Superimpose_Pdbs.cc File Reference

#include <basic/options/util.hh>
#include <devel/init.hh>
#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/chemical/ResidueType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Atom.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/options/option.hh>
#include <core/id/AtomID_Map.hh>
#include <utility/file/FileName.hh>
#include <numeric/xyzVector.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rms_util.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <protocols/task_operations/RestrictToInterfaceOperation.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <utility/vector1.functions.hh>
#include <utility/vector1.hh>
#include <sstream>
#include <iomanip>
#include <iostream>
#include <fstream>
#include <utility/io/izstream.hh>
#include <string>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <core/pose/util.hh>
#include <core/import_pose/import_pose.hh>

Namespaces
	align

Functions
bool	read_master_pose_range (std::string const &filename, utility::vector1< std::pair< Size, Size > > &master_ranges)
bool	read_list_pose_range (std::string const &filename, utility::vector1< std::pair< Size, Size > > &list_ranges)
core::pack::task::TaskFactoryOP	generate_factory ()
	Create task factory for rotamer trials mover. More...
int	main (int argc, char *argv[])
	Main function////////////////////////////////////////////////////////////////////////////////////////. More...

Variables
FileOptionKey const	align::master_pose_range ("align::master_pose_range")
FileOptionKey const	align::list_pose_range ("align::list_pose_range")

Function Documentation

generate_factory()

core::pack::task::TaskFactoryOP generate_factory

(

)

Create task factory for rotamer trials mover.

References vancomycin::task.

Referenced by main().

main()

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

Main function////////////////////////////////////////////////////////////////////////////////////////.

References argv, utility::io::oc::cout, test.T009_Exceptions::e, PREcst::fname, generate_factory(), create_a3b_hbs::i, basic::init(), create_a3b_hbs::j, align::list_pose_range, align::master_pose_range, max(), min(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::in::file::native, in::file::native(), basic::options::option, option, erraser_single_res_analysis::out, p2, test.Workshop6test::pack_mover, predPRE::pdbname, pdbs, basic::options::OptionKeys::pepspec::pep_chain, pyrosetta.distributed.io::pose_from_file, read_list_pose_range(), read_master_pose_range(), average_rmsds::rmsd, basic::options::OptionKeys::in::file::s, oop_conformations::scorefxn, basic::options::start_files(), superimpose_pose(), and value.

read_list_pose_range()

bool read_list_pose_range	(	std::string const &	filename,
		utility::vector1< std::pair< Size, Size > > &	list_ranges
	)

Reads in file that specifies which residues in list pose will be aligned Each line of the file list_pose_range should have start and end position to align

References begin, utility::io::oc::cerr, utility::io::oc::cout, data, end, lactamize::filename, getline(), line, and range.

Referenced by main().

read_master_pose_range()

bool read_master_pose_range	(	std::string const &	filename,
		utility::vector1< std::pair< Size, Size > > &	master_ranges
	)

Reads in file that specifies which residues in master pose will be aligned Each line of the file master_pose_range should have start and end position to align

References begin, utility::io::oc::cerr, utility::io::oc::cout, data, end, lactamize::filename, getline(), line, and range.

Referenced by main().