mp_domain_assembly.cc File Reference

Build a full-length membrane protein model from a bunch of poses and a fasta file. More...

#include <devel/init.hh>
#include <protocols/moves/Mover.hh>
#include <core/conformation/membrane/Span.hh>
#include <core/conformation/membrane/SpanningTopology.hh>
#include <protocols/membrane/util.hh>
#include <protocols/membrane/AddMembraneMover.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/pack_rotamers.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/mp.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/relax.OptionKeys.gen.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/util.hh>
#include <core/pose/annotated_sequence.hh>
#include <protocols/relax/membrane/MPRangeRelaxMover.hh>
#include <protocols/simple_moves/SwitchResidueTypeSetMover.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/simple_moves/SuperimposeMover.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/Energies.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <protocols/moves/MonteCarlo.fwd.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/simple_moves/FragmentMover.hh>
#include <core/fragment/FragSet.hh>
#include <core/fragment/FragmentIO.hh>
#include <apps/benchmark/performance/init_util.hh>
#include <core/types.hh>
#include <numeric/xyzVector.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/util.hh>
#include <core/pose/variant_util.hh>
#include <core/pose/subpose_manipulation_util.hh>
#include <core/conformation/util.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/Job.hh>
#include <basic/Tracer.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/string_util.hh>
#include <utility/io/ozstream.hh>
#include <protocols/jd2/util.hh>
#include <utility/minmax.hh>
#include <numeric/random/random.hh>
#include <cstdlib>
#include <string>
#include <cmath>

Classes
class	MPDomainAssembly

Typedefs
using	MPDomainAssemblyOP = utility::pointer::shared_ptr< MPDomainAssembly >

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

Variables
static basic::Tracer	TR ("apps.public.mp_domain_assembly")

Detailed Description

Build a full-length membrane protein model from a bunch of poses and a fasta file.

Author

JKLeman (julia.nosp@m..koe.nosp@m.hler..nosp@m.lema.nosp@m.n@gma.nosp@m.il.c.nosp@m.om)

Typedef Documentation

using MPDomainAssemblyOP = utility::pointer::shared_ptr<MPDomainAssembly>

Function Documentation

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

References utility::io::oc::cout, test.T009_Exceptions::e, devel::init(), MPDomainAssembly::MPDomainAssembly(), utility::excn::Exception::msg(), and demo.D010_Pose_structure::pose.

Variable Documentation

basic::Tracer TR("apps.public.mp_domain_assembly")

static

Referenced by MPDomainAssembly::apply(), MPDomainAssembly::init_from_cmd(), and MPDomainAssembly::print_score().