contact_map_from_homologs.cc File Reference

#include <utility/exit.hh>
#include <utility/string_util.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <devel/init.hh>
#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <basic/Tracer.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/id/SequenceMapping.hh>
#include <core/sequence/util.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/scoring/rms_util.hh>
#include <core/kinematics/FoldTree.hh>
#include <protocols/comparative_modeling/coord_util.hh>
#include <protocols/comparative_modeling/PartialThreadingMover.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <ObjexxFCL/format.hh>
#include <fstream>
#include <map>
#include <set>
#include <vector>
#include <sstream>
#include <algorithm>
#include <core/import_pose/import_pose.hh>
#include <core/pose/annotated_sequence.hh>

Functions
vector1< SequenceAlignment >	generateRankedAlignments (map< string, SequenceAlignment > &alns, Real THRESHOLD_FOR_E_VAL)
	@detail converts string to upper case More...
map< string, Pose >	poses_from_cmd_line (utility::vector1< std::string > const &fn_list)
	@detail gathers the poses More...
multimap< Size, Size >	calc_contacts (core::pose::Pose pose, SequenceAlignment aln, Real cutoff_dist, Size aa_separation)
	@detail calculates contact map without having a mapping. More...
int	main (int argc, char *argv[])
	@detail calculates contact map More...

Variables
static basic::Tracer	tr ("contact_map_from_homologs.main")

Function Documentation

calc_contacts()

multimap<Size,Size> calc_contacts	(	core::pose::Pose	pose,
		SequenceAlignment	aln,
		Real	cutoff_dist,
		Size	aa_separation
	)

@detail calculates contact map without having a mapping.

References aln, basic::options::OptionKeys::evaluation::contact_map, build_jacobian::distance, create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, pna::resi, and basic::options::OptionKeys::cmiles::jumping::resj.

Referenced by main().

generateRankedAlignments()

vector1< SequenceAlignment > generateRankedAlignments	(	map< string, SequenceAlignment > &	alns,
		Real	THRESHOLD_FOR_E_VAL
	)

@detail converts string to upper case

@detail gets the aligment from file and ranks them.

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, data, cm::ev_map(), file_exists(), lactamize::filename, getline(), cm::hh_map(), subloop_histogram::iterator, line, option, tr, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by main().

main()

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

@detail calculates contact map

References in::file::alignment(), aln, cm::aln_format(), argv, calc_contacts(), basic::options::OptionKeys::chemical::chemical, utility::io::ozstream::close(), utility::io::oc::cout, run::debug(), test.T009_Exceptions::e, in::file::fasta(), lactamize::filename, generateRankedAlignments(), create_a3b_hbs::ii, basic::init(), subloop_histogram::iterator, beta_nonlocal::jj, kk, max(), in::file::native(), docking::native_pose, out::file::o(), option, bin_torsions::output, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::mp::assembly::poses, poses_from_cmd_line(), basic::options::OptionKeys::relax::sequence, ObjexxFCL::string_of(), and in::file::template_pdb().

poses_from_cmd_line()

map< string, Pose > poses_from_cmd_line

(

utility::vector1< std::string > const &

fn_list

)

@detail gathers the poses

References basic::options::OptionKeys::chemical::chemical, end, utility::file_basename(), utility::file::file_exists(), file_exists(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and basic::options::OptionKeys::mp::assembly::poses.

Referenced by main().

Variable Documentation

tr

basic::Tracer tr("contact_map_from_homologs.main") ( "contact_map_from_homologs.main"  )

static

Referenced by generateRankedAlignments().