BuildFloppyTail.cc File Reference

#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/disulfide_util.hh>
#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/util.hh>
#include <core/scoring/Energies.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/options/option.hh>
#include <core/options/keys/in.OptionKeys.gen.hh>
#include <core/options/keys/run.OptionKeys.gen.hh>
#include <utility/vector1.hh>
#include <utility>
#include <core/conformation/Conformation.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/chemical/ResidueTypeSelector.hh>
#include <core/chemical/util.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <basic/Tracer.hh>
#include <core/options/util.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <numeric/xyzVector.hh>
#include <numeric/random/random.hh>
#include <core/options/keys/out.OptionKeys.gen.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/util.hh>

Functions
void	append_sequence_to_pose (pose::Pose &pose, std::string const &sequence_in, chemical::ResidueTypeSet const &residue_set, bool const auto_termini)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("BuildFloppyTail")

Function Documentation

append_sequence_to_pose()

void append_sequence_to_pose	(	pose::Pose &	pose,
		std::string const &	sequence_in,
		chemical::ResidueTypeSet const &	residue_set,
		bool const	auto_termini
	)

Given a Pose, a protein sequence where each character represents an amino acid, and a ResidueTypeSet, give the Pose a conformation of covalently linked residues that match the sequence. NOTE: support making pose from a fully annotated sequence now, that is, for each residue variant or ligand which cannot be deduced from one letter code directly, a [] is added directly following the one letter code containig the residue's fullname, e.g. K[lys:NtermProteinFull]ADFGCH[HIS_D]QNVE[glu:CtermProteinFull]Z[ZN]. This allows a pose to be constructed with full features from a silent output file, such as with distiguished HIS tautomers, various chain termini and cutpoint variants etc. Currently not working with disulfide variant CYD, but this is on to-do list.

References utility::io::oc::cerr, basic::options::OptionKeys::chemical::chemical, basic::Tracer::Error, create_a3b_hbs::i, oop_conformations::length, beta_nonlocal::pose, residue_types_from_sequence(), TR, and utility_exit_with_message.

Referenced by main().

main()

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

References append_sequence_to_pose(), argv, basic::options::OptionKeys::chemical::chemical, test.T009_Exceptions::e, in::file::fasta(), create_a3b_hbs::i, basic::init(), option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::in::file::residue_type_set, runtime_assert, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), and TR.

Variable Documentation

TR

basic::Tracer TR("BuildFloppyTail") ( "BuildFloppyTail"  )

static

Referenced by append_sequence_to_pose(), and main().