david_align_append_and_recompute_score_and_rmsd.cc File Reference

#include <iostream>
#include <fstream>
#include <sstream>
#include <core/pose/Pose.hh>
#include <core/pose/init_id_map.hh>
#include <core/conformation/Residue.hh>
#include <devel/init.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <basic/options/util.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/Tracer.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/rms_util.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <string>
#include <ObjexxFCL/FArray2D.hh>
#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <utility/excn/Exceptions.hh>
#include <numeric/model_quality/rms.hh>

Functions
void	define_interface (core::pose::Pose &ref_pose)
bool	is_interface_heavyatom (core::pose::Pose const &pose, core::pose::Pose const &, core::Size resno, core::Size atomno)
bool	is_interface_bbatom (core::pose::Pose const &pose, core::pose::Pose const &, core::Size resno, core::Size atomno)
Real	calpha_pdb_superimpose_pose (pose::Pose &mod_pose, pose::Pose const &ref_pose)
Real	iface_pdb_superimpose_pose (pose::Pose &mod_pose, pose::Pose const &ref_pose)
template<class T >
Real	interface_rmsd (pose::Pose &mod_pose, pose::Pose const &ref_pose, T *predicate)
int	main (int argc, char *argv[])
	General testing code. More...

Variables
static basic::Tracer	TR ("apps.pilot.david_recompute_score_and_rmsd.main")
std::set< std::string >	interface
core::Size	lig_res_num

Function Documentation

calpha_pdb_superimpose_pose()

Real calpha_pdb_superimpose_pose	(	pose::Pose &	mod_pose,
		pose::Pose const &	ref_pose
	)

References create_a3b_hbs::ii, beta_nonlocal::jj, and superimpose_pose().

define_interface()

void define_interface

(

core::pose::Pose &

ref_pose

)

References test.T200_Scoring::emap, utility::options::OptionKeys::options::exit, utility::graph::Edge::get_node(), pyrosetta.distributed.io::get_score_function(), interface, create_a3b_hbs::j, lig_res_num, utility::graph::Node::lower_edge_list_end(), predPRE::resnum, oop_conformations::scorefxn, and TR.

Referenced by main().

iface_pdb_superimpose_pose()

Real iface_pdb_superimpose_pose	(	pose::Pose &	mod_pose,
		pose::Pose const &	ref_pose
	)

References create_a3b_hbs::ii, is_interface_heavyatom(), beta_nonlocal::jj, and superimpose_pose().

Referenced by main().

interface_rmsd()

template<class T >

Real interface_rmsd	(	pose::Pose &	mod_pose,
		pose::Pose const &	ref_pose,
		T *	predicate
	)

References create_a3b_hbs::i, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::jj, create_a3b_hbs::k, natoms(), and numeric::model_quality::rms_wrapper().

Referenced by main().

is_interface_bbatom()

bool is_interface_bbatom	(	core::pose::Pose const &	pose,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References interface, and beta_nonlocal::pose.

Referenced by main().

is_interface_heavyatom()

bool is_interface_heavyatom	(	core::pose::Pose const &	pose,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References interface, and beta_nonlocal::pose.

Referenced by iface_pdb_superimpose_pose(), and main().

main()

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

General testing code.

References job_manager::app, argv, utility::vectorL< L, T, A >::at(), utility::io::ozstream::clear(), utility::io::ozstream::close(), utility::io::oc::cout, define_interface(), test.T009_Exceptions::e, basic::options::OptionKeys::score::empty, utility::options::OptionKeys::options::exit, create_a3b_hbs::f, getline(), iface_pdb_superimpose_pose(), basic::init(), interface_rmsd(), is_interface_bbatom(), is_interface_heavyatom(), NEW_OPT, utility::io::ozstream::open(), option, erraser_single_res_analysis::out, drrafter_rna::output_tag, pyrosetta.distributed.io::pose_from_file(), basic::options::start_files(), tag, and TR.

Variable Documentation

interface

std::set<std::string> interface

Referenced by define_interface(), is_interface_bbatom(), and is_interface_heavyatom().

lig_res_num

core::Size lig_res_num

Referenced by define_interface().

TR

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

static

Referenced by define_interface(), and main().