calculate_distances.cc File Reference

Calculate distances in RNA/protein structures for score function development. More...

#include <core/pose/Pose.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/import_pose/pose_stream/PoseInputStream.hh>
#include <core/import_pose/pose_stream/PoseInputStream.fwd.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <core/import_pose/import_pose.hh>
#include <core/conformation/Residue.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <utility/pointer/owning_ptr.hh>
#include <basic/Tracer.hh>
#include <numeric/xyzMatrix.hh>
#include <iostream>
#include <fstream>
#include <devel/init.hh>
#include <basic/options/option_macros.hh>
#include <core/chemical/rna/util.hh>

Functions
void	get_distances (core::pose::Pose const &pose, std::string struct_name, std::ofstream &out_file)
void	get_atom_vdw (core::pose::Pose const &poseFA, std::ofstream &out_file, utility::vector1< std::string > const &RNA_atoms_common, utility::vector1< std::string > const &protein_atoms, utility::vector1< std::string > const &RNA_atoms_A, utility::vector1< std::string > const &RNA_atoms_C, utility::vector1< std::string > const &RNA_atoms_G, utility::vector1< std::string > const &RNA_atoms_U, core::Real const &cutoff=20.0, bool const &include_base_cen=false)
void	get_distance_around_rna_base (core::pose::Pose const &poseFA, std::string const &struct_name, std::ofstream &out_file)
void	get_distances_around_rna_backbone (core::pose::Pose const &poseFA, std::string const &struct_name, std::ofstream &out_file)
utility::vector1< std::pair< core::Size, bool > >	get_interface_type (core::pose::Pose const &poseFA)
utility::vector1< std::pair< core::Size, core::Size > >	get_num_nbrs (core::pose::Pose const &poseFA)
void	write_to_restype_file (std::ofstream &restype_file, utility::vector1< std::pair< core::Size, bool > > is_interface, utility::vector1< std::pair< core::Size, core::Size > > num_nbrs, std::string const &pdb_name)
void	test_actcoord (core::pose::Pose const &pose)
void	calculate_distances ()
int	main (int argc, char **argv)

Variables
static basic::Tracer	TR ("apps.pilot.kkappel.calculate_distances")

Detailed Description

Calculate distances in RNA/protein structures for score function development.

score RNA/protein complex with low-res score function

see what's going on with protein centroid with RNA FA

Author

Kalli Kappel kappe.nosp@m.l@st.nosp@m.anfor.nosp@m.d.ed.nosp@m.u

Function Documentation

calculate_distances()

void calculate_distances

(

)

References ObjexxFCL::blank(), utility::io::oc::cout, basic::options::OptionKeys::ddg::dump_pdbs, get_atom_vdw(), add_xyz_to_pose::get_dist(), get_distance_around_rna_base(), get_distances_around_rna_backbone(), get_interface_type(), get_num_nbrs(), gaussian-sampling::input, num_nbrs(), basic::options::option, drrafter_rna::output_tag, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, docking::s, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::in::file::silent, tag, tag_from_pose(), basic::options::OptionKeys::in::file::tags, basic::options::OptionKeys::inout::dbms::user, and write_to_restype_file().

Referenced by main().

get_atom_vdw()

void get_atom_vdw	(	core::pose::Pose const &	poseFA,
		std::ofstream &	out_file,
		utility::vector1< std::string > const &	RNA_atoms_common,
		utility::vector1< std::string > const &	protein_atoms,
		utility::vector1< std::string > const &	RNA_atoms_A,
		utility::vector1< std::string > const &	RNA_atoms_C,
		utility::vector1< std::string > const &	RNA_atoms_G,
		utility::vector1< std::string > const &	RNA_atoms_U,
		core::Real const &	cutoff = 20.0,
		bool const &	include_base_cen = false
	)

References extract_by_sidechain_sasa_score::cutoff, build_jacobian::distance, basic::options::option, beta_nonlocal::pose, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by calculate_distances().

get_distance_around_rna_base()

void get_distance_around_rna_base	(	core::pose::Pose const &	poseFA,
		std::string const &	struct_name,
		std::ofstream &	out_file
	)

References numeric::xyzMatrix< T >::col_x(), numeric::xyzMatrix< T >::col_y(), numeric::xyzMatrix< T >::col_z(), build_jacobian::distance, vector::dot_product(), basic::options::option, beta_nonlocal::pose, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by calculate_distances().

get_distances()

void get_distances	(	core::pose::Pose const &	pose,
		std::string	struct_name,
		std::ofstream &	out_file
	)

References build_jacobian::distance, oop_conformations::length, natoms(), beta_nonlocal::pose, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

get_distances_around_rna_backbone()

void get_distances_around_rna_backbone	(	core::pose::Pose const &	poseFA,
		std::string const &	struct_name,
		std::ofstream &	out_file
	)

References build_jacobian::distance, basic::options::option, beta_nonlocal::pose, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by calculate_distances().

get_interface_type()

utility::vector1< std::pair< core::Size, bool > > get_interface_type

(

core::pose::Pose const &

poseFA

)

References build_jacobian::distance, oop_conformations::length, basic::options::option, beta_nonlocal::pose, and test.T200_Scoring::rsd2.

Referenced by calculate_distances().

get_num_nbrs()

utility::vector1< std::pair< core::Size, core::Size > > get_num_nbrs

(

core::pose::Pose const &

poseFA

)

References build_jacobian::distance, oop_conformations::length, basic::options::OptionKeys::frags::contacts::neighbors, basic::options::option, beta_nonlocal::pose, and test.T200_Scoring::rsd2.

Referenced by calculate_distances().

main()

int main	(	int	argc,
		char **	argv
	)

References argv, calculate_distances(), basic::options::OptionKeys::ddg::dump_pdbs, test.T009_Exceptions::e, add_xyz_to_pose::get_dist(), basic::init(), and NEW_OPT.

test_actcoord()

void test_actcoord

(

core::pose::Pose const &

pose

)

References val2thr::atom, basic::options::OptionKeys::in::file::centroid, utility::io::oc::cout, create_a3b_hbs::i, oop_conformations::length, natoms(), beta_nonlocal::pose, docking::s, and subloop_histogram::size.

write_to_restype_file()

void write_to_restype_file	(	std::ofstream &	restype_file,
		utility::vector1< std::pair< core::Size, bool > >	is_interface,
		utility::vector1< std::pair< core::Size, core::Size > >	num_nbrs,
		std::string const &	pdb_name
	)

References create_a3b_hbs::i, and num_nbrs().

Referenced by calculate_distances().

Variable Documentation

TR

basic::Tracer TR("apps.pilot.kkappel.calculate_distances") ( "apps.pilot.kkappel.calculate_distances"  )

static