef2() [2/2]

◆ read_coef2_default()

◆ read_coef2_user()

◆ read_database()

◆ read_undefined_coef1() [1/3]

◆ read_undefined_coef1() [2/3]

◆ read_undefined_coef1() [3/3]

◆ read_undefined_coef2() [1/3]

◆ read_undefined_coef2() [2/3]

◆ read_undefined_coef2() [3/3]

◆ tolerance() [1/2]

◆ tolerance() [2/2]

◆ write_database()

◆ write_undefined_coef1() [1/3]

◆ write_undefined_coef1() [2/3]

◆ write_undefined_coef1() [3/3]

◆ write_undefined_coef2() [1/3]

◆ write_undefined_coef2() [2/3]

◆ write_undefined_coef2() [3/3]

Member Data Documentation

◆ bond_angle_residue_type_param_set_

◆ coef1_

◆ coef2_

◆ coef_map1_

◆ coef_map2_

◆ initialized_

◆ mm_bondangle_library_

◆ tolerance_

◆ undefined_coef1_

◆ undefined_coef2_