PeptideDeriver.cc File Reference

#include <core/types.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueSelector.hh>
#include <core/chemical/util.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <basic/Tracer.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/PDBInfo.hh>
#include <basic/options/util.hh>
#include <core/init/init.hh>
#include <core/io/pdb/pose_io.hh>
#include <numeric/xyzVector.hh>
#include <numeric/random/random.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/util.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/conformation/Conformation.hh>
#include <core/chemical/VariantType.hh>
#include <core/util/disulfide_util.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <protocols/scoring/Interface.hh>
#include <basic/options/option.hh>
#include <devel/init.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/pdb/file_data.hh>
#include <utility/excn/Exceptions.hh>

Namespaces
	peptide_deriver

Functions
core::pose::PoseOP	get_subPose (core::pose::PoseOP, core::pose::PoseOP, core::Size, core::Size, char)
Real	calculateInterfaceScore (core::pose::Pose, core::scoring::ScoreFunctionOP)
core::pose::PoseOP	twoChainPose (core::pose::Pose const &src, Size chainA, Size chainB)
core::pose::PoseOP	oneChainPose (core::pose::Pose const &src, Size chainA)
void	derive (core::pose::Pose const &pose)
int	main (int argc, char *argv[])

Variables
basic::options::StringOptionKey	peptide_deriver::chain_to_derive_from ("peptide_deriver:chain_to_derive_from")
basic::options::RealOptionKey	peptide_deriver::length_to_derive ("peptide_deriver:length_to_derive")
basic::options::BooleanOptionKey	peptide_deriver::optimize ("peptide_deriver:optimize")
basic::options::StringOptionKey	peptide_deriver::dump_peptide_pdb ("peptide_deriver:dump_peptide_pdb")
static basic::Tracer	TR ("PeptideDeriver")

Function Documentation

calculateInterfaceScore()

Real calculateInterfaceScore	(	core::pose::Pose	pose,
		core::scoring::ScoreFunctionOP	scorefxn
	)

References beta_nonlocal::pose, and basic::options::OptionKeys::enzdes::trans_magnitude.

derive()

void derive

(

core::pose::Pose const &

pose

)

References a, compute_difference::b, create_a3b_hbs::best_pose, calculateInterfaceScore(), chain_end(), peptide_deriver::chain_to_derive_from, chains, basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, pyrosetta::create_score_function, dist(), peptide_deriver::dump_peptide_pdb, get_subPose(), create_a3b_hbs::i, peptide_deriver::length_to_derive, peptide_deriver::optimize, option, basic::options::OptionKeys::pepspec::pep_chain, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

get_subPose()

core::pose::PoseOP get_subPose	(	core::pose::PoseOP	chainA,
		core::pose::PoseOP	chainB,
		core::Size	pep_start,
		core::Size	pep_end,
		char	pep_chain
	)

References basic::options::OptionKeys::chemical::chemical, create_a3b_hbs::i, basic::options::OptionKeys::pepspec::pep_chain, pep_end(), and beta_nonlocal::pose.

main()

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

References argv, peptide_deriver::chain_to_derive_from, chains, basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, pyrosetta::create_score_function, derive(), peptide_deriver::dump_peptide_pdb, test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, func, create_a3b_hbs::i, basic::init(), create_a3b_hbs::j, peptide_deriver::length_to_derive, basic::options::OptionKeys::in::file::movemap, peptide_deriver::optimize, option, beta_nonlocal::pose, pyrosetta.io::pose_from_pdb(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), TR, and twoChainPose().

oneChainPose()

core::pose::PoseOP oneChainPose	(	core::pose::Pose const &	src,
		Size	chainA
	)

References create_a3b_hbs::i, and beta_nonlocal::pose.

twoChainPose()

core::pose::PoseOP twoChainPose	(	core::pose::Pose const &	src,
		Size	chainA,
		Size	chainB
	)

References create_a3b_hbs::i, and beta_nonlocal::pose.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("PeptideDeriver") ( "PeptideDeriver"  )

static

Referenced by derive(), and main().