script to add residues to a PDB. This script is NOT intended to make a good conformation - just the sequence-correct PDB for other modes (loop modeling, etc) More...

#include <core/pose/Pose.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/PDBPoseMap.hh>
#include <core/pose/PDBInfo.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <devel/init.hh>
#include <utility/io/izstream.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <string>

Namespaces
	basic
	Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input.

	basic::options

	basic::options::OptionKeys

Functions
void	read_in_extension (core::pose::Pose const &pose, core::Size &loop_start, std::string &extension)
	helper parses extension file More...

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

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

utility::options::FileOptionKey const	basic::options::OptionKeys::extension ("extension")

Detailed Description

script to add residues to a PDB. This script is NOT intended to make a good conformation - just the sequence-correct PDB for other modes (loop modeling, etc)

Author: Steven Lewis

Function Documentation

◆ main()

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

References utility::options::OptionCollection::add(), argv, utility::options::ScalarOption_T_< K, T >::def(), test.T009_Exceptions::e, basic::options::OptionKeys::extension, create_a3b_hbs::i, basic::init(), pivot_selection::loop_start, beta_sc_scan::name3, basic::options::option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file(), read_in_extension(), basic::options::OptionKeys::in::file::residue_type_set, basic::options::start_file(), basic::options::TR, and utility_exit_with_message.

◆ read_in_extension()

void read_in_extension	(	core::pose::Pose const &	pose,
		core::Size &	loop_start,
		std::string &	extension
	)

helper parses extension file

References predPRE::chain, basic::Error(), basic::options::OptionKeys::extension, utility::io::izstream::fail(), lactamize::filename, pivot_selection::loop_start, basic::options::option, beta_nonlocal::pose, utility_exit, and value.

Referenced by main().

Variable Documentation

◆ TR

basic::Tracer TR("apps.pilot.smlewis.Extender") ( "apps.pilot.smlewis.Extender" )

static

Namespaces