disulfide_handoff.cc File Reference

Removes disulfides from a structure and tries to replace them. More...

#include <devel/init.hh>
#include <utility/vector1.hh>
#include <core/pose/Pose.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <basic/options/util.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/pack_rotamers.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/disulfides/FullatomDisulfidePotential.hh>
#include <core/scoring/constraints/BoundConstraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <apps/pilot/blivens/disulfides.hh>
#include <utility>
#include <basic/Tracer.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/util.hh>
#include <core/util/SwitchResidueTypeSet.hh>

Functions
int	usage (char *msg)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("pilot_apps.blivens.disulfide_handoff")

Detailed Description

Removes disulfides from a structure and tries to replace them.

Author

Spencer Bliven blive.nosp@m.ns@u.nosp@m..wash.nosp@m.ingt.nosp@m.on.ed.nosp@m.u

Date

Created September 2008

This app was written to experiment with techniques for preserving disulfide bonds during the handoff between centroid and full atom. Techniques tried include repacking, minimization, constraints.

Command Line

disulfide_staple -s input.pdb -o output.pdb -database db 

Function Documentation

main()

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

References actual_disulfide(), argv, test.T009_Exceptions::e, create_a3b_hbs::i, basic::init(), create_a3b_hbs::j, beta_nonlocal::mm, out::file::o(), option, lactamize::outfile, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, res, in::file::s(), test.T120_core::sfxn, basic::options::start_file(), vancomycin::task, TR, usage(), and basic::options::OptionKeys::inout::dbms::user.

usage()

int usage

(

char *

msg

)

References utility::options::OptionKeys::options::exit, and TR.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("pilot_apps.blivens.disulfide_handoff") ( "pilot_apps.blivens.disulfide_handoff"  )

static

Referenced by main(), and usage().