tgtres_polar_sho_energies.cc File Reference

#include <core/scoring/geometric_solvation/ExactOccludedHbondSolEnergy.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/io/pdb/pose_io.hh>
#include <core/pose/PDBInfo.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/Pose.hh>
#include <core/chemical/ResidueType.hh>
#include <basic/Tracer.hh>
#include <basic/options/util.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/pose_metrics.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/after_opts.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/types.hh>
#include <fstream>

Functions
void	load_set (std::string setf, utility::vector1< Size > &rset, core::pose::Pose &ps)
	loads a set of residues from file. The file format is as follows: More...
void	print_atom_info (Size ato_idx, Size res_idx, core::pose::Pose const &ps)
	prints an atom's identifier More...
Real	accum_hbdon_shoene (Size const base_idx, Size const res_idx, core::pose::Pose const &ps, core::scoring::geometric_solvation::ExactOccludedHbondSolEnergyCOP const &sho_meth)
	accumulates the SHO energies of a residue's polar hydrogens that share a common base atom More...
int	main (int argc, char *argv[])
	MAIN. More...

Variables
static basic::Tracer	TR ("apps.pilot.tgtres_polar_sho_energies")
	prints the SHO energies of the polar atoms of selected residues. More...

Function Documentation

accum_hbdon_shoene()

Real accum_hbdon_shoene	(	Size const	base_idx,
		Size const	res_idx,
		core::pose::Pose const &	ps,
		core::scoring::geometric_solvation::ExactOccludedHbondSolEnergyCOP const &	sho_meth
	)

accumulates the SHO energies of a residue's polar hydrogens that share a common base atom

Parameters

[in]	base_idx	index of the base atom in the residue
[in]	res_idx	index of the residue in the pose
[in]	ps	the pose
[in]	sho_meth	energy method to compute SHO energies

Returns

the accumulated energy of such hydrogens

References res.

Referenced by main().

load_set()

void load_set	(	std::string	setf,
		utility::vector1< Size > &	rset,
		core::pose::Pose &	ps
	)

loads a set of residues from file. The file format is as follows:

C1 R1 I1
... CN RN IN
Here, Ci, Ri, and Ii indicate the chain identifier, residue index, and insertion code (as specified in the pose's input PDB file) of the ith residue in the set (i=1,...,N; N>=1).

Parameters

[in]	path	to the input file.
[out]	rset	vector to hold the residues. The vector must be passed empty.
[in]	ps	the pose.

: after this function has been called, rset[i] is the pose index of the residue specified by the ith input line (i=1,...,N).

: blank chain identifiers and insertion codes must be specified with the '_' character.

References utility::options::OptionKeys::options::exit, kmeans_adaptive_kernel_density_bb_dependent_rotlib::idx, and basic::options::TR.

Referenced by main().

main()

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

MAIN.

References accum_hbdon_shoene(), argv, test.T009_Exceptions::e, create_a3b_hbs::i, basic::init(), create_a3b_hbs::j, load_set(), N, NEW_OPT, basic::options::option, pyrosetta.io::pose_from_pdb(), print_atom_info(), res, oop_conformations::scorefxn, basic::options::start_file(), and basic::options::TR.

print_atom_info()

void print_atom_info	(	Size	ato_idx,
		Size	res_idx,
		core::pose::Pose const &	ps
	)

prints an atom's identifier

Parameters

[in]	ato_idx	index of the atom in its residue
[in]	res_idx	index of the residue in the pose
[in]	ps	the pose

References basic::options::TR.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("apps.pilot.tgtres_polar_sho_energies") ( "apps.pilot.tgtres_polar_sho_energies"  )

static

prints the SHO energies of the polar atoms of selected residues.

Author

Andrea Bazzoli (bazzo.nosp@m.li@k.nosp@m.u.edu)

ARGUMENTS —> -s <POSE_PDB> —> -tgt_set <TGT_SET>, where <TGT_SET> is the path to a file describing the set of selected residues. The format of the file is specified in the comments to fuction load_set() (see below).

The output can be seen as a sequence of N blocks, where N is the number of residues in <TGT_SET> that contain at least one polar heavy atom. The ith block contains atom ids and sho energies of the ith such residue (i=1,...,N). Within each block, the jth line contains the atom id and sho energy of the residue's jth polar heavy atom (j=0,...,H-1).