shobuns.cc File Reference

#include <protocols/pose_metric_calculators/SHOBuriedUnsatisfiedPolarsCalculator.fwd.hh>
#include <protocols/pose_metric_calculators/SHOBuriedUnsatisfiedPolarsCalculator.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <basic/Tracer.hh>
#include <basic/MetricValue.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/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/pose/PDBInfo.hh>
#include <core/id/AtomID.hh>
#include <core/conformation/Residue.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/pose/Pose.hh>
#include <core/types.hh>

Functions
int	main (int argc, char *argv[])
	MAIN. More...

Variables
static basic::Tracer	TR ("apps.public.analysis.shobuns.main")
	computes, using the SHO solvation model, the buried unsatisfied atoms among a target set of polar atoms More...

Function Documentation

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

MAIN.

References utility::io::oc::cerr, basic::options::OptionKeys::cp::cutoff, test.T009_Exceptions::e, devel::init(), utility::excn::Exception::msg(), option, pyrosetta.distributed.io::pose_from_file, res, basic::options::OptionKeys::DisulfideInsertion::scorefxn, basic::options::OptionKeys::pose_metrics::shobuns::sho_cutoff, basic::options::start_file(), basic::options::OptionKeys::pose_metrics::shobuns::tgt_amino, basic::options::OptionKeys::pose_metrics::shobuns::tgt_atom, basic::options::OptionKeys::pose_metrics::shobuns::tgt_res, and basic::options::OptionKeys::inout::dbms::user.

Variable Documentation

basic::Tracer TR("apps.public.analysis.shobuns.main")

static

computes, using the SHO solvation model, the buried unsatisfied atoms among a target set of polar atoms

Author

Andrea Bazzoli (ndrbz.nosp@m.z@gm.nosp@m.ail.c.nosp@m.om)

The program accepts only the following combinations of program-specific flags:

1. -tgt_amino <AMINO> -tgt_atom <ATOM> , to select all polar atoms named <ATOM> in all residues of type <AMINO>, where <AMINO> is a one-letter amino acid code; if <AMINO> is equal to "any", then the program selects atom <ATOM> from all residues that have it;
2. -tgt_res <TGTFIL> , to select all polar atoms from the residues specified in file <TGTFIL>. The format of <TGTFIL> is specified in the comments to function protocols::pose_metric_calculators::residue_subset() in file "protocols/pose_metric_calculators/SHOBuriedUnsatisfiedPolarsCalculator.cc";
3. [NO FLAGS], to select all polar atoms in the pose.

NOTE: flags -tgt_amino, -tgt_atom, -tgt_res are all in namespace pose_metrics:shobuns.

NOTE: flags that activate SHO within a scoring function, like '-score:patch occ_Hbond_sol_exact_talaris', are irrelevant to determining whether a polar atom is buried unsatisfied or not.