simple_cm.cc File Reference

#include <core/types.hh>
#include <devel/init.hh>
#include <basic/prof.hh>
#include <basic/Tracer.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <basic/options/option.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceProfile.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/sequence/NWAligner.hh>
#include <core/sequence/SWAligner.hh>
#include <core/sequence/L1ScoringScheme.hh>
#include <core/sequence/MatrixScoringScheme.hh>
#include <core/sequence/SimpleScoringScheme.hh>
#include <core/sequence/ScoringScheme.fwd.hh>
#include <core/sequence/ScoringSchemeFactory.hh>
#include <core/scoring/rms_util.hh>
#include <core/pose/Pose.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentStructFactory.hh>
#include <protocols/comparative_modeling/ThreadingMover.hh>
#include <protocols/comparative_modeling/AlignmentSet.hh>
#include <protocols/jobdist/standard_mains.hh>
#include <protocols/jobdist/not_universal_main.hh>
#include <utility/vector1.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/char.functions.hh>
#include <ObjexxFCL/string.functions.hh>
#include <numeric/random/random.hh>
#include <map>
#include <fstream>
#include <iostream>
#include <string>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/frags.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <utility/excn/Exceptions.hh>

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

Function Documentation

main()

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

References in::file::alignment(), out::file::alignment(), argv, utility::file::FileName::base(), basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, test.T009_Exceptions::e, end, create_a3b_hbs::i, basic::init(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, basic::options::OptionKeys::cm::max_gap_extend, basic::options::OptionKeys::cm::max_gap_open, basic::options::OptionKeys::cm::min_gap_extend, basic::options::OptionKeys::cm::min_gap_open, option, bin_torsions::output, pyrosetta.distributed.io::pose_from_file, frags::scoring::profile_score(), in::file::pssm(), in::file::residue_type_set(), challenge::ss, ObjexxFCL::string_of(), in::file::template_pdb(), and basic::options::OptionKeys::inout::dbms::user.