convert_pdb_to_silent_file.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueTypeSelector.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AtomType.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <basic/database/open.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/pose/util.hh>
#include <core/import_pose/import_pose.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.fwd.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/cluster.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/after_opts.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/util.hh>
#include <basic/options/option_macros.hh>
#include <protocols/idealize/idealize.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <protocols/viewer/viewers.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/EnergyMap.fwd.hh>
#include <basic/basic.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/conversions.hh>
#include <string>
#include <map>
#include <protocols/rna/denovo/util.hh>
#include <protocols/rna/denovo/RNA_BasePairClassifier.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <protocols/rna/denovo/RNA_LoopCloser.hh>
#include <protocols/rna/denovo/RNA_LoopCloser.fwd.hh>
#include <core/scoring/rna/RNA_BaseDoubletClasses.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <fstream>
#include <iostream>
#include <sstream>
#include <algorithm>
#include <cctype>
#include <iomanip>
#include <cstdlib>
#include <ctime>
#include <list>
#include <stdio.h>
#include <math.h>
#include <basic/Tracer.hh>

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
std::string	get_tag_from_pdb_filename (std::string const pdb_filename)
void	pdb_to_silent_file_simple ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

get_tag_from_pdb_filename()

std::string get_tag_from_pdb_filename

(

std::string const

pdb_filename

)

References demo.D010_Pose_structure::pdb_filename, and tag.

Referenced by align_pdbs(), minimize_pdb(), pdb_to_silent_file(), and pdb_to_silent_file_simple().

main()

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

References argv, test.T009_Exceptions::e, basic::init(), my_main(), NEW_OPT, and viewer_main().

my_main()

void* my_main

(

void *

)

References utility::options::OptionKeys::options::exit, and pdb_to_silent_file_simple().

Referenced by main().

pdb_to_silent_file_simple()

void pdb_to_silent_file_simple

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, get_tag_from_pdb_filename(), basic::options::OptionKeys::optimization::optimization, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, docking::R, docking::s, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, tag, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by my_main().