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Rosetta
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Rosetta
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A protocol which outputs sequence recovery statistics ala the table in the "Native sequences are close to optimal" paper. More...
#include <devel/init.hh>#include <core/conformation/PointGraph.hh>#include <core/conformation/find_neighbors.hh>#include <core/io/pdb/pose_io.hh>#include <core/pack/task/PackerTask.hh>#include <core/pack/task/operation/TaskOperations.hh>#include <core/pack/task/operation/TaskOperationFactory.hh>#include <core/pack/task/TaskFactory.hh>#include <core/pose/Pose.hh>#include <core/pose/PDBInfo.hh>#include <core/conformation/Residue.hh>#include <core/scoring/EnergyMap.hh>#include <core/scoring/ScoreType.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/ScoreFunctionFactory.hh>#include <basic/Tracer.hh>#include <basic/prof.hh>#include <basic/options/util.hh>#include <basic/datacache/DataMap.hh>#include <utility/file/file_sys_util.hh>#include <utility/io/ozstream.hh>#include <utility/vector1.hh>#include <utility/excn/Exceptions.hh>#include <basic/options/keys/run.OptionKeys.gen.hh>#include <ObjexxFCL/format.hh>#include <ObjexxFCL/FArray2D.hh>#include <sstream>#include <core/conformation/PointGraphData.hh>#include <core/graph/UpperEdgeGraph.hh>#include <core/import_pose/import_pose.hh>#include <protocols/filters/Filter.fwd.hh>#include <utility/vector0.hh>Go to the source code of this file.
Namespaces | |
| sequence_recovery | |
Functions | |
| static THREAD_LOCAL basic::Tracer | TR ("sequence_recovery") |
| void | init_usage_prompt (std::string exe) |
| core::pack::task::TaskFactoryOP | setup_tf (core::pack::task::TaskFactoryOP task_factory_) |
| load custom TaskOperations according to an xml-like utility::tag file More... | |
| void | fill_num_neighbors (pose::Pose &pose, utility::vector1< core::Size > &num_nbs) |
| helper method which uses the tenA nb graph in the pose object to fill a vector with nb counts More... | |
| std::set< Size > | fill_designable_set (pose::Pose &pose, pack::task::TaskFactoryOP &tf) |
| return the set of residues that are designable based given pose More... | |
| void | measure_sequence_recovery (utility::vector1< core::pose::Pose > &native_poses, utility::vector1< core::pose::Pose > &redesign_poses) |
| iterates over all designed positions and determines identity to native. outputs recoveries to file. More... | |
| void | measure_rotamer_recovery (utility::vector1< core::pose::Pose > &, utility::vector1< core::pose::Pose > &) |
| int | main (int argc, char *argv[]) |
Variables | |
| FileOptionKey const | sequence_recovery::native_pdb_list ("sequence_recovery::native_pdb_list") |
| FileOptionKey const | sequence_recovery::redesign_pdb_list ("sequence_recovery::redesign_pdb_list") |
| FileOptionKey const | sequence_recovery::parse_taskops_file ("sequence_recovery::parse_taskops_file") |
| BooleanOptionKey const | sequence_recovery::rotamer_recovery ("sequence_recovery::rotamer_recovery") |
| StringOptionKey const | sequence_recovery::seq_recov_filename ("sequence_recovery::seq_recov_filename") |
| StringOptionKey const | sequence_recovery::sub_matrix_filename ("sequence_recovery::sub_matrix_filename") |
| IntegerOptionKey const | sequence_recovery::se_cutoff ("sequence_recovery::se_cutoff") |
| std::string | usage_string |
A protocol which outputs sequence recovery statistics ala the table in the "Native sequences are close to optimal" paper.
Definition in file sequence_recovery.cc.
| std::set< Size > fill_designable_set | ( | pose::Pose & | pose, |
| pack::task::TaskFactoryOP & | tf | ||
| ) |
return the set of residues that are designable based given pose
Definition at line 161 of file sequence_recovery.cc.
References test.T200_Scoring::ii, option, sequence_recovery::parse_taskops_file, app.surface_docking.surface_docking::pose, PyMOL_demo::scorefxn, TR(), and utility::options::OptionKeys::options::user.
Referenced by measure_sequence_recovery().
| void fill_num_neighbors | ( | pose::Pose & | pose, |
| utility::vector1< core::Size > & | num_nbs | ||
| ) |
helper method which uses the tenA nb graph in the pose object to fill a vector with nb counts
Definition at line 136 of file sequence_recovery.cc.
References test.T200_Scoring::ii.
Referenced by measure_sequence_recovery().
| void init_usage_prompt | ( | std::string | exe | ) |
Definition at line 403 of file sequence_recovery.cc.
References utility::io::oc::cout, utility::file::file_exists(), ObjexxFCL::getline(), devel::init(), init_usage_prompt(), measure_rotamer_recovery(), measure_sequence_recovery(), utility::excn::EXCN_Base::msg(), sequence_recovery::native_pdb_list, test.Workshop7test::native_pose, option, sequence_recovery::parse_taskops_file, sequence_recovery::redesign_pdb_list, sequence_recovery::rotamer_recovery, sequence_recovery::se_cutoff, sequence_recovery::seq_recov_filename, sequence_recovery::sub_matrix_filename, TR(), usage_string, utility::options::OptionKeys::options::user, utility_exit_with_message, utility_exit_with_message_status, and value.
| void measure_rotamer_recovery | ( | utility::vector1< core::pose::Pose > & | , |
| utility::vector1< core::pose::Pose > & | |||
| ) |
Definition at line 399 of file sequence_recovery.cc.
Referenced by main().
| void measure_sequence_recovery | ( | utility::vector1< core::pose::Pose > & | native_poses, |
| utility::vector1< core::pose::Pose > & | redesign_poses | ||
| ) |
iterates over all designed positions and determines identity to native. outputs recoveries to file.
Definition at line 188 of file sequence_recovery.cc.
References end, ObjexxFCL::format::F(), fill_designable_set(), fill_num_neighbors(), test.T200_Scoring::ii, test.Workshop7test::native_pose, usec::native_sequence, clean_pdb_keep_ligand::nres, option, sequence_recovery::se_cutoff, sequence_recovery::seq_recov_filename, setup_tf(), sequence_recovery::sub_matrix_filename, and value.
Referenced by main().
| core::pack::task::TaskFactoryOP setup_tf | ( | core::pack::task::TaskFactoryOP | task_factory_ | ) |
load custom TaskOperations according to an xml-like utility::tag file
The sequence recovery app can only handle taskops that do not use ResidueSelectors, unless they are anonymous (i.e. unnamed) ResidueSelectors that are declared as subtags of TaskOperations.
Definition at line 114 of file sequence_recovery.cc.
References option, sequence_recovery::parse_taskops_file, test.G204_Module_ScoreAnalysis::tops, and utility::options::OptionKeys::options::user.
Referenced by measure_sequence_recovery().
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static |
Referenced by fill_designable_set(), and main().
| std::string usage_string |
Definition at line 87 of file sequence_recovery.cc.
Referenced by init_usage_prompt(), and main().
1.8.7