#include <devel/init.hh>
#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/import_pose/import_pose.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ElementSet.hh>
#include <core/chemical/MMAtomTypeSet.hh>
#include <core/chemical/orbitals/OrbitalTypeSet.hh>
#include <core/chemical/AtomRefMapping.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/residue_io.hh>
#include <core/chemical/MutableResidueType.fwd.hh>
#include <core/chemical/rdkit/util.hh>
#include <core/chemical/rdkit/RDMolToRestype.hh>
#include <core/chemical/rdkit/RestypeToRDMol.hh>
#include <core/chemical/ResidueGraphTypes.hh>
#include <rdkit/GraphMol/ROMol.h>
#include <rdkit/GraphMol/FileParsers/MolWriters.h>
#include <rdkit/GraphMol/FileParsers/FileParsers.h>
#include <rdkit/GraphMol/MonomerInfo.h>
#include <core/conformation/Residue.hh>
#include <core/conformation/util.hh>
#include <core/id/AtomID.hh>
#include <core/types.hh>
#include <utility/options/FileVectorOption.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <numeric/model_quality/rms.hh>
#include <set>
#include <fstream>
#include <string>

Typedefs
typedef utility::vector1< std::pair< core::Size, core::Size > >	SizePairVec

typedef utility::keys::Key4Tuple< core::Size, core::Size, core::Size, core::Size >	DihedralAtomTuple

typedef std::map< utility::keys::Key4Tuple< core::Size, core::Size, core::Size, core::Size >, core::Size >	DihedralAtomTuple2ChiIdxMap

Functions
void	align_pose (core::pose::Pose const &template_pose, core::pose::Pose &ligand_pose, std::map< core::Size, core::Size > const &pair_indices_map, core::Size const &template_idx, core::Size const &ligand_idx)

void	set_torsion_and_align (core::pose::Pose const &template_pose, core::pose::Pose &ligand_pose, std::map< core::Size, core::Size > const &pair_indices_map, core::Size const &template_idx, core::Size const &ligand_idx)

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

Variables
static basic::Tracer	TR ("apps.align_substructure")

Typedef Documentation

◆ DihedralAtomTuple

typedef utility::keys::Key4Tuple< core::Size, core::Size, core::Size, core::Size > DihedralAtomTuple

◆ DihedralAtomTuple2ChiIdxMap

typedef std::map< utility::keys::Key4Tuple< core::Size, core::Size, core::Size, core::Size >, core::Size> DihedralAtomTuple2ChiIdxMap

◆ SizePairVec

typedef utility::vector1<std::pair<core::Size, core::Size> > SizePairVec

Function Documentation

◆ align_pose()

void align_pose	(	core::pose::Pose const &	template_pose,
		core::pose::Pose &	ligand_pose,
		std::map< core::Size, core::Size > const &	pair_indices_map,
		core::Size const &	template_idx,
		core::Size const &	ligand_idx
	)

References numeric::model_quality::findUU(), create_a3b_hbs::i, and docking::R.

Referenced by StepWiseJobQueen::complete_larval_job_maturation(), create_theozyme_pdb(), rna_fullatom_minimize_test(), run_pep_prep(), set_torsion_and_align(), stepwise_lores_test(), stepwise_monte_carlo_legacy(), and stepwise_template_test().

◆ main()

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

References argv, val2thr::atom, basic::options::OptionKeys::chemical::chemical, test.T009_Exceptions::e, basic::init(), basic::options::OptionKeys::docking::ligand::ligand, basic::options::OptionKeys::in::file::native, NEW_OPT, basic::options::option, pyrosetta.distributed.io::pose_from_file, set_torsion_and_align(), basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

◆ set_torsion_and_align()

void set_torsion_and_align	(	core::pose::Pose const &	template_pose,
		core::pose::Pose &	ligand_pose,
		std::map< core::Size, core::Size > const &	pair_indices_map,
		core::Size const &	template_idx,
		core::Size const &	ligand_idx
	)