cartesian_ddg.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/Energies.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <core/pack/task/ResfileReader.hh>
#include <core/pose/PDBInfo.hh>
#include <basic/options/util.hh>
#include <basic/options/after_opts.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/ddg.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/database/open.hh>
#include <devel/init.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyz.functions.hh>
#include <fstream>
#include <iostream>
#include <sstream>
#include <cstdlib>
#include <string>
#include <ObjexxFCL/format.hh>
#include <protocols/ddg/ddGMover.hh>
#include <protocols/scoring/Interface.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/relax/FastRelax.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/toolbox/pose_manipulation/pose_manipulation.hh>
#include <protocols/ddg/CartesianddG.hh>
#include <core/import_pose/import_pose.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>
#include <utility/exit.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <basic/Tracer.hh>

Typedefs
using	mutations = utility::vector1< core::chemical::AA >
using	bools = utility::vector1< bool >

Functions
void	find_neighbors (bools const &is_mutated, Pose const &pose, bools &is_flexible, Real const heavyatom_distance_threshold=6.0)
void	find_neighbors_directional (bools const &neighborin, Pose const &pose, bools &neighbor, Real const K=8.0)
void	read_in_mutations (utility::vector1< mutations > &res_to_mut, bools &is_mutated, std::string filename, Pose &pose)
	The input file is a list of mutation blocks. Usually, this will be a set of point mutations. where each "block" lists a single mutation. However, it is possible to specify multiple mutations together in a single block. More...
void	compute_folding_energies (ScoreFunctionOP fa_scorefxn, Pose &pose, bools const &is_flexible, bools const &is_mutpos, Size bbnbrs=0)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.public.cartesian_ddg")

Typedef Documentation

using bools = utility::vector1<bool>

using mutations = utility::vector1<core::chemical::AA>

Function Documentation

void compute_folding_energies	(	ScoreFunctionOP	fa_scorefxn,
		Pose &	pose,
		bools const &	is_flexible,
		bools const &	is_mutpos,
		Size	bbnbrs = 0
	)

References basic::options::OptionKeys::ddg::bbnbrs, ddg::cartesian(), basic::options::OptionKeys::carbohydrates::glycan_sampler::cartmin, basic::options::OptionKeys::abinitio::fastrelax, basic::options::OptionKeys::frags::j, basic::options::OptionKeys::in::file::movemap, option, options, and runtime_assert.

Referenced by main().

void find_neighbors	(	bools const &	is_mutated,
		Pose const &	pose,
		bools &	is_flexible,
		Real const	heavyatom_distance_threshold = 6.0
	)

References basic::options::OptionKeys::frags::j, clean_pdb_keep_ligand::nres, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, and numeric::square().

Referenced by main().

void find_neighbors_directional	(	bools const &	neighborin,
		Pose const &	pose,
		bools &	neighbor,
		Real const	K = 8.0
	)

References erraser_analysis::angle1, erraser_analysis::angle2, numeric::angle_degrees(), basic::options::OptionKeys::score::fiber_diffraction::b, basic::options::OptionKeys::frags::j, make_symmdef_file_denovo::length, clean_pdb_keep_ligand::nres, demo.D010_Pose_structure::pose, mutant_modeler::protein_residues, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by main().

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

References utility::file::FileName::base(), basic::options::OptionKeys::ddg::bbnbrs, utility::io::izstream::close(), utility::io::ozstream::close(), compute_folding_energies(), utility::io::oc::cout, basic::options::OptionKeys::cp::cutoff, basic::Tracer::Debug, basic::options::OptionKeys::ddg::dump_pdbs, test.T009_Exceptions::e, utility::io::izstream::eof(), ObjexxFCL::format::F(), basic::options::OptionKeys::ddg::fd_mode, utility::file::file_exists(), test.G202_Module_PythonPDB::filename, find_neighbors(), find_neighbors_directional(), utility::io::getline(), utility::io::izstream::good(), devel::init(), basic::options::OptionKeys::ddg::interface_ddg, basic::options::OptionKeys::ddg::iterations, basic::options::OptionKeys::frags::j, basic::options::OptionKeys::ddg::legacy, line, utility::excn::Exception::msg(), basic::options::OptionKeys::ddg::mut_file, basic::options::OptionKeys::ddg::mut_only, basic::options::OptionKeys::casp::num_iterations, utility::io::izstream::open(), utility::io::ozstream::open(), utility::io::ozstream::open_append(), basic::options::OptionKeys::casp::opt_radius, basic::options::option, option, options, demo.D050_Packer_task::packer_task(), demo.D010_Pose_structure::pose, pyrosetta.distributed.io::pose_from_file, read_in_mutations(), basic::options::OptionKeys::run::run, runtime_assert, basic::options::start_file(), tag, test.G200_Module_Region::task, TR, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, value, and basic::options::OptionKeys::ddg::wt_only.

void read_in_mutations	(	utility::vector1< mutations > &	res_to_mut,
		bools &	is_mutated,
		std::string	filename,
		Pose &	pose
	)

The input file is a list of mutation blocks. Usually, this will be a set of point mutations. where each "block" lists a single mutation. However, it is possible to specify multiple mutations together in a single block.

The file format is: "total N" followed by N blocks, where each block is "M" specifying followed by M lines of wt/resid/mutaa triples "wtaa resid mutaa" N, M and resid are all supposed to be integers. wtaa, and mutaa are supposed to be 1-letter amino acid codes.

References basic::Tracer::Debug, debug_assert, basic::Tracer::Error, basic::options::OptionKeys::mp::mutate_relax::mutation, clean_pdb_keep_ligand::resnum, runtime_assert, TR, and revert_app::wt.

Referenced by main().

Variable Documentation

basic::Tracer TR("apps.public.cartesian_ddg")

static

Referenced by main(), and read_in_mutations().