pack_ddg.cc File Reference

#include <devel/init.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/MMAtomTypeSet.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <basic/Tracer.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/viewer/viewers.hh>
#include <core/scoring/packstat/compute_sasa.hh>
#include <utility/vector1.hh>
#include <numeric/xyzVector.hh>
#include <numeric/random/random.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <fstream>
#include <sstream>
#include <iostream>
#include <string>
#include <map>
#include <ctime>
#include <core/import_pose/import_pose.hh>

Functions
std::map< std::string, std::string >	get_resname1to3 ()
core::conformation::ResidueOP	get_residue (std::string name)
void	refine_pose (Pose &pose, int seqpos=0)
void	mutate_residue (Pose &pose, int const seqpos, std::string res_to)
Real	packing_score (Pose const &pose, core::Size const rsd_id=0)
void	test_ddg (Pose const orig, std::string pdb, int seqpos, std::string from_res, std::string to_res, Real ddg1, Real ddg2)
void	read_ddg_file (std::string pdb, std::string fname)
int	main (int argc, char *argv[])

Function Documentation

get_residue()

core::conformation::ResidueOP get_residue

(

std::string

name

)

References get_resname1to3(), and basic::options::OptionKeys::in::file::residue_type_set.

Referenced by mutate_residue().

get_resname1to3()

std::map<std::string,std::string> get_resname1to3

(

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::m.

Referenced by get_residue(), and test_ddg().

main()

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

References argv, test.T009_Exceptions::e, basic::init(), and read_ddg_file().

mutate_residue()

void mutate_residue	(	Pose &	pose,
		int const	seqpos,
		std::string	res_to
	)

References get_residue(), beta_nonlocal::pose, and create_a3b_hbs::r.

Referenced by test_ddg().

packing_score()

Real packing_score	(	Pose const &	pose,
		core::Size const	rsd_id = 0
	)

References beta_nonlocal::pose.

Referenced by output_packstat(), and test_ddg().

read_ddg_file()

void read_ddg_file	(	std::string	pdb,
		std::string	fname
	)

References cal_vdw_radius_pool::buf, utility::io::oc::cerr, PREcst::fname, basic::options::OptionKeys::in::in, test.T008_Serialization::iss, kic_runner::pdb, pyrosetta.distributed.io::pose_from_file(), and test_ddg().

Referenced by main().

refine_pose()

void refine_pose	(	Pose &	pose,
		int	seqpos = 0
	)

References create_a3b_hbs::i, enumerate_junctions::int, beta_nonlocal::mm, beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by test_ddg().

test_ddg()

void test_ddg	(	Pose const	orig,
		std::string	pdb,
		int	seqpos,
		std::string	from_res,
		std::string	to_res,
		Real	ddg1,
		Real	ddg2
	)

References utility::io::oc::cerr, utility::io::oc::cout, get_resname1to3(), mutate_residue(), packing_score(), kic_runner::pdb, beta_nonlocal::pose, and refine_pose().

Referenced by read_ddg_file().