protocol to assign sequence More...

#include <map>
#include <stdio.h>
#include <devel/init.hh>
#include <core/types.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pose/util.hh>
#include <core/pose/PDBInfo.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/Edge.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rms_util.hh>
#include <core/fragment/FragSet.hh>
#include <core/fragment/SecondaryStructure.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/viewer/viewers.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/relax/loop/LoopRelaxMover.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/simple_moves/rational_mc/RationalMonteCarlo.hh>
#include <protocols/rigid/RigidBodyMotionMover.hh>
#include <protocols/constraint_movers/ConstraintSetMover.hh>
#include <protocols/nonlocal/StarTreeBuilder.hh>
#include <protocols/nonlocal/util.hh>
#include <protocols/medal/MedalMover.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <numeric/random/random.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/model_quality/maxsub.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/rigid.OptionKeys.gen.hh>
#include <utility/excn/Exceptions.hh>
#include <apps/pilot/yfsong/util.hh>
#include <basic/Tracer.hh>

Classes
class	SecondaryStructureChunk

class	ChallengeMover

Namespaces
	challenge

Functions
void	copy_xyz_by_chunk (core::pose::Pose &mod_pose, core::Size const mod_seqpos_start, core::pose::Pose const &ref_pose, core::Size const ref_seqpos_start, core::Size const length)

Real	superimpose_pose (pose::Pose &mod_pose, std::list< Size > const &residue_list, pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map)

void	get_superposition_transformation (pose::Pose const &mod_pose, pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map, numeric::xyzMatrix< core::Real > &R, numeric::xyzVector< core::Real > &preT, numeric::xyzVector< core::Real > &postT)

void	apply_transform (pose::Pose &mod_pose, std::list< Size > const &residue_list, numeric::xyzMatrix< core::Real > const &R, numeric::xyzVector< core::Real > const &preT, numeric::xyzVector< core::Real > const &postT)

void	superimpose_pose_transform (pose::Pose &mod_pose, std::list< Size > const &residue_list, pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map)

void	align_backbone_by_chunk (core::pose::Pose &pose, core::Size const residue_seq_start, core::Size const residue_seq_end, core::pose::Pose const &ref_pose, std::map< core::Size, core::Size > const &seqpos_alignment, int const registry_shift=0, core::Size MAX_TRIAL=100)

void	extract_ss_chunks_from_seq (std::string const secstructs, core::pose::Pose const &pose, std::string const extracted_ss_types, utility::vector1< SecondaryStructureChunk > &ss_chunks, core::Size max_gap_in_continuous_chunk=1, core::Size minimum_length_of_chunk=3, core::Real CA_CA_distance_cutoff=4.0)

void	read_template_structures (utility::vector1< core::pose::PoseOP > &template_structures)

void	split_pdb_into_ss_chunks (core::pose::PoseOP const pose, utility::vector1< SecondaryStructureChunk > &ss_chunks)

void *	my_main (void *)

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

Variables
static basic::Tracer	TR ("pilot.yfsong.challenge")

basic::options::FileVectorOptionKey	challenge::template_structure ("challenge:template_structure")

basic::options::BooleanOptionKey	challenge::close_loops ("challenge:close_loops")

Detailed Description

protocol to assign sequence

Author: Yifan Song

Function Documentation

◆ align_backbone_by_chunk()

void align_backbone_by_chunk	(	core::pose::Pose &	pose,
		core::Size const	residue_seq_start,
		core::Size const	residue_seq_end,
		core::pose::Pose const &	ref_pose,
		std::map< core::Size, core::Size > const &	seqpos_alignment,
		int const	registry_shift = `0`,
		core::Size	MAX_TRIAL = `100`
	)

References demo.D060_Folding::counter, test.T110_numeric::I, beta_nonlocal::pose, numeric::random::RandomGenerator::random_range(), numeric::random::rg(), superimpose_pose_transform(), and TR.

Referenced by ChallengeMover::initialize_pose(), and ChallengeMover::realign().

◆ apply_transform()

void apply_transform	(	pose::Pose &	mod_pose,
		std::list< Size > const &	residue_list,
		numeric::xyzMatrix< core::Real > const &	R,
		numeric::xyzVector< core::Real > const &	preT,
		numeric::xyzVector< core::Real > const &	postT
	)

References natoms(), and docking::R.

Referenced by superimpose_pose_transform().

◆ copy_xyz_by_chunk()

void copy_xyz_by_chunk	(	core::pose::Pose &	mod_pose,
		core::Size const	mod_seqpos_start,
		core::pose::Pose const &	ref_pose,
		core::Size const	ref_seqpos_start,
		core::Size const	length
	)

References oop_conformations::length, and natoms().

◆ extract_ss_chunks_from_seq()

void extract_ss_chunks_from_seq	(	std::string const	secstructs,
		core::pose::Pose const &	pose,
		std::string const	extracted_ss_types,
		utility::vector1< SecondaryStructureChunk > &	ss_chunks,
		core::Size	max_gap_in_continuous_chunk = `1`,
		core::Size	minimum_length_of_chunk = `3`,
		core::Real	CA_CA_distance_cutoff = `4.0`
	)

References utility::vectorL< L, T, A >::append(), oop_conformations::length, beta_nonlocal::pose, SecondaryStructureChunk::set_sequence(), SecondaryStructureChunk::set_start_seqpos(), challenge::ss, and SecondaryStructureChunk::start_seqpos().

Referenced by split_pdb_into_ss_chunks().

◆ get_superposition_transformation()

void get_superposition_transformation	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		id::AtomID_Map< id::AtomID > const &	atom_map,
		numeric::xyzMatrix< core::Real > &	R,
		numeric::xyzVector< core::Real > &	preT,
		numeric::xyzVector< core::Real > &	postT
	)

References numeric::model_quality::findUU(), run_backbone::float, create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, natoms(), and docking::R.

Referenced by apps::pilot::AlignChunkMover::align_chunk(), and superimpose_pose_transform().

◆ main()

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

References challenge::aligned, argv, challenge::chunk_mapping, challenge::close_loops, test.T009_Exceptions::e, basic::init(), challenge::max_registry_shift, my_main(), option, challenge::revert_real_loops, challenge::ss, challenge::template_structure, viewer_main(), and challenge::virtual_loops.

◆ my_main()

void* my_main ( void * )

References utility::io::oc::cerr, challenge::close_loops, basic::options::OptionKeys::constraints::cst_file, basic::options::option, basic::options::OptionKeys::remodel::rama, numeric::random::rg(), oop_conformations::scorefxn, utility::excn::Exception::show(), challenge::template_structure, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and basic::options::OptionKeys::remodel::vdw.

Referenced by main().

◆ read_template_structures()

void read_template_structures ( utility::vector1< core::pose::PoseOP > & template_structures )

References basic::options::option, pyrosetta.distributed.io::pose_from_file, challenge::template_structure, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by ChallengeMover::initialize_template_structures(), and apps::pilot::SampleSecondaryStructureAlignmentMover::SampleSecondaryStructureAlignmentMover().

◆ split_pdb_into_ss_chunks()

void split_pdb_into_ss_chunks	(	core::pose::PoseOP const	pose,
		utility::vector1< SecondaryStructureChunk > &	ss_chunks
	)

References extract_ss_chunks_from_seq(), beta_nonlocal::pose, secstruct(), and TR.

◆ superimpose_pose()

Real superimpose_pose	(	pose::Pose &	mod_pose,
		std::list< Size > const &	residue_list,
		pose::Pose const &	ref_pose,
		id::AtomID_Map< id::AtomID > const &	atom_map
	)

References ObjexxFCL::abs(), numeric::model_quality::COMAS(), test.T009_Exceptions::e, detail::find(), create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, natoms(), loops_kic::rms, numeric::model_quality::rmsfitca2(), runtime_assert, and orn_macrocycle::wt.

Referenced by addcyclicconstraints(), ClusterCycDisulf::align_clusters(), align_conformations(), align_helix(), PoseWrap::align_orig_pose(), align_pdbs_function(), align_pose_general(), align_poses(), align_with_offset(), alignhelix(), calc_nonlocal_segment_bb_rmsd(), calpha_pdb_superimpose_pose(), InterfaceStrandFinderMover::dock_strands(), drrafter_error_estimation(), fit_helix_in_map(), fix_cyclic_termini(), generate_combined_model(), get_min_frag_rmsd(), get_rmsd(), go(), homolog_finder(), iface_pdb_superimpose_diff_prot(), iface_pdb_superimpose_pose(), main(), ExposedStrandMover::move_superimpose(), pep_rmsd_analysis(), perturb(), run(), run_3bpy(), run_pep_prep(), stepwise_template_test(), superimpose_A_to_all(), abbinding::superimpose_antigen(), superimpose_pdb(), superimpose_pose_using_aln(), superimpose_smotifs(), superimpose_via_alignment(), and superimposebb().

◆ superimpose_pose_transform()

void superimpose_pose_transform	(	pose::Pose &	mod_pose,
		std::list< Size > const &	residue_list,
		pose::Pose const &	ref_pose,
		id::AtomID_Map< id::AtomID > const &	atom_map
	)