MSA_design.cc File Reference

test app for packer design that is biased toward a multiple sequence alignment/PSSM More...

#include <devel/init.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <basic/options/option.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/operation/OperateOnCertainResidues.hh>
#include <core/pack/task/operation/ResLvlTaskOperations.hh>
#include <core/pack/task/operation/ResFilters.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/dna/setup.hh>
#include <protocols/viewer/viewers.hh>
#include <core/sequence/SequenceProfile.hh>
#include <core/scoring/constraints/SequenceProfileConstraint.hh>
#include <basic/Tracer.hh>
#include <utility/io/izstream.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/file/FileName.hh>
#include <utility/exit.hh>
#include <utility/vector1.hh>
#include <iostream>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>

Functions
void	MSA_design (pose::PoseOP pose)
void *	MSA_design_main (void *)
int	main (int argc, char *argv[])

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

Detailed Description

test app for packer design that is biased toward a multiple sequence alignment/PSSM

Author

ashworth

Function Documentation

main()

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

References argv, test.T009_Exceptions::e, basic::init(), MSA_design_main(), and viewer_main().

MSA_design()

void MSA_design

(

pose::PoseOP

pose

)

References demo.D060_Folding::counter, basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, end, lactamize::filename, basic::options::OptionKeys::packing::ndruns, option, beta_nonlocal::pose, basic::options::OptionKeys::run::profile, basic::options::OptionKeys::in::file::pssm, basic::options::OptionKeys::packing::resfile, oop_conformations::scorefxn, challenge::ss, test.G200_Module_Region::tf, TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by MSA_design_main().

MSA_design_main()

void* MSA_design_main

(

void *

)

References utility::io::oc::cerr, utility::io::oc::cout, utility::file::file_exists(), lactamize::filename, in::file::l(), basic::options::OptionKeys::in::file::list, MSA_design(), option, predPRE::pdbname, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("apps.pilot.MSA_design") ( "apps.pilot.MSA_design"  )

static

Referenced by MSA_design(), and MSA_design_main().