find_buns.cc File Reference

Application that finds buried unsatisfied hydrogen bonding groups in proteins using the variable- distance to solvent logic. Outputs a kinemage that highlights the buried-unsatisfied polar groups and also displays all the exposed dots. More...

#include <devel/init.hh>
#include <protocols/vardist_solaccess/VarSolDRotamerDots.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueKinWriter.hh>
#include <core/id/AtomID.hh>
#include <basic/options/util.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/import_pose/import_pose.hh>
#include <protocols/jobdist/Jobs.hh>
#include <protocols/jobdist/standard_mains.hh>
#include <utility/file/FileName.hh>
#include <fstream>

Functions
utility::vector1< protocols::vardist_solaccess::VarSolDRotamerDotsOP >	varsoldist_rotamer_dots_for_pose (protocols::vardist_solaccess::VarSolDistSasaCalculatorCOP calc, core::pose::Pose const &pose)
std::list< core::id::AtomID >	buns_for_pose (core::pose::Pose const &pose, utility::vector1< protocols::vardist_solaccess::VarSolDRotamerDotsOP > const &rotamer_dots, core::scoring::hbonds::HBondSet const &hbset)
core::Vector	pose_nbratom_center_of_mass (core::pose::Pose const &pose)
void	write_buns_and_dots_kinemage (std::string const &outfile_name, std::string const &structure_tag, core::pose::Pose const &pose, utility::vector1< protocols::vardist_solaccess::VarSolDRotamerDotsOP > const &rotamer_dots, std::list< core::id::AtomID > const &buns)
int	main (int argc, char *argv[])

Detailed Description

Application that finds buried unsatisfied hydrogen bonding groups in proteins using the variable- distance to solvent logic. Outputs a kinemage that highlights the buried-unsatisfied polar groups and also displays all the exposed dots.

Author

Andrew Leaver-Fay (aleav.nosp@m.erfa.nosp@m.y@gma.nosp@m.il.c.nosp@m.om)

Function Documentation

buns_for_pose()

std::list< core::id::AtomID > buns_for_pose	(	core::pose::Pose const &	pose,
		utility::vector1< protocols::vardist_solaccess::VarSolDRotamerDotsOP > const &	rotamer_dots,
		core::scoring::hbonds::HBondSet const &	hbset
	)

References create_a3b_hbs::ii, beta_nonlocal::jj, kk, beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by main().

main()

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

References argv, utility::file::FileName::base(), buns_for_pose(), basic::options::OptionKeys::chemical::chemical, test.T009_Exceptions::e, create_a3b_hbs::ii, basic::init(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::frags::scoring::scoring, test.T120_core::sfxn, varsoldist_rotamer_dots_for_pose(), and write_buns_and_dots_kinemage().

pose_nbratom_center_of_mass()

core::Vector pose_nbratom_center_of_mass

(

core::pose::Pose const &

pose

)

References create_a3b_hbs::ii, and beta_nonlocal::pose.

Referenced by write_buns_and_dots_kinemage().

varsoldist_rotamer_dots_for_pose()

utility::vector1< protocols::vardist_solaccess::VarSolDRotamerDotsOP > varsoldist_rotamer_dots_for_pose	(	protocols::vardist_solaccess::VarSolDistSasaCalculatorCOP	calc,
		core::pose::Pose const &	pose
	)

References create_a3b_hbs::ii, beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by main().

write_buns_and_dots_kinemage()

void write_buns_and_dots_kinemage	(	std::string const &	outfile_name,
		std::string const &	structure_tag,
		core::pose::Pose const &	pose,
		utility::vector1< protocols::vardist_solaccess::VarSolDRotamerDotsOP > const &	rotamer_dots,
		std::list< core::id::AtomID > const &	buns
	)

References val2thr::fout, create_a3b_hbs::ii, beta_nonlocal::pose, and pose_nbratom_center_of_mass().

Referenced by main().