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unalignedEvaluate.cc File Reference

This takes an alignment file, fasta file, and a silent file. It then evaluates the qualities of the loops. 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 <basic/Tracer.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/id/SequenceMapping.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/import_pose.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/func/Func.hh>
#include <core/scoring/func/Func.fwd.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/constraints/Constraint.fwd.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/electron_density/util.hh>
#include <core/scoring/electron_density/FastDensEnergy.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/types.hh>
#include <devel/init.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <utility/options/keys/FileOptionKey.fwd.hh>
#include <utility/options/keys/FileOptionKey.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.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 <utility/options/keys/BooleanOptionKey.fwd.hh>
#include <utility/options/keys/BooleanOptionKey.hh>
#include <protocols/comparative_modeling/util.hh>
#include <protocols/electron_density/SetupForDensityScoringMover.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <numeric/xyzVector.hh>
#include <apps/pilot/brunette/tj_util.hh>
#include <iostream>
#include <fstream>

Namespaces

 unalignedEvaluate
 

Functions

Real region_density_score (Pose &pose, Pose const templatePose, SequenceAlignment aln, Size start_res, Size end_res)
 
Real region_constraint_score (Pose &pose, Size start_res, Size end_res, ConstraintSetOP cstSet_)
 
Real region_score (Pose &pose, Size start_res, Size end_res)
 
Real region_rmsd_structures_aligned (Pose &mod_pose, Pose const &ref_pose, SequenceAlignment aln, Size start_res, Size end_res)
 
Real two_region_rmsd (Pose &mod_pose, Pose const &ref_pose, SequenceAlignment aln, Size start_res, Size end_res, Size region2_start_res, Size region2_end_res)
 
Real region_rmsd (Pose &mod_pose, Pose const &ref_pose, SequenceAlignment aln, Size start_res, Size end_res)
 
bool present_in_native (Size start_res, Size end_res, SequenceAlignment native_aln)
 
void score_loop (Pose &pose, Pose const &native_pose, SequenceAlignment native_aln, SequenceAlignment template_aln, Pose native_relaxed_pose, Size start_res, Size end_res, ConstraintSetOP cstSet_, ConstraintSetOP lookBackCstSet_, Pose const templatePose, std::ostream &out)
 
void score_loops (Pose pose, Loops const unalignedLoops, Pose native_pose, SequenceAlignment native_alignment, SequenceAlignment template_alignment, Pose native_relaxed_pose, Pose const templatePoseData, ConstraintSetOP cstSet_, ConstraintSetOP lookBackCstSet_, std::ostream &out)
 
int main (int argc, char *argv[])
 

Variables

static basic::Tracer tr ("unalignedEvaluate")
 @usage: -in:file:alignent <alignment> -in:file:s <decoy.out> -in:file:native <native pose> -in:file:fasta <fasta> -unalignedEvaluate:pair_silent_all_aln -cm:aln_format grishin -in:file:template_pdb <templates> More...
 
basic::options::FileOptionKey unalignedEvaluate::relaxed_native ("unalignedEvaluate:relaxed_native")
 
basic::options::FileOptionKey unalignedEvaluate::core_pdb ("unalignedEvaluate:core_pdb")
 
basic::options::FileOptionKey unalignedEvaluate::lookback_csts ("unalignedEvaluate:lookback_csts")
 

Detailed Description

This takes an alignment file, fasta file, and a silent file. It then evaluates the qualities of the loops.

Function Documentation

◆ main()

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

◆ present_in_native()

bool present_in_native ( Size  start_res,
Size  end_res,
SequenceAlignment  native_aln 
)

◆ region_constraint_score()

Real region_constraint_score ( Pose pose,
Size  start_res,
Size  end_res,
ConstraintSetOP  cstSet_ 
)

◆ region_density_score()

Real region_density_score ( Pose pose,
Pose const  templatePose,
SequenceAlignment  aln,
Size  start_res,
Size  end_res 
)

◆ region_rmsd()

Real region_rmsd ( Pose mod_pose,
Pose const &  ref_pose,
SequenceAlignment  aln,
Size  start_res,
Size  end_res 
)

◆ region_rmsd_structures_aligned()

Real region_rmsd_structures_aligned ( Pose mod_pose,
Pose const &  ref_pose,
SequenceAlignment  aln,
Size  start_res,
Size  end_res 
)

◆ region_score()

Real region_score ( Pose pose,
Size  start_res,
Size  end_res 
)

◆ score_loop()

void score_loop ( Pose pose,
Pose const &  native_pose,
SequenceAlignment  native_aln,
SequenceAlignment  template_aln,
Pose  native_relaxed_pose,
Size  start_res,
Size  end_res,
ConstraintSetOP  cstSet_,
ConstraintSetOP  lookBackCstSet_,
Pose const  templatePose,
std::ostream &  out 
)

◆ score_loops()

void score_loops ( Pose  pose,
Loops const  unalignedLoops,
Pose  native_pose,
SequenceAlignment  native_alignment,
SequenceAlignment  template_alignment,
Pose  native_relaxed_pose,
Pose const  templatePoseData,
ConstraintSetOP  cstSet_,
ConstraintSetOP  lookBackCstSet_,
std::ostream &  out 
)

◆ two_region_rmsd()

Real two_region_rmsd ( Pose mod_pose,
Pose const &  ref_pose,
SequenceAlignment  aln,
Size  start_res,
Size  end_res,
Size  region2_start_res,
Size  region2_end_res 
)

Variable Documentation

◆ tr

basic::Tracer tr("unalignedEvaluate") ( "unalignedEvaluate"  )
static

@usage: -in:file:alignent <alignment> -in:file:s <decoy.out> -in:file:native <native pose> -in:file:fasta <fasta> -unalignedEvaluate:pair_silent_all_aln -cm:aln_format grishin -in:file:template_pdb <templates>

Author
TJ Brunette