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IterativeOptEDriver.cc File Reference

Implementation of iterative weight fitting protocol. More...

#include <protocols/optimize_weights/IterativeOptEDriver.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreTypeManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreType.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/SingleResidueDunbrackLibrary.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibraryFactory.hh>
#include <protocols/simple_moves/SwitchResidueTypeSetMover.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <core/scoring/UnfoldedStatePotential.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/rms_util.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/operation/TaskOperationFactory.hh>
#include <core/pack/task/operation/ReplicateTask.hh>
#include <core/pack/task/ResfileReader.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/rotamer_set/RotamerSetFactory.hh>
#include <core/pack/packer_neighbors.hh>
#include <protocols/optimize_weights/OptEData.hh>
#include <protocols/optimize_weights/NestedEnergyTermOptEData.hh>
#include <protocols/optimize_weights/DGBindOptEData.hh>
#include <protocols/optimize_weights/DDGBindOptEData.hh>
#include <protocols/optimize_weights/PNatLigPoseOptEData.hh>
#include <utility/graph/Graph.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/scoring/mm/MMTorsionLibrary.fwd.hh>
#include <core/optimization/types.hh>
#include <core/optimization/Multifunc.hh>
#include <protocols/optimize_weights/OptEMultifunc.hh>
#include <core/optimization/Minimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/optimization/ParticleSwarmMinimizer.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <basic/options/util.hh>
#include <basic/Tracer.hh>
#include <basic/datacache/DataMap.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/MinPackMover.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/denovo_design/movers/FastDesign.hh>
#include <utility/io/izstream.hh>
#include <utility/vector1.hh>
#include <utility/vector1.functions.hh>
#include <utility/exit.hh>
#include <utility/file/FileName.hh>
#include <utility/file/PathName.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/string_util.hh>
#include <utility/pointer/owning_ptr.hh>
#include <utility/VirtualBase.hh>
#include <numeric/xyzVector.hh>
#include <numeric/statistics/functions.hh>
#include <numeric/random/random.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <algorithm>
#include <sstream>
#include <basic/options/option.hh>
#include <basic/options/keys/optE.OptionKeys.gen.hh>
#include <basic/options/keys/relax.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <utility/vector0.hh>
#include <ObjexxFCL/format.hh>

Classes

class  protocols::optimize_weights::ScaleAnnealerTemperatureOperation
 

Namespaces

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::optimize_weights
 

Functions

static basic::Tracer protocols::optimize_weights::TR ("protocols.optimize_weights.IterativeOptEDriver")
 
static basic::Tracer protocols::optimize_weights::TR_VERBOSE ("protocols.optimize_weights.IterativeOptEDriver.verbose")
 
void protocols::optimize_weights::attach_debugger ()
 for parallel applications. Wait at a specific point and stay there until you can attach a gdb process (with the –pid <ID> flag in gdb) and internally modify the variable "i" to some non-zero value with a "set var i = 7" command. More...
 
void protocols::optimize_weights::load_component_weights (utility::vector1< core::Real > &component_weights)
 Read options[ optE::component_weights ] file from input file. Not a member of the above driver class since its independent of the driver; possibly belongs in a separate source file. Any component specified in the weights file is set to the corresponding weight. Any component not specified in the weights file is set to 1. More...
 

Detailed Description

Implementation of iterative weight fitting protocol.

Author
Andrew Leaver-Fay – emulating a protocol by Jim Havranek and Brian Kuhlman.