erraser_minimizer.cc File Reference

#include <protocols/farna/util.hh>
#include <core/pose/rna/RNA_IdealCoord.hh>
#include <protocols/stepwise/modeler/rna/util.hh>
#include <protocols/stepwise/modeler/output_util.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/init/init.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/util.hh>
#include <basic/options/option_macros.hh>
#include <protocols/viewer/viewers.hh>
#include <core/id/AtomID.hh>
#include <core/id/NamedAtomID.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/full_model_info/util.hh>
#include <core/pose/full_model_info/FullModelInfo.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/rna/RNA_TorsionPotential.hh>
#include <core/pose/rna/util.hh>
#include <core/chemical/rna/util.hh>
#include <core/io/silent/SilentFileData.fwd.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/rotamer_set/RotamerCouplings.hh>
#include <core/pack/rotamer_set/WaterAnchorInfo.hh>
#include <core/pack/rotamer_set/WaterPackingInfo.hh>
#include <core/pack/rotamer_set/WaterPackingInfo.fwd.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/Mover.fwd.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/util.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.hh>
#include <basic/options/keys/rna.OptionKeys.gen.hh>
#include <core/pose/PDBInfo.hh>
#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <numeric/conversions.hh>
#include <numeric/xyz.functions.hh>
#include <iostream>
#include <string>
#include <utility/excn/Exceptions.hh>

Functions
bool	check_num_in_vector (int input_num, utility::vector1< int > const &input_vector)
void	translate_residue (conformation::Residue &rsd, Vector const &nbr_atom_xyz)
bool	check_in_bonded_list (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, utility::vector1< std::pair< core::id::AtomID, core::id::AtomID > > &bonded_atom_list)
bool	check_in_bond_angle_list (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, core::id::AtomID const &atom_id3, utility::vector1< std::pair< core::id::AtomID, std::pair< core::id::AtomID, core::id::AtomID > > > &bond_angle_list)
void	apply_ideal_coordinates (pose::Pose const &pose, pose::Pose &pose_reference)
void	add_bond_constraint (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, utility::vector1< std::pair< core::id::AtomID, core::id::AtomID > > &bonded_atom_list, core::pose::Pose const &pose, core::pose::Pose const &pose_reference, core::scoring::constraints::ConstraintSetOP &cst_set)
void	add_bond_angle_constraint (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, core::id::AtomID const &atom_id3, utility::vector1< std::pair< core::id::AtomID, std::pair< core::id::AtomID, core::id::AtomID > > > &bond_angle_list, core::pose::Pose const &pose, core::pose::Pose const &pose_reference, core::scoring::constraints::ConstraintSetOP &cst_set)
bool	check_if_really_connected (core::pose::Pose const &pose, core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2)
bool	i_want_this_atom_to_move (conformation::Residue const &residue2, Size const &k)
bool	i_want_this_atom_to_move (pose::Pose const &pose, core::id::AtomID const &atom_id)
bool	is_atom_exist_in_reference (pose::Pose const &pose, pose::Pose const &pose_reference, core::id::AtomID const &atom_id)
void	create_pose_reference (pose::Pose const &pose, pose::Pose &pose_reference)
void	vary_bond_geometry (core::kinematics::MoveMap &mm, pose::Pose &pose, pose::Pose const &pose_reference, ObjexxFCL::FArray1D< bool > &allow_insert_)
int	add_virtual_res (core::pose::Pose &pose)
void	setup_fold_tree (pose::Pose &pose, utility::vector1< core::Size > const &cutpoint_list)
bool	is_elem_in_list (core::Size const elem, utility::vector1< core::Size > const &list)
void	setup_fold_tree_sample_res (pose::Pose &pose, utility::vector1< core::Size > const &sample_res_list)
void	pyrimidine_flip_trial (pose::Pose &pose, utility::vector1< Size > const &fixed_res_list, scoring::ScoreFunctionOP scorefxn)
void	pdb_minimizer ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Function Documentation

void add_bond_angle_constraint	(	core::id::AtomID const &	atom_id1,
		core::id::AtomID const &	atom_id2,
		core::id::AtomID const &	atom_id3,
		utility::vector1< std::pair< core::id::AtomID, std::pair< core::id::AtomID, core::id::AtomID > > > &	bond_angle_list,
		core::pose::Pose const &	pose,
		core::pose::Pose const &	pose_reference,
		core::scoring::constraints::ConstraintSetOP &	cst_set
	)

References numeric::angle_radians(), check_in_bond_angle_list(), basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, numeric::conversions::degrees(), has, numeric::conversions::radians(), basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::in::file::xyz.

Referenced by vary_bond_geometry().

void add_bond_constraint	(	core::id::AtomID const &	atom_id1,
		core::id::AtomID const &	atom_id2,
		utility::vector1< std::pair< core::id::AtomID, core::id::AtomID > > &	bonded_atom_list,
		core::pose::Pose const &	pose,
		core::pose::Pose const &	pose_reference,
		core::scoring::constraints::ConstraintSetOP &	cst_set
	)

References check_in_bonded_list(), basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, has, make_symmdef_file_denovo::length, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::in::file::xyz.

Referenced by vary_bond_geometry().

int add_virtual_res

(

core::pose::Pose &

pose

)

References basic::options::OptionKeys::mh::match::aa, utility::io::oc::cout, and clean_pdb_keep_ligand::nres.

Referenced by nucleobase_probe_score_test(), and pdb_minimizer().

void apply_ideal_coordinates	(	pose::Pose const &	pose,
		pose::Pose &	pose_reference
	)

References basic::options::OptionKeys::rna::corrected_geo, option, and basic::options::OptionKeys::full_model::rna::rna.

Referenced by create_pose_reference().

bool check_if_really_connected	(	core::pose::Pose const &	pose,
		core::id::AtomID const &	atom_id1,
		core::id::AtomID const &	atom_id2
	)

References test.T220_AtomAtomPairEnergies::atom1, and test.T220_AtomAtomPairEnergies::atom2.

Referenced by vary_bond_geometry().

bool check_in_bond_angle_list	(	core::id::AtomID const &	atom_id1,
		core::id::AtomID const &	atom_id2,
		core::id::AtomID const &	atom_id3,
		utility::vector1< std::pair< core::id::AtomID, std::pair< core::id::AtomID, core::id::AtomID > > > &	bond_angle_list
	)

References assign_charges::first.

Referenced by add_bond_angle_constraint().

bool check_in_bonded_list	(	core::id::AtomID const &	atom_id1,
		core::id::AtomID const &	atom_id2,
		utility::vector1< std::pair< core::id::AtomID, core::id::AtomID > > &	bonded_atom_list
	)

References assign_charges::first.

Referenced by add_bond_constraint().

bool check_num_in_vector	(	int	input_num,
		utility::vector1< int > const &	input_vector
	)

Referenced by pdb_minimizer(), and pyrimidine_flip_trial().

void create_pose_reference	(	pose::Pose const &	pose,
		pose::Pose &	pose_reference
	)

References apply_ideal_coordinates(), and basic::options::OptionKeys::chemical::chemical.

Referenced by pdb_minimizer().

bool i_want_this_atom_to_move	(	conformation::Residue const &	residue2,
		Size const &	k
	)

Referenced by i_want_this_atom_to_move(), and vary_bond_geometry().

bool i_want_this_atom_to_move	(	pose::Pose const &	pose,
		core::id::AtomID const &	atom_id
	)

References i_want_this_atom_to_move().

bool is_atom_exist_in_reference	(	pose::Pose const &	pose,
		pose::Pose const &	pose_reference,
		core::id::AtomID const &	atom_id
	)

References utility::io::oc::cout, and has.

Referenced by vary_bond_geometry().

bool is_elem_in_list	(	core::Size const	elem,
		utility::vector1< core::Size > const &	list
	)

Referenced by setup_fold_tree_sample_res().

int main	(	int	argc,
		char *	argv[]
	)

References utility::io::oc::cout, basic::options::OptionKeys::full_model::cutpoint_open, basic::options::OptionKeys::stepwise::fixed_res, basic::init(), utility::excn::EXCN_Base::msg(), my_main(), NEW_OPT, basic::options::OptionKeys::stepwise::skip_minimize, and basic::options::OptionKeys::rna::vary_geometry.

void* my_main

(

void *

)

References utility::options::OptionKeys::options::exit, and pdb_minimizer().

Referenced by main().

void pdb_minimizer

(

)

References add_virtual_res(), check_num_in_vector(), basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, create_pose_reference(), basic::options::OptionKeys::full_model::cutpoint_open, basic::options::OptionKeys::stepwise::fixed_res, basic::options::OptionKeys::in::file::fold_tree, test.T200_Scoring::ii, basic::options::OptionKeys::frags::j, max(), min(), app.delta_score_per_mutation::mm, in::file::native(), clean_pdb_keep_ligand::nres, basic::options::OptionKeys::optimization::optimization, option, app.surface_docking.surface_docking::pose, pyrimidine_flip_trial(), basic::options::OptionKeys::in::file::residue_type_set, basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::AnchoredDesign::filters::score, PyMOL_demo::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_fold_tree(), show(), basic::options::OptionKeys::stepwise::skip_minimize, app.surface_docking.surface_docking::start_pose, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, vary_bond_geometry(), basic::options::OptionKeys::rna::vary_geometry, and basic::options::OptionKeys::score::weights.

Referenced by my_main().

void pyrimidine_flip_trial	(	pose::Pose &	pose,
		utility::vector1< Size > const &	fixed_res_list,
		scoring::ScoreFunctionOP	scorefxn
	)

References check_num_in_vector(), basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, test.Workshop4test::new_score, app.surface_docking.surface_docking::pose, app.delta_score_per_mutation::res, basic::options::OptionKeys::full_model::rna::rna, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by pdb_minimizer().

void setup_fold_tree	(	pose::Pose &	pose,
		utility::vector1< core::Size > const &	cutpoint_list
	)

References basic::options::OptionKeys::chemical::chemical, demo.D060_Folding::f, clean_pdb_keep_ligand::nres, basic::options::OptionKeys::full_model::rna::rna, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by pdb_minimizer().

void setup_fold_tree_sample_res	(	pose::Pose &	pose,
		utility::vector1< core::Size > const &	sample_res_list
	)

References basic::options::OptionKeys::chemical::chemical, demo.D060_Folding::f, is_elem_in_list(), clean_pdb_keep_ligand::nres, and basic::options::OptionKeys::frags::scoring::scoring.

void translate_residue	(	conformation::Residue &	rsd,
		Vector const &	nbr_atom_xyz
	)

void vary_bond_geometry	(	core::kinematics::MoveMap &	mm,
		pose::Pose &	pose,
		pose::Pose const &	pose_reference,
		ObjexxFCL::FArray1D< bool > &	allow_insert_
	)

References add_bond_angle_constraint(), add_bond_constraint(), check_if_really_connected(), utility::options::BooleanOptionKey::clone(), basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, i_want_this_atom_to_move(), is_atom_exist_in_reference(), basic::options::OptionKeys::frags::j, clean_pdb_keep_ligand::nres, test.Workshop4test::PHI, basic::options::OptionKeys::hotspot::residue, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by pdb_minimizer().