genmatch.cc File Reference

#include <basic/database/open.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/parser.OptionKeys.gen.hh>
#include <basic/options/keys/smhybrid.OptionKeys.gen.hh>
#include <basic/options/keys/willmatch.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <basic/Tracer.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/symmetry/SymDof.hh>
#include <core/conformation/symmetry/SymmData.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/conformation/symmetry/VirtualCoordinate.hh>
#include <core/fragment/BBTorsionSRFD.hh>
#include <core/fragment/ConstantLengthFragSet.hh>
#include <core/fragment/FragData.hh>
#include <core/fragment/FragmentIO.hh>
#include <core/fragment/FragSet.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/Stub.hh>
#include <core/pack/dunbrack/DunbrackRotamer.fwd.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>
#include <core/pack/optimizeH.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/Pose.hh>
#include <core/pose/symmetry/util.hh>
#include <core/pose/util.hh>
#include <core/scoring/constraints/AmbiguousConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/MultiConstraint.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/func/XYZ_Func.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/electron_density/util.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/packstat/compute_sasa.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyz.io.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <protocols/simple_moves/FragmentMover.hh>
#include <protocols/electron_density/util.hh>
#include <protocols/flxbb/DesignLayerOperation.fwd.hh>
#include <protocols/flxbb/DesignLayerOperation.hh>
#include <protocols/flxbb/FlxbbDesign.hh>
#include <protocols/jobdist/standard_mains.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/symmetry/SetupForSymmetryMover.hh>
#include <protocols/minimization_packing/symmetry/SymMinMover.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/scoring/ImplicitFastClashCheck.hh>
#include <protocols/symmetry/SymDockingInitialPerturbation.hh>
#include <protocols/symmetric_docking/SymDockingLowRes.hh>
#include <protocols/viewer/viewers.hh>
#include <sstream>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <apps/pilot/will/will_util.ihh>
#include <apps/pilot/will/mynamespaces.ihh>

Functions
Real const	sqr (Real const r)
Real	sigmoidish_neighbor (Real const &sqdist)
Real	iface_check_c3 (Pose &pose, Size nres, vector1< Size > const &iface_candidates)
vector1< Size >	read_res_list (string fn)
void	repack (Pose &pose, Size nres, ScoreFunctionOP sf)
void	design (Pose &pose, Size nres, ScoreFunctionOP sf)
void	design_dyad (Pose &pose, Size const r1, Size const r2, ScoreFunctionOP sf, bool ex=false)
void	minimize (Pose &pose, Size nres, Size, ScoreFunctionOP sf, int bb=0)
std::pair< Size, Size >	makesplitwork_3bpy (Size total)
std::pair< vector1< Size >, vector1< Size > >	makesplitwork (Size total, Size total2=0)
std::pair< vector1< Size >, vector1< Size > >	makesplitwork (utility::vector1< Size > res1, utility::vector1< Size > res2)
void	myoptH (Pose &pose, ScoreFunctionOP sf)
void	run_3bpy ()
void	run_zn2his ()
void	run_tyr_his ()
void	align_carboxyl_diiron_OLD (core::pose::Pose &pose, Size irsd, Size jrsd, Vec cen)
void	align_carboxyl_diiron (core::pose::Pose &pose, Size irsd, Size jrsd, Vec cen, Vec mori, bool posneg=true)
void	run_diiron_glu ()
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("genmatch")

Function Documentation

align_carboxyl_diiron()

void align_carboxyl_diiron	(	core::pose::Pose &	pose,
		Size	irsd,
		Size	jrsd,
		Vec	cen,
		Vec	mori,
		bool	posneg = true
	)

References a, docking::a2, compute_difference::b, docking::b2, basic::options::OptionKeys::out::file::o, beta_nonlocal::pose, numeric::projection_matrix(), create_a3b_hbs::r, and numeric::rotation_matrix_degrees().

Referenced by run_diiron_glu().

align_carboxyl_diiron_OLD()

void align_carboxyl_diiron_OLD	(	core::pose::Pose &	pose,
		Size	irsd,
		Size	jrsd,
		Vec	cen
	)

References docking::a1, docking::a2, docking::a3, angle_degrees(), create_a3b_hbs::i, create_a3b_hbs::j, basic::options::OptionKeys::out::file::o, beta_nonlocal::pose, and numeric::rotation_matrix_degrees().

design()

void design	(	Pose &	pose,
		Size	nres,
		ScoreFunctionOP	sf
	)

References basic::options::OptionKeys::smhybrid::design_hydrophobic, basic::options::OptionKeys::willmatch::design_interface, basic::options::OptionKeys::willmatch::exclude_ala, detail::find(), basic::options::OptionKeys::willmatch::fixed_res, create_a3b_hbs::i, basic::options::OptionKeys::in::in, interface, create_a3b_hbs::j, create_a3b_hbs::nres, option, beta_nonlocal::pose, repack(), basic::options::OptionKeys::AnchoredDesign::filters::sasa, basic::options::OptionKeys::out::sf, vancomycin::task, TR, basic::options::OptionKeys::inout::dbms::user, and basic::options::OptionKeys::in::file::xyz.

Referenced by run_3bpy().

design_dyad()

void design_dyad	(	Pose &	pose,
		Size const	r1,
		Size const	r2,
		ScoreFunctionOP	sf,
		bool	ex = false
	)

References numeric::xyzVector< T >::distance_squared(), create_a3b_hbs::i, beta_nonlocal::pose, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, repack(), basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by run_tyr_his().

iface_check_c3()

Real iface_check_c3	(	Pose &	pose,
		Size	nres,
		vector1< Size > const &	iface_candidates
	)

References create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::nres, beta_nonlocal::pose, and sigmoidish_neighbor().

Referenced by run_3bpy().

main()

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

References argv, test.T009_Exceptions::e, basic::init(), and run_zn2his().

makesplitwork() [1/2]

std::pair<vector1<Size>,vector1<Size> > makesplitwork	(	Size	total,
		Size	total2 = 0
	)

References create_a3b_hbs::i, create_a3b_hbs::j, basic::options::option, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::willmatch::splitwork, basic::options::TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by run_diiron_glu(), run_tyr_his(), and run_zn2his().

makesplitwork() [2/2]

std::pair<vector1<Size>,vector1<Size> > makesplitwork	(	utility::vector1< Size >	res1,
		utility::vector1< Size >	res2
	)

References create_a3b_hbs::i, create_a3b_hbs::j, basic::options::option, erraser_analysis::res1, erraser_analysis::res2, basic::options::OptionKeys::willmatch::splitwork, basic::options::TR, and basic::options::OptionKeys::inout::dbms::user.

makesplitwork_3bpy()

std::pair<Size,Size> makesplitwork_3bpy

(

Size

total

)

References basic::options::option, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::willmatch::splitwork, basic::options::TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by run_3bpy().

minimize()

void minimize	(	Pose &	pose,
		Size	nres,
		Size	,
		ScoreFunctionOP	sf,
		int	bb = 0
	)

References test.T009_Exceptions::e, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, basic::options::OptionKeys::in::file::movemap, create_a3b_hbs::nres, beta_nonlocal::pose, and basic::options::OptionKeys::out::sf.

Referenced by run_3bpy().

myoptH()

void myoptH	(	Pose &	pose,
		ScoreFunctionOP	sf
	)

References beta_nonlocal::pose, and basic::options::OptionKeys::out::sf.

Referenced by run_tyr_his(), and run_zn2his().

read_res_list()

vector1<Size> read_res_list

(

string

fn

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, basic::options::OptionKeys::in::in, extract_by_sidechain_sasa_score::l, create_a3b_hbs::r, and utility_exit_with_message.

Referenced by run_3bpy().

repack()

void repack	(	Pose &	pose,
		Size	nres,
		ScoreFunctionOP	sf
	)

References create_a3b_hbs::i, create_a3b_hbs::nres, beta_nonlocal::pose, basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by design(), design_dyad(), and run_3bpy().

run_3bpy()

void run_3bpy

(

)

References basic::options::OptionKeys::smhybrid::add_cavities, orn_macrocycle::ala, basic::options::OptionKeys::willmatch::chi1_increment, basic::options::OptionKeys::willmatch::chi2_increment, basic::options::OptionKeys::willmatch::chilist, basic::options::OptionKeys::willmatch::clash_dis, clashcheck(), design(), basic::options::OptionKeys::willmatch::exclude_res1, ObjexxFCL::format::F(), utility::file_basename(), detail::find(), PREcst::fname, test.T020_Pose_Bindings::ft, create_a3b_hbs::i, test.T110_numeric::I, iface_check_c3(), basic::options::OptionKeys::in::in, basic::options::OptionKeys::willmatch::interface_size, create_a3b_hbs::j, makesplitwork_3bpy(), max(), min(), minimize(), natoms(), create_a3b_hbs::nres, basic::options::option, erraser_single_res_analysis::out, output_packstat_pdb(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, read_res_list(), repack(), basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::AnchoredDesign::filters::sasa, basic::options::OptionKeys::out::sf, binder::split(), ObjexxFCL::string_of(), superimpose_pose(), predPRE::t, basic::options::TR, kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

run_diiron_glu()

void run_diiron_glu

(

)

References orn_macrocycle::ala, align_carboxyl_diiron(), basic::options::OptionKeys::hotspot::angle, angle_degrees(), CHI1, basic::options::OptionKeys::willmatch::chi1_increment, CHI2, basic::options::OptionKeys::willmatch::chi2_increment, clash(), basic::options::OptionKeys::willmatch::clash_dis, clashcheck(), count, numeric::xyzVector< T >::cross(), numeric::conversions::degrees(), numeric::dihedral_degrees(), numeric::distance_squared(), numeric::xyzVector< T >::distance_squared(), measure_params::dot(), numeric::xyzVector< T >::dot(), ObjexxFCL::format::F(), utility::file_basename(), detail::find(), PREcst::fname, create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, create_a3b_hbs::k, makesplitwork(), basic::options::OptionKeys::willmatch::match_overlap_ang, basic::options::OptionKeys::willmatch::match_overlap_dis, basic::options::OptionKeys::willmatch::max_ang_metal, basic::options::OptionKeys::willmatch::max_dis_metal, create_a3b_hbs::nres, basic::options::OptionKeys::out::file::o, numeric::constants::f::one, basic::options::option, adapt_rotamers::ori, erraser_single_res_analysis::out, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, numeric::projection_matrix(), create_a3b_hbs::r, docking::R, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, numeric::conversions::radians(), execute::residues, basic::options::OptionKeys::willmatch::residues, numeric::rotation_matrix_degrees(), basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::stepwise::s1, basic::options::OptionKeys::stepwise::s2, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::willmatch::splitwork, ObjexxFCL::string_of(), stub(), tag, basic::options::TR, numeric::constants::f::two, basic::options::OptionKeys::inout::dbms::user, numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

run_tyr_his()

void run_tyr_his

(

)

References orn_macrocycle::ala, basic::options::OptionKeys::hotspot::angle, basic::options::OptionKeys::edensity::atom_mask, CHI1, basic::options::OptionKeys::willmatch::chi1_increment, CHI2, basic::options::OptionKeys::willmatch::chi2_increment, clash(), basic::options::OptionKeys::willmatch::clash_dis, clashcheck(), count, measure_params::cross(), numeric::conversions::degrees(), design_dyad(), build_jacobian::distance, numeric::xyzVector< T >::distance(), numeric::distance_squared(), numeric::xyzVector< T >::distance_squared(), measure_params::dot(), numeric::xyzVector< T >::dot(), utility::file_basename(), detail::find(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, PREcst::fname, basic::options::OptionKeys::willmatch::forbid_residues, hd(), create_a3b_hbs::i, basic::Tracer::Info, create_a3b_hbs::j, oop_conformations::length, makesplitwork(), basic::options::OptionKeys::willmatch::match_overlap_ang, basic::options::OptionKeys::willmatch::match_overlap_dis, numeric::max(), basic::options::OptionKeys::willmatch::max_dis_hb, basic::options::OptionKeys::willmatch::max_dis_hb_colinear, numeric::min(), basic::options::OptionKeys::willmatch::min_dis_hb, myoptH(), surface_app::native, numeric::xyzVector< T >::normalized(), create_a3b_hbs::nres, numeric::constants::f::one, basic::options::option, adapt_rotamers::ori, erraser_single_res_analysis::out, p2, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, numeric::conversions::radians(), execute::residues, basic::options::OptionKeys::willmatch::residues, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::stepwise::s1, basic::options::OptionKeys::stepwise::s2, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::willmatch::splitwork, ObjexxFCL::string_of(), stub(), tag, basic::options::TR, numeric::constants::f::two, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

run_zn2his()

void run_zn2his

(

)

References orn_macrocycle::ala, basic::options::OptionKeys::hotspot::angle, CHI1, basic::options::OptionKeys::willmatch::chi1_increment, CHI2, basic::options::OptionKeys::willmatch::chi2_increment, clash(), basic::options::OptionKeys::willmatch::clash_dis, clashcheck(), count, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, numeric::conversions::degrees(), build_jacobian::distance, numeric::distance_squared(), numeric::xyzVector< T >::distance_squared(), numeric::xyzVector< T >::dot(), ObjexxFCL::format::F(), utility::file_basename(), detail::find(), PREcst::fname, hd(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, makesplitwork(), basic::options::OptionKeys::willmatch::match_overlap_ang, basic::options::OptionKeys::willmatch::match_overlap_dis, basic::options::OptionKeys::willmatch::max_ang_metal, basic::options::OptionKeys::willmatch::max_dis_metal, myoptH(), numeric::xyzVector< T >::normalized(), create_a3b_hbs::nres, numeric::constants::f::one, basic::options::option, adapt_rotamers::ori, erraser_single_res_analysis::out, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, numeric::conversions::radians(), execute::residues, basic::options::OptionKeys::willmatch::residues, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::stepwise::s1, basic::options::OptionKeys::stepwise::s2, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::willmatch::splitwork, ObjexxFCL::string_of(), stub(), tag, basic::options::TR, numeric::constants::f::two, basic::options::OptionKeys::inout::dbms::user, numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

Referenced by main().

sigmoidish_neighbor()

Real sigmoidish_neighbor ( Real const &  sqdist )

inline

References dist(), and sqr().

Referenced by iface_check_c3().

sqr()

Real const sqr ( Real const  r )

inline

References create_a3b_hbs::r.

Referenced by sigmoidish_neighbor().

Variable Documentation

TR

basic::Tracer TR("genmatch") ( "genmatch"  )

static

Referenced by design().