aln_to_disulf.cc File Reference

#include <core/types.hh>
#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <core/chemical/util.hh>
#include <core/id/SequenceMapping.hh>
#include <basic/options/option.hh>
#include <utility/io/ozstream.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pose/annotated_sequence.hh>
#include <utility/exit.hh>
#include <utility/vector1.hh>
#include <utility/string_util.hh>
#include <utility/file/file_sys_util.hh>
#include <map>
#include <iostream>
#include <string>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <core/conformation/Residue.hh>

Namespaces
	aln_to_disulf

Functions
utility::vector1< std::pair< Size, Size > >	get_disulfides_from_aln (core::pose::Pose templatePose, core::sequence::SequenceAlignment aln)
std::map< std::string, core::pose::Pose >	poses_from_cmd_line (utility::vector1< std::string > const &fn_list)
int	main (int argc, char *argv[])

Variables
basic::options::FileVectorOptionKey	aln_to_disulf::coordCstFiles ("minimalCstHomology:coordCstFiles")
basic::options::BooleanOptionKey	aln_to_disulf::only_res_out ("minimalCstHomology:only_res_out")

Detailed Description

Author

TJ Brunette

Function Documentation

get_disulfides_from_aln()

utility::vector1< std::pair< Size, Size> > get_disulfides_from_aln	(	core::pose::Pose	templatePose,
		core::sequence::SequenceAlignment	aln
	)

References aln, dist(), end, basic::options::OptionKeys::in::file::fullatom, create_a3b_hbs::ii, oop_conformations::length, and basic::options::OptionKeys::loops::ccd::tolerance.

Referenced by main().

main()

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

References basic::options::OptionKeys::in::file::alignment, basic::options::OptionKeys::cm::aln_format, argv, basic::options::OptionKeys::chemical::chemical, test.T009_Exceptions::e, end, get_disulfides_from_aln(), basic::init(), subloop_histogram::iterator, basic::options::OptionKeys::out::file::o, basic::options::option, bin_torsions::output, pair, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::mp::assembly::poses, poses_from_cmd_line(), basic::options::OptionKeys::relax::sequence, basic::options::OptionKeys::in::file::template_pdb, tr, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

poses_from_cmd_line()

std::map< std::string, core::pose::Pose > poses_from_cmd_line

(

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

fn_list

)

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().