helix_from_sequence.cc File Reference

#include <devel/init.hh>
#include <core/conformation/membrane/SpanningTopology.hh>
#include <protocols/pose_creation/HelixFromSequence.hh>
#include <protocols/membrane/AddMembraneMover.hh>
#include <protocols/membrane/OptimizeProteinEmbeddingMover.hh>
#include <protocols/membrane/TransformIntoMembraneMover.hh>
#include <protocols/relax/membrane/MPRangeRelaxMover.hh>
#include <protocols/simple_moves/ScoreMover.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/util.hh>
#include <core/chemical/ChemicalManager.fwd.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/types.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/mp.OptionKeys.gen.hh>
#include <basic/options/keys/relax.OptionKeys.gen.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <basic/Tracer.hh>
#include <string>

Functions
std::string	read_fasta ()
bool	read_membrane ()
bool	optimize_embedding ()
bool	skipping_relax ()
void	helix_from_sequence ()
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.pilot.jkleman.helix_from_sequence")

Detailed Description

Creates a helix pose from the sequence only, works for soluble and membrane proteins; the latter will be transformed into the membrane

Author

JKLeman (julia.nosp@m..koe.nosp@m.hler1.nosp@m.982@.nosp@m.gmail.nosp@m..com)

Function Documentation

helix_from_sequence()

void helix_from_sequence

(

)

References create_a3b_hbs::i, basic::options::OptionKeys::abinitio::membrane, optimize_embedding(), beta_nonlocal::pose, read_fasta(), read_membrane(), basic::options::OptionKeys::abinitio::relax, create_a3b_hbs::score, beta_sc_scan::seq, skip_relax, skipping_relax(), basic::options::TR, and basic::options::OptionKeys::mp::transform::transform.

main()

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

References argv, test.T009_Exceptions::e, basic::init(), and basic::options::OptionKeys::abinitio::membrane.

optimize_embedding()

bool optimize_embedding

(

)

References peptide_deriver::optimize, basic::options::OptionKeys::mp::transform::optimize_embedding, basic::options::option, basic::options::TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by helix_from_sequence(), and main().

read_fasta()

std::string read_fasta

(

)

References CREATE_EXCEPTION, basic::options::OptionKeys::in::file::fasta, basic::options::option, basic::options::OptionKeys::relax::sequence, basic::options::TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by helix_from_sequence().

read_membrane()

bool read_membrane

(

)

References basic::options::OptionKeys::abinitio::membrane, basic::options::option, basic::options::TR, basic::options::OptionKeys::mp::setup::transform_into_membrane, and basic::options::OptionKeys::inout::dbms::user.

Referenced by helix_from_sequence().

skipping_relax()

bool skipping_relax

(

)

References basic::options::option, skip_relax, basic::options::OptionKeys::relax::range::skip_relax, basic::options::TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by helix_from_sequence().

Variable Documentation

TR

basic::Tracer TR("apps.pilot.jkleman.helix_from_sequence") ( "apps.pilot.jkleman.helix_from_sequence"  )

static