atom_tree_check.cc File Reference

Check retreeing with core::kinematics::tree. More...

#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/AtomICoor.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/residue_io.hh>
#include <core/id/AtomID.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/kinematics/tree/BondedAtom.hh>
#include <core/kinematics/tree/JumpAtom.hh>
#include <core/id/types.hh>
#include <core/types.hh>
#include <devel/init.hh>
#include <utility/options/FileVectorOption.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <fstream>
#include <utility/graph/DFS_sort.hh>
#include <numeric/xyzVector.io.hh>
#include <boost/graph/depth_first_search.hpp>
#include <boost/graph/properties.hpp>

Classes
class	RerootRestypeVisitor
class	RerootEdgeSorter
	Edge sorting: More...

Typedefs
typedef std::map< core::chemical::VD, core::kinematics::tree::AtomOP >	VdTreeatomMap

Functions
void	tweak_coords (core::kinematics::tree::AtomOP atom)
void	print_tree (core::kinematics::tree::AtomCOP atom, core::pose::Pose const &pose)
void	print_tree (core::kinematics::tree::AtomCOP atom, core::chemical::ResidueType const &restype)
core::kinematics::tree::AtomOP	rebuild (core::kinematics::tree::AtomCOP atom)
void	reroot_restype (core::chemical::ResidueType &restype, core::chemical::VD root)
	Doing a depth first search here because that's what molfile_to_params.py does: "Protein residues appear to go depth first, so that all chi angles ride on each other." RM: Doing a breadth first search would likely result in a shallower tree, but with possibly different behavior on how ring atom trees are built. More...
bool	comp (core::Real x, core::Real y)
int	main (int argc, char *argv[])

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

Detailed Description

Check retreeing with core::kinematics::tree.

Author

Rocco Moretti (rmore.nosp@m.ttia.nosp@m.se@gm.nosp@m.ail..nosp@m.com)

Typedef Documentation

VdTreeatomMap

typedef std::map< core::chemical::VD, core::kinematics::tree::AtomOP > VdTreeatomMap

Function Documentation

comp()

bool comp	(	core::Real	x,
		core::Real	y
	)

References test.T009_Exceptions::e, x, and predPRE::y.

Referenced by main(), margin(), and numeric::model_quality::rmsfitca3().

main()

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

References argv, center, basic::options::OptionKeys::chemical::chemical, test.T009_Exceptions::e, basic::options::OptionKeys::in::file::extra_res_fa, lactamize::filename, PREcst::fname, create_a3b_hbs::i, basic::init(), basic::options::option, beta_nonlocal::pose, test.T008_Serialization::pose2, print_tree(), rebuild(), reroot_restype(), res, erraser_analysis::res2, build_restypes::restype, basic::options::OptionKeys::mh::filter::restype2, utility::options::VectorOption_T_< K, T >::size(), and basic::options::TR.

print_tree() [1/2]

void print_tree	(	core::kinematics::tree::AtomCOP	atom,
		core::chemical::ResidueType const &	restype
	)

References val2thr::atom, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, basic::options::OptionKeys::optE::fixed, create_a3b_hbs::ii, PHI, basic::Tracer::precision(), print_tree(), build_restypes::restype, stub(), THETA, and basic::options::TR.

print_tree() [2/2]

void print_tree	(	core::kinematics::tree::AtomCOP	atom,
		core::pose::Pose const &	pose
	)

References val2thr::atom, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, basic::options::OptionKeys::optE::fixed, create_a3b_hbs::ii, PHI, beta_nonlocal::pose, basic::Tracer::precision(), stub(), THETA, and basic::options::TR.

Referenced by main(), and print_tree().

rebuild()

core::kinematics::tree::AtomOP rebuild

(

core::kinematics::tree::AtomCOP

atom

)

References val2thr::atom, and create_a3b_hbs::ii.

Referenced by main(), my_main(), and picking_test().

reroot_restype()

void reroot_restype	(	core::chemical::ResidueType &	restype,
		core::chemical::VD	root
	)

Doing a depth first search here because that's what molfile_to_params.py does: "Protein residues appear to go depth first, so that all chi angles ride on each other." RM: Doing a breadth first search would likely result in a shallower tree, but with possibly different behavior on how ring atom trees are built.

Assumes:

• All bonds and atoms exist in the graph,
• The graph is completely connected.
• All ideal xyz coordinates are updated.

References basic::options::OptionKeys::hotspot::angle, val2thr::atom, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, utility::graph::depth_first_search_sort(), oop_conformations::phi, PHI, build_restypes::restype, THETA, internal_coordinates::torsion(), basic::options::TR, utility_exit_with_message, and basic::Tracer::Warning.

Referenced by main().

tweak_coords()

void tweak_coords

(

core::kinematics::tree::AtomOP

atom

)

References val2thr::atom, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, create_a3b_hbs::ii, PHI, and THETA.

Variable Documentation

TR

basic::Tracer TR("apps.atomtreeprint") ( "apps.atomtreeprint"  )

static