crossmatch.cc File Reference

#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/smhybrid.OptionKeys.gen.hh>
#include <basic/options/keys/enzdes.OptionKeys.gen.hh>
#include <basic/options/keys/crossmatch.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/util.hh>
#include <core/conformation/symmetry/SymmData.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/Stub.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/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <core/pose/symmetry/util.hh>
#include <core/pose/util.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/func/CircularHarmonicFunc.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/ResidueTypeConstraint.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/packstat/compute_sasa.hh>
#include <core/scoring/packstat/sasa_dot_locations.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyz.io.hh>
#include <numeric/NumericTraits.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/symmetry/SymMinMover.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <protocols/toolbox/SwitchResidueTypeSet.hh>
#include <sstream>
#include <utility/excn/Exceptions.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/string_util.hh>
#include <apps/pilot/will/will_util.ihh>

Classes
struct	Tags
struct	Filter
struct	NullFilter
struct	ListFilter
struct	MatchAlignInfo
struct	MatchAligner
struct	Tet4HMatchAligner
struct	MatchBase
struct	MatchLig
struct	MatchSet

Typedefs
typedef numeric::xyzMatrix< Real >	Mat
typedef numeric::xyzVector< Real >	Vec
typedef utility::vector1< Vec >	Vecs
typedef utility::pointer::owning_ptr< MatchAligner >	MatchAlignerOP
typedef utility::pointer::owning_ptr< MatchBase >	MatchBaseOP
typedef utility::pointer::owning_ptr< const MatchBase >	MatchBaseCOP

Functions
vector1< Size >	read_res_list (string fn)
Vec	randvec ()
void	minimize (Pose &pose, ScoreFunctionOP sf, vector1< Size > matchres)
void	myoptH (Pose &pose, ScoreFunctionOP sf)
void	design (Pose &pose, ScoreFunctionOP sf, Size end_of_prot_1, vector1< Size > const &matchres, Size end_of_prot_2=0, bool designall=false)
void	repack (Pose &pose, ScoreFunctionOP sf, Size, vector1< Size > const &matchres, Size end_of_prot_2=0)
void	design_homodimer (Pose &pose, ScoreFunctionOP sf, vector1< Size > const &matchres, bool designall=false)
std::ostream &	operator<< (std::ostream &out, MatchAlignInfo &ai)
void	setup_favor_native (core::pose::Pose &pose, core::pose::Pose const &native)
std::pair< vector1< Size >, vector1< Size > >	makesplitwork (Size total, Size total2=0)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("crossmatch")
static core::io::silent::SilentFileData	sfd

Typedef Documentation

Mat

typedef numeric::xyzMatrix<Real> Mat

MatchAlignerOP

typedef utility::pointer::owning_ptr<MatchAligner> MatchAlignerOP

MatchBaseCOP

typedef utility::pointer::owning_ptr<const MatchBase> MatchBaseCOP

MatchBaseOP

typedef utility::pointer::owning_ptr<MatchBase> MatchBaseOP

Vec

typedef numeric::xyzVector<Real> Vec

Vecs

typedef utility::vector1<Vec> Vecs

Function Documentation

design()

void design	(	Pose &	pose,
		ScoreFunctionOP	sf,
		Size	end_of_prot_1,
		vector1< Size > const &	matchres,
		Size	end_of_prot_2 = 0,
		bool	designall = false
	)

References basic::options::OptionKeys::willmatch::cb_sasa_thresh, 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, and basic::options::OptionKeys::inout::dbms::user.

Referenced by MatchSet::cross().

design_homodimer()

void design_homodimer	(	Pose &	pose,
		ScoreFunctionOP	sf,
		vector1< Size > const &	matchres,
		bool	designall = false
	)

References basic::options::OptionKeys::smhybrid::design_hydrophobic, 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::out::sf, vancomycin::task, and basic::options::OptionKeys::inout::dbms::user.

Referenced by MatchSet::cross_homodimer().

main()

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

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, argv, MatchAlignInfo::axis, CA, MatchAlignInfo::cen, CHI1, basic::options::OptionKeys::willmatch::chi1_increment, CHI2, basic::options::OptionKeys::willmatch::chi2_increment, clash(), MatchSet::cross(), numeric::xyzVector< T >::cross(), MatchSet::cross_homodimer(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, numeric::distance_squared(), numeric::xyzVector< T >::dot(), test.T009_Exceptions::e, basic::options::OptionKeys::willmatch::exclude_res1, basic::options::OptionKeys::willmatch::exclude_res2, filter, detail::find(), PREcst::fname, test.T020_Pose_Bindings::ft, h, basic::options::OptionKeys::willmatch::homodimer, create_a3b_hbs::i, MatchSet::iface_candidates, basic::options::OptionKeys::in::in, basic::init(), MatchSet::init(), create_a3b_hbs::j, oop_conformations::length, MatchSet::ligs, makesplitwork(), basic::options::OptionKeys::ms::ms, surface_app::native, basic::options::OptionKeys::willmatch::native1, basic::options::OptionKeys::willmatch::native2, numeric::xyzVector< T >::normalized(), basic::options::option, MatchAlignInfo::ortho, pi, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::mp::assembly::poses, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, numeric::conversions::radians(), read_res_list(), residue, rot, rot_pose(), numeric::rotation_matrix(), numeric::rotation_matrix_degrees(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::stepwise::s1, basic::options::OptionKeys::stepwise::s2, subloop_histogram::size, basic::options::OptionKeys::willmatch::splitwork, MatchAlignInfo::sqp, ObjexxFCL::string_of(), basic::options::OptionKeys::willmatch::symmetry_d2, tag, basic::options::OptionKeys::willmatch::taglist, basic::options::TR, trans_pose(), numeric::xyzMatrix< T >::transposed(), numeric::random::uniform(), basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, basic::options::OptionKeys::willmatch::write_reduced_matchset, MatchSet::write_to_file(), numeric::xyzVector< T >::x(), numeric::x_rotation_matrix_degrees(), xform_pose(), xform_pose_rev(), basic::options::OptionKeys::in::file::xyz, numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

makesplitwork()

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 main().

minimize()

void minimize	(	Pose &	pose,
		ScoreFunctionOP	sf,
		vector1< Size >	matchres
	)

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

Referenced by MatchSet::cross().

myoptH()

void myoptH	(	Pose &	pose,
		ScoreFunctionOP	sf
	)

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

Referenced by MatchSet::cross(), MatchSet::cross_homodimer(), and MatchSet::init().

operator<<()

std::ostream& operator<<	(	std::ostream &	out,
		MatchAlignInfo &	ai
	)

References MatchAlignInfo::axis, MatchAlignInfo::cen, MatchAlignInfo::ortho, and erraser_single_res_analysis::out.

randvec()

Vec randvec ( )

inline

References numeric::random::uniform(), and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by MatchSet::cross().

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 main().

repack()

void repack	(	Pose &	pose,
		ScoreFunctionOP	sf,
		Size	,
		vector1< Size > const &	matchres,
		Size	end_of_prot_2 = 0
	)

References detail::find(), create_a3b_hbs::i, beta_nonlocal::pose, basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by MatchSet::cross(), design(), and design_homodimer().

setup_favor_native()

void setup_favor_native	(	core::pose::Pose &	pose,
		core::pose::Pose const &	native
	)

References basic::options::OptionKeys::constraints::constraints, basic::options::OptionKeys::enzdes::favor_native_res, create_a3b_hbs::i, basic::Tracer::Info, surface_app::native, basic::options::option, beta_nonlocal::pose, and basic::options::TR.

Variable Documentation

sfd

core::io::silent::SilentFileData sfd

static

Referenced by MatchSet::cross(), and MatchSet::cross_homodimer().

TR

basic::Tracer TR("crossmatch") ( "crossmatch"  )

static

Referenced by minimize().