sel_hbonds.cc File Reference

#include <basic/Tracer.hh>
#include <basic/options/util.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <core/conformation/Residue.hh>
#include <core/id/AtomID.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/PDBInfo.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/HBondDatabase.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/HBEvalTuple.hh>
#include <core/scoring/hbonds/hbonds_geom.hh>
#include <core/scoring/hbonds/constants.hh>
#include <core/scoring/hbonds/types.hh>
#include <devel/init.hh>
#include <numeric/xyzVector.hh>
#include <iomanip>
#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...
bool	is_donor_h (AtomID const &aid, Pose const &ps)
	Tells whether a hydrogen atom may be an hbond donor. More...
bool	is_acceptor (AtomID const &aid, Pose const &ps)
	Tells whether an atom may be an hbond acceptor. More...
bool	is_hbond (AtomID const &don, AtomID const &acc, Pose const &ps, HBondDatabase const &database, HBondSet const &hbond_set)
	Tells whether two atoms form a hydrogen bond. More...
void	print_hbond (string const &ndon, int const idon, char const cdon, string const &nacc, int const iacc, char const cacc)
	Prints an hbond identifier. More...
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.pilot.sel_hbonds.main")
	Outputs selected hydrogen bonds from a pose. 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 TR.

Referenced by main().

is_acceptor()

bool is_acceptor	(	AtomID const &	aid,
		Pose const &	ps
	)

Tells whether an atom may be an hbond acceptor.

Parameters

[in]	aid	atom identifier in its pose.
[in]	ps	the pose.

Returns

true if the atom may be an acceptor atom; false otherwise.

Referenced by main().

is_donor_h()

bool is_donor_h	(	AtomID const &	aid,
		Pose const &	ps
	)

Tells whether a hydrogen atom may be an hbond donor.

Parameters

[in]	aid	atom identifier in its pose.
[in]	ps	the pose.

Returns

true if the atom is a polar hydrogen bond; false otherwise.

Referenced by main().

is_hbond()

bool is_hbond	(	AtomID const &	don,
		AtomID const &	acc,
		Pose const &	ps,
		HBondDatabase const &	database,
		HBondSet const &	hbond_set
	)

Tells whether two atoms form a hydrogen bond.

Parameters

[in]	don	candidate donor atom.
[in]	acc	candidate acceptor atom.
[in]	ps	pose containing the atoms.
[in]	database	hbond database.
[in]	hbond_set	dummy hbond set (will not be filled in).

Returns

true if the two atoms form a hydrogen bond; false otherwise.

It is assumed that don is a polar hydrogen atom and acc may accept hydrogen bonds.

References test.T005_Bindings::base, kic_runner::database, numeric::xyzVector< T >::distance_squared(), and test.T200_Scoring::hbond_set.

Referenced by main().

main()

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

References argv, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, utility::graph::Node::const_edge_list_end(), test.T009_Exceptions::e, utility::graph::Edge::get_node(), get_pose_resnum(), create_a3b_hbs::i, basic::init(), is_acceptor(), is_donor_h(), is_hbond(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, NEW_OPT, option, pi, pyrosetta.distributed.io::pose_from_file, print_hbond(), oop_conformations::scorefxn, basic::options::start_file(), and TR.

print_hbond()

void print_hbond	(	string const &	ndon,
		int const	idon,
		char const	cdon,
		string const &	nacc,
		int const	iacc,
		char const	cacc
	)

Prints an hbond identifier.

Parameters

[in]	ndon	name of the donor atom.
[in]	idon	PDB index of the donor residue.
[in]	cdon	PDB chain identifier of the donor residue.
[in]	nacc	name of the acceptor atom.
[in]	iacc	PDB index of the acceptor residue.
[in]	cacc	PDB chain identifier of the acceptor residue.

References TR.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("apps.pilot.sel_hbonds.main") ( "apps.pilot.sel_hbonds.main"  )

static

Outputs selected hydrogen bonds from a pose.

Parameters

[in]	-s	<PDB>, where <PDB> is the path to the PDB file containing the pose.
[in]	-bond_fil	<BOFIL>, where <BOFIL> is the path to a file specifying the hbonds to be searched for in the pose. The file has the following format:

C1 I1 A1, c1 i1 a1
... CM IM AM, cM iM aM
Here, M is the number of hydrogen bonds to be searched for. Ci, Ii, and Ai indicate, respectively, the chain identifier, residue index, and name of the DONOR atom in the ith hbond to be searched for (i=1,...,M); ci, ii, and ai indicate, respectively, the chain identifier, residue index and name of the ACCEPTOR atom in the ith hbond to be searched for (i=1,...,M).

Parameters

[in]

-atom_fil

<ATFIL>, where <ATFIL> is the path to a file specifying the atoms whose hbonds are to be searched for. The file has the following format:

C1 I1 A1
... CN IN AN
Here Ci, Ii, and Ai indicate, respectively, the chain identifier, residue index, and name of the ith atom whose hbonds are to be searched for (i=1,...,N, where N is the number of such atoms).

If both the -bond_fil and -atom_fil options are specified, only the former will be applied.

In the case of option -bond_fil, the ith output line indicates the ith hbond from the input list (i=0,...,N-1, where N is the number of such hbonds).

In the case of option -atom_fil, the output can be seen as a sequence of S blocks, where the ith block lists the hbond identifiers of the ith input atom that forms any hydrogen bonds (i=1,...,S).

Author

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

Referenced by get_pose_resnum(), main(), and print_hbond().