cyclic_sampler.cc File Reference

run Monte Carlo for sampling protein conformation More...

#include <core/chemical/AA.hh>
#include <core/chemical/Atom.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/util.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentStructFactory.hh>
#include <core/types.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/import_pose/import_pose.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/bbg.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/basic.hh>
#include <basic/Tracer.hh>
#include <numeric/random/random.hh>
#include <numeric/constants.hh>
#include <utility/vector1.hh>
#include <utility/fixedsizearray1.hh>
#include <core/optimization/CartesianMinimizer.hh>
#include <core/optimization/Minimizer.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/moves/PyMOLMover.hh>
#include <protocols/moves/Mover.fwd.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/simple_moves/BBGaussianMover.hh>
#include <protocols/simple_moves/sidechain_moves/SidechainMover.hh>
#include <protocols/simple_moves/sidechain_moves/SidechainMCMover.hh>
#include <protocols/canonical_sampling/PDBTrajectoryRecorder.hh>
#include <protocols/jd2/Job.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/util.hh>
#include <protocols/jd2/InnerJob.hh>

Classes
class	BBG_Cyclic_Mover
class	MyProtocol

Functions
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static numeric::random::RandomGenerator	RG (62331911)
basic::Tracer	TR ("pilot.wendao.cyclic")

Detailed Description

run Monte Carlo for sampling protein conformation

Author

Yuan Liu

Modified backbone Gaussian sampler for cyclic peptide 0. currently only work for full-atom

1. randomly select N(>=4) hinge residues
2. restrain the CYS-CYS distance (tune factor A/B)
3. repack CYS CYS
4. simulated annealing or cartmin

Function Documentation

main()

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

References argv, test.T009_Exceptions::e, basic::init(), local::mc_temperature, my_main(), NEW_OPT, and viewer_main().

my_main()

void* my_main

(

void *

)

Referenced by main().

Variable Documentation

RG

numeric::random::RandomGenerator RG(62331911) ( 62331911  )

static

TR

basic::Tracer TR("pilot.wendao.cyclic")

(

"pilot.wendao.cyclic"

)