minimalCstRelax.cc File Reference

For the first structure in the alignment compare the deviation between native and the relaxed native structure. Then constraints are modified and coordinate constraints are added. If an alignment is given only the residues from the beginning to end of the alignment are used. More...

#include <utility/exit.hh>
#include <utility/string_util.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <core/types.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/simple_moves/MissingDensityToJumpMover.hh>
#include <protocols/simple_moves/MissingDensityToJumpMover.fwd.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/func/Func.hh>
#include <core/scoring/func/Func.fwd.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rms_util.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <basic/Tracer.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <protocols/relax/FastRelax.hh>
#include <protocols/relax/cst_util.hh>
#include <utility/options/keys/FileOptionKey.fwd.hh>
#include <utility/options/keys/FileOptionKey.hh>
#include <utility/options/keys/FileVectorOptionKey.fwd.hh>
#include <utility/options/keys/FileVectorOptionKey.hh>
#include <devel/init.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/relax.OptionKeys.gen.hh>
#include <ObjexxFCL/format.hh>
#include <fstream>
#include <map>
#include <set>
#include <sstream>
#include <devel/cstEnergyBalance/minimalCstRelaxUtil.hh>

Namespaces
	minimalCstRelax

Functions
void	get_poseToRelax (core::pose::PoseOP &toRelax_poseOP, core::pose::PoseOP &input_poseOP, core::import_pose::pose_stream::MetaPoseInputStream input, std::map< string, SequenceAlignment > alns, Size &offset)
	: gets the pose to relax.Returns either the input pose or if alignments exists a subset of the input pose More...
	if (alns.find(pdbid)==alns.end())
	get_terminal_aln_res (aln, 2, firstRes, lastRes)
void	output_caAtomsToConstraint (const std::set< Size > caAtomsToConstrain, const Size offset, const string coordCstFile, const core::pose::PoseOP input_poseOP)
	: outputs the ca atoms to constrain either with taking account the offset More...
int	main (int argc, char *argv[])

Variables
static basic::Tracer	tr ("minimalCstRelax")
basic::options::IntegerOptionKey	minimalCstRelax::coordinate_cst_gap ("minimalCstRelax:coordinate_cst_gap")
basic::options::BooleanOptionKey	minimalCstRelax::relax_pdb ("minimalCstRelax:relax_pdb")
	else
SequenceAlignment	aln = alns.find(pdbid)->second
	toRelax_poseOP = new core::pose::Pose(*input_poseOP,firstRes,lastRes)
	offset = firstRes-1

Detailed Description

For the first structure in the alignment compare the deviation between native and the relaxed native structure. Then constraints are modified and coordinate constraints are added. If an alignment is given only the residues from the beginning to end of the alignment are used.

Function Documentation

get_poseToRelax()

void get_poseToRelax	(	core::pose::PoseOP &	toRelax_poseOP,
		core::pose::PoseOP &	input_poseOP,
		core::import_pose::pose_stream::MetaPoseInputStream	input,
		std::map< string, SequenceAlignment >	alns,
		Size &	offset
	)

: gets the pose to relax.Returns either the input pose or if alignments exists a subset of the input pose

References basic::options::OptionKeys::chemical::chemical, utility::file_basename(), utility::file::file_basename(), gaussian-sampling::input, offset, tag_from_pose(), and toRelax_poseOP.

Referenced by main().

get_terminal_aln_res()

get_terminal_aln_res	(	aln	,
		2	,
		firstRes	,
		lastRes
	)

Referenced by removeConstraintsNearGap().

if()

if

(

alns.

findpdbid = = alns.end()

)

References utility_exit_with_message.

Referenced by enumerate_junctions.Design::append_component(), enumerate_junctions.Design::attach_valid(), get_junctions_from_legos::collect_junctions(), TCDock::dump_top_hits(), erraser_util::extract_pdb(), PREcst::fit(), enumerate_junctions::generate_all_dhr_attach_permutations(), enumerate_junctions::generate_all_junction_attach_permutations(), enumerate_junctions::generate_all_terminal_pdb_permutations(), enumerate_junctions::generate_dhrs_txt_file(), enumerate_junctions::generate_junctions_txt_file(), enumerate_junctions::generate_starting_round_structures(), enumerate_junctions::generate_structures(), enumerate_junctions.Design::get_current_c_term_dhr(), enumerate_junctions.Design::get_current_n_term_dhr(), build::get_defines(), enumerate_junctions::get_terminal_pdb(), enumerate_junctions::listener(), combine_ContactMaps::main(), main(), pyrosetta.mpi::MPIJobDistributor(), my_main(), enumerate_junctions.Design::number_of_components(), enumerate_junctions.Design::output_valid(), erraser_util::parse_options(), TCDock::run(), add_xyz_to_pose::select_area(), enumerate_junctions.Component::set_c_term_seq(), enumerate_junctions.Component::set_n_term_seq(), enumerate_junctions.Component::set_term_seq(), erraser_wrapper::SWA_rebuild_erraser(), build::update_source_file(), update_ui_project::update_source_file(), and rosetta_binders::xyzMatrix_add_on_binder().

main()

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

References argv, basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, minimalCstRelax::coordinate_cst_gap, test.T009_Exceptions::e, utility::file_basename(), utility::file::file_basename(), basic::options::OptionKeys::cluster::gdtmm, get_poseToRelax(), basic::init(), gaussian-sampling::input, input_alignmentsMapped(), offset, option, output_caAtomsToConstraint(), minimalCstRelax::relax_pdb, basic::options::OptionKeys::frags::scoring::scoring, sfd, basic::options::OptionKeys::in::file::silent, out::file::silent(), challenge::ss, tag_from_pose(), and toRelax_poseOP.

output_caAtomsToConstraint()

void output_caAtomsToConstraint	(	const std::set< Size >	caAtomsToConstrain,
		const Size	offset,
		const string	coordCstFile,
		const core::pose::PoseOP	input_poseOP
	)

: outputs the ca atoms to constrain either with taking account the offset

References subloop_histogram::iterator, offset, and erraser_single_res_analysis::out.

Referenced by main().

Variable Documentation

aln

SequenceAlignment aln = alns.find(pdbid)->second

Referenced by ComputeProfileMover::apply(), calc_blosum_scores(), calc_contacts(), calc_dgaps(), get_disulfides_from_aln(), main(), region_density_score(), region_rmsd(), region_rmsd_structures_aligned(), removeConstraintsNearGap(), save_per_residue_scores(), superimpose_pose_using_aln(), superimpose_via_alignment(), and two_region_rmsd().

else

else

Initial value:

{
  Size firstRes,lastRes

offset

offset = firstRes-1

Referenced by ObjexxFCL::FArray2< T >::a(), ObjexxFCL::FArray2A< T >::a(), ObjexxFCL::FArray2D< T >::a(), ObjexxFCL::FArray2P< T >::a(), ObjexxFCL::FArray3< T >::a(), ObjexxFCL::FArray3A< T >::a(), ObjexxFCL::FArray3D< T >::a(), ObjexxFCL::FArray3P< T >::a(), ObjexxFCL::FArray4< T >::a(), ObjexxFCL::FArray4A< T >::a(), ObjexxFCL::FArray4D< T >::a(), ObjexxFCL::FArray4P< T >::a(), ObjexxFCL::FArray5< T >::a(), ObjexxFCL::FArray5A< T >::a(), ObjexxFCL::FArray5D< T >::a(), ObjexxFCL::FArray5P< T >::a(), ObjexxFCL::FArray6< T >::a(), ObjexxFCL::FArray6A< T >::a(), ObjexxFCL::FArray6D< T >::a(), ObjexxFCL::FArray6P< T >::a(), ObjexxFCL::KeyFArray2D< T >::a(), ObjexxFCL::KeyFArray3D< T >::a(), ObjexxFCL::KeyFArray4D< T >::a(), ObjexxFCL::KeyFArray5D< T >::a(), ObjexxFCL::KeyFArray6D< T >::a(), align_with_offset(), MPDomainAssembly::apply(), atom_tree_torsion_test(), CA_cst_generator(), calc_dist(), ScoreFragmentSetMover::clash_score(), ScoreFragmentSetMover::closability_score(), coarse_frag_test(), utility::graph::LowMemGraph< _LMNode, _LMEdge >::delete_edge(), delete_protein_from_pose(), delete_RNA_from_pose(), utility::graph::LowMemGraph< _LMNode, _LMEdge >::drop_all_edges_for_node(), fastpow2(), utility::graph::LowMemNode::find_edge(), generate_from_point(), apps::pilot::MultiTemplateAlignChunkMover::get_alignment_from_chunk_mapping(), detail::dragonbox::cache_accessor< double >::get_cached_power(), get_poseToRelax(), utility::graph::LowMemGraph< _LMNode, _LMEdge >::internal_create_new_edge(), utility::graph::LowMemNode::internal_find_edge(), utility::graph::LowMemGraph< _LMNode, _LMEdge >::internal_get_edge(), invariants_for_cyclic_permutation(), latticeHit::latticeHit(), loop_modeling_test(), main(), numeric::interpolation::multilinear_interpolation(), utility::nmers_worker(), detail::normalize(), nosuper_CA_rmsd(), output_caAtomsToConstraint(), ScoreFragmentSetMover::overlap_score(), overlap_score(), prepare_threaded_model(), numeric::geometry::hashing::SixDCoordinateBinner::radial_bin_index(), reconstruct_lattice_pose_info(), utility::json_spirit::remove_trailing(), numeric::MathNTensor< T, N >::replace_layer(), ScoreFragmentSetMover::run(), SolutionRescoreMover::run(), set_pattern(), UniformPerturber::set_pose_after_closure(), setup_CA_constraints(), setup_mask(), setup_repeat_symminfo(), slidearound(), detail::snprintf_float(), and soft_overlap_score().

toRelax_poseOP

toRelax_poseOP = new core::pose::Pose(*input_poseOP,firstRes,lastRes)

Referenced by get_poseToRelax(), and main().

tr

basic::Tracer tr("minimalCstRelax") ( "minimalCstRelax"  )

static

@usage: -in:file:s <pdb files> [options: -minimalCstRelax:coordinate_cst_gap in first round of relax gap between CA coordinate constraints] -in::file::alignmen [alignment.filt file]

Author

TJ Brunette