create_disulf_file.cc File Reference

Given a pdb file, detect disulfides and output to a disulfide file. More...

#include <apps/pilot/blivens/disulfides.hh>
#include <devel/init.hh>
#include <core/pose/Pose.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/pose/util.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <basic/options/util.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <utility/vector1.hh>
#include <basic/Tracer.hh>
#include <fstream>
#include <utility>
#include <core/import_pose/import_pose.hh>

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

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

Detailed Description

Given a pdb file, detect disulfides and output to a disulfide file.

Author

Spencer Bliven blive.nosp@m.ns@u.nosp@m..wash.nosp@m.ingt.nosp@m.on.ed.nosp@m.u

Date

Created 3/22/2009

Creates a file pairs of numbers giving rosetta residue indices for each disulfide bond. This file can then be used with -fix_disulf

Only detects disulfides which have the right rotamer for each Cys.

Note

requires a full atom input pdb

Command Line

create_disulf_file -database db -s in.pdb -o out.disulf 

Function Documentation

main()

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

References argv, test.T009_Exceptions::e, find_disulfides(), basic::init(), out::file::o(), option, erraser_single_res_analysis::out, lactamize::outfile, clean_pdb_keep_ligand::pdbfile, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), basic::options::start_file(), usage(), and basic::options::OptionKeys::inout::dbms::user.

usage()

int usage

(

string

msg

)

References utility::options::OptionKeys::options::exit, and TR.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("apps.pilot.blivens.create_disulf_file") ( "apps.pilot.blivens.create_disulf_file"  )

static

Referenced by usage().