list_cnl_ngbs.cc File Reference

#include <protocols/neighbor/Neighborhood.hh>
#include <basic/Tracer.hh>
#include <basic/options/util.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <fstream>
#include <string>

Functions
Size	get_pose_resnum (int const pdbnum, char const pdbchn, Pose &ps)
	Returns the residue number of a residue in a pose. More...
void	print_res_ids (vector1< Size > const &vec, Pose const &ps, basic::Tracer &tr)
	: prints the identifiers of a set of residues More...
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.pilot.list_cnl_ngbs")
	Lists the residues that are neighbor to a given constellation. More...

Function Documentation

get_pose_resnum()

Size get_pose_resnum	(	int const	pdbnum,
		char const	pdbchn,
		Pose &	ps
	)

Returns the residue number of a residue in a pose.

@parm[in] pdbnum residue number of the residue in its PDB file. @parm[in] pdbchn chain identifier of the residue in the PDB file. @parm[in] ps pose that the residue has been loaded into.

References utility::options::OptionKeys::options::exit, create_a3b_hbs::j, and basic::options::TR.

Referenced by main().

main()

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

References argv, test.T009_Exceptions::e, get_pose_resnum(), basic::init(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, NEW_OPT, basic::options::option, pyrosetta.distributed.io::pose_from_file, print_res_ids(), basic::options::start_file(), and basic::options::TR.

print_res_ids()

void print_res_ids	(	vector1< Size > const &	vec,
		Pose const &	ps,
		basic::Tracer &	tr
	)

: prints the identifiers of a set of residues

Parameters

[in]

References create_a3b_hbs::i, tr, and vec().

Referenced by main().

Variable Documentation

TR

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

static

Lists the residues that are neighbor to a given constellation.

Parameters

[in]	-s	<PDBFIL>, where <PDBFIL> is the path to the PDB file containing the protein.
[in]	-cnl_resfile	<CNLFIL>, where <CNLFIL> is the path to a file enumerating the residues that form the constellation. The file has the following format: I1 C1 ... IN CN , where Ii and Ci are the residue index and the chain ID, respectively, of the ith residue forming the constellation (i=1,...,N).

The ith output line contains the identifier of the ith residue in the pose that is neighbor to the constellation (i=1,...,M, where M is the number of neighbors).

In the current implementation, a residue is neighbor to the constellation iff it is neighbor to at least one residue in the constellation; in particular, residue B is neighbor to constellation residue A iff protocols::neighbor::in_ngbat_sphere(A, B, pose) returns true.

A chain identifier in <CNLFIL> that is equal to '_' indicates a chain identifier of ' ' in <PDBFIL>.

Author

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