torsional_potential_corrections.cc File Reference

#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/util.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/CartesianMinimizer.hh>
#include <core/optimization/symmetry/SymAtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/task/RotamerSampleOptions.hh>
#include <core/pack/packer_neighbors.hh>
#include <core/pack/rotamer_set/RotamerSetFactory.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/SingleResidueDunbrackLibrary.hh>
#include <core/pack/dunbrack/DunbrackRotamer.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>
#include <core/pack/optimizeH.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibraryFactory.hh>
#include <core/io/CrystInfo.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/types.hh>
#include <devel/init.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <protocols/jd2/Job.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <utility>
#include <utility/vector1.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/mpistream.hh>
#include <utility/string_util.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <numeric/random/random.hh>
#include <numeric/NumericTraits.hh>
#include <numeric/fourier/FFT.hh>
#include <numeric/constants.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyzVector.io.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <ObjexxFCL/format.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/after_opts.hh>
#include <basic/options/option_macros.hh>
#include <basic/basic.hh>
#include <basic/database/open.hh>
#include <basic/datacache/CacheableString.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>
#include <boost/algorithm/string.hpp>
#include <fstream>
#include <iostream>
#include <cmath>
#include <sstream>
#include <string>
#include <queue>
#include <cstdarg>

Classes
struct	FragInfo
struct	ScoreFragInfo

Functions
core::Size	getRotID (core::Size r1, core::Size r2=0, core::Size r3=0, core::Size r4=0)
core::Real	distance (FragInfo const &f1, FragInfo const &f2)
core::Size	getbin (core::Real theta)
void	read_rama_map_file (std::string const &filename, utility::vector1< ObjexxFCL::FArray2D< Real > > &data)
bool	is_semi_rot (core::chemical::AA aa)
void	mutate_to_ala (core::pose::Pose &pose, int center)
template<class C >
void	dump_table (ObjexxFCL::FArray2D< C > const &table, std::string const &filename, std::string const &tag)
void	correct_rama ()
void	calc_rama_scores ()
void	correct_dunbrack ()
void	calc_scores ()
void	make_fragments ()
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("torsion.corrections")

Function Documentation

void calc_rama_scores

(

)

References basic::options::OptionKeys::in::file::dssp, getbin(), test.T150_PyMOL_Integration::i, test.T200_Scoring::ii, basic::options::OptionKeys::frags::j, min(), loops_kic::mm, option, options, erraser_single_res_analysis::out, test.T150_PyMOL_Integration::phi, demo.D010_Pose_structure::pose, test.T150_PyMOL_Integration::psi, basic::options::OptionKeys::remodel::rama, test.T200_Scoring::score_types, basic::options::OptionKeys::out::file::scorefile, basic::options::OptionKeys::DisulfideInsertion::scorefxn, basic::options::OptionKeys::mh::match::ss, utility::to_string(), TR, and basic::options::OptionKeys::optE::weights.

Referenced by main().

void calc_scores

(

)

References basic::options::OptionKeys::mh::match::aa, basic::options::OptionKeys::mp::setup::center, basic::options::OptionKeys::chemical::chemical, basic::Tracer::Debug, utility::pointer::dynamic_pointer_cast(), basic::options::OptionKeys::cutoutdomain::end, getRotID(), test.T200_Scoring::ii, is_semi_rot(), min(), loops_kic::mm, option, options, erraser_single_res_analysis::out, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, runtime_assert, basic::options::OptionKeys::out::file::scorefile, basic::options::OptionKeys::DisulfideInsertion::scorefxn, basic::options::OptionKeys::cutoutdomain::start, utility::string_split(), tag, test.G200_Module_Region::tf, TR, and basic::options::OptionKeys::sc::weight.

Referenced by main().

void correct_dunbrack

(

)

References basic::options::OptionKeys::mh::match::aa, basic::options::OptionKeys::loodo::cap, basic::options::OptionKeys::chemical::chemical, clean_pdb_keep_ligand::count, erraser_single_res_analysis::data, utility::pointer::dynamic_pointer_cast(), numeric::fourier::fft2(), getRotID(), test.T150_PyMOL_Integration::i, ScoreFragInfo::id_, numeric::fourier::ifft2(), test.T200_Scoring::ii, basic::options::OptionKeys::in::in, is_semi_rot(), basic::options::OptionKeys::frags::j, min(), option, erraser_single_res_analysis::outfile, test.T150_PyMOL_Integration::phi, demo.D010_Pose_structure::pose, test.T150_PyMOL_Integration::psi, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, basic::options::OptionKeys::mh::filter::restype, basic::options::OptionKeys::out::file::scorefile, basic::options::OptionKeys::out::path::scratch, basic::options::OptionKeys::cutoutdomain::start, basic::options::OptionKeys::full_model::working_res, numeric::crick_equations::x(), and numeric::crick_equations::y().

Referenced by main().

void correct_rama

(

)

References basic::options::OptionKeys::mh::match::aa, basic::options::OptionKeys::loodo::cap, utility::io::oc::cerr, basic::options::OptionKeys::chemical::chemical, clean_pdb_keep_ligand::count, erraser_single_res_analysis::data, ObjexxFCL::FArray2D< typename >::dimension(), numeric::fourier::fft2(), test.T150_PyMOL_Integration::i, ScoreFragInfo::id_, numeric::fourier::ifft2(), basic::options::OptionKeys::in::in, basic::options::OptionKeys::frags::j, numeric::log(), max(), min(), basic::options::option, option, erraser_single_res_analysis::outfile, basic::options::OptionKeys::corrections::score::rama_pp_map, read_rama_map_file(), basic::options::OptionKeys::out::file::scorefile, basic::options::OptionKeys::inout::dbms::user, numeric::crick_equations::x(), and numeric::crick_equations::y().

Referenced by main().

core::Real distance	(	FragInfo const &	f1,
		FragInfo const &	f2
	)

References FragInfo::center_, and FragInfo::pose_.

Referenced by make_fragments().

template<class C >

void dump_table	(	ObjexxFCL::FArray2D< C > const &	table,
		std::string const &	filename,
		std::string const &	tag
	)

References test.T150_PyMOL_Integration::i, basic::options::OptionKeys::frags::j, erraser_single_res_analysis::out, utility::options::OptionKeys::options::table::table, and ObjexxFCL::FArray2D< typename >::u1().

core::Size getbin

(

core::Real

theta

)

Referenced by calc_rama_scores(), and make_fragments().

core::Size getRotID	(	core::Size	r1,
		core::Size	r2 = 0,
		core::Size	r3 = 0,
		core::Size	r4 = 0
	)

References basic::options::OptionKeys::motifs::r1, and basic::options::OptionKeys::motifs::r2.

Referenced by calc_scores(), and correct_dunbrack().

bool is_semi_rot

(

core::chemical::AA

aa

)

References basic::options::OptionKeys::chemical::chemical.

Referenced by calc_scores(), and correct_dunbrack().

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

References calc_rama_scores(), calc_scores(), basic::options::OptionKeys::loodo::cap, basic::options::OptionKeys::cluster::energy_based_clustering::cluster_radius, correct_dunbrack(), correct_rama(), utility::excn::Exception::display(), test.T009_Exceptions::e, packing::flip_HNQ(), devel::init(), make_fragments(), min(), in::missing_density_to_jump(), basic::options::OptionKeys::dna::specificity::mode, NEW_OPT, packing::no_optH(), option, basic::options::OptionKeys::out::file::scorefile, and in::file::silent_struct_type().

void make_fragments

(

)

References a, basic::options::OptionKeys::mp::setup::center, basic::options::OptionKeys::cluster::energy_based_clustering::cluster_radius, utility::graph::Node::const_edge_list_end(), basic::options::OptionKeys::in::path::database, debug_assert, distance(), basic::options::OptionKeys::in::file::dssp, utility::graph::Edge::get_node(), getbin(), test.T150_PyMOL_Integration::i, basic::options::OptionKeys::frags::j, min(), mutate_to_ala(), basic::options::OptionKeys::ddg::nfrags, option, erraser_single_res_analysis::outfile, test.T150_PyMOL_Integration::phi, demo.D010_Pose_structure::pose, test.T150_PyMOL_Integration::psi, basic::options::OptionKeys::DisulfideInsertion::scorefxn, basic::options::OptionKeys::mh::match::ss, utility::to_string(), and numeric::crick_equations::x().

Referenced by main().

void mutate_to_ala	(	core::pose::Pose &	pose,
		int	center
	)

References test.T150_PyMOL_Integration::i, basic::options::OptionKeys::in::file::residue_type_set, and TR.

Referenced by make_fragments().

void read_rama_map_file	(	std::string const &	filename,
		utility::vector1< ObjexxFCL::FArray2D< Real > > &	data
	)

References basic::options::OptionKeys::mh::match::aa, utility::io::izstream::close(), erraser_single_res_analysis::data, utility::io::izstream::eof(), utility::io::izstream::getline(), utility::io::izstream::good(), test.T150_PyMOL_Integration::i, basic::options::OptionKeys::frags::j, line, basic::database::open(), utility::io::izstream::open(), test.T150_PyMOL_Integration::phi, test.T150_PyMOL_Integration::psi, and utility_exit_with_message.

Referenced by correct_rama().

Variable Documentation

basic::Tracer TR("torsion.corrections")

static

Referenced by calc_rama_scores(), calc_scores(), and mutate_to_ala().