Rosetta 3.3
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run backrub Monte Carlo More...
#include <protocols/branch_angle/BranchAngleOptimizer.hh>
#include <protocols/jobdist/Jobs.hh>
#include <protocols/jobdist/standard_mains.hh>
#include <protocols/moves/BackboneMover.hh>
#include <protocols/moves/BackrubMover.hh>
#include <protocols/moves/MinMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/PackRotamersMover.hh>
#include <protocols/moves/SidechainMover.hh>
#include <protocols/moves/TrajectoryRecorder.hh>
#include <protocols/viewer/viewers.hh>
#include <core/chemical/ResidueType.hh>
#include <core/kinematics/MoveMap.hh>
#include <protocols/init.hh>
#include <core/io/pdb/pose_io.hh>
#include <core/scoring/mm/MMBondAngleResidueTypeParamSet.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/types.hh>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>
#include <numeric/random/random.hh>
#include <platform/types.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/backrub.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <protocols/moves/MoverStatistics.hh>
#include <utility/io/mpistream.hh>
#include <fstream>
Functions | |
void * | my_main (void *) |
int | main (int argc, char *argv[]) |
bool | read_fold_tree_from_file (core::kinematics::FoldTree &foldtree, std::string filepath) |
bool | read_fold_tree_from_file (core::pose::Pose &pose, std::string filepath) |
void | append_fold_tree_to_file (core::kinematics::FoldTree const &foldtree, std::string file_path) |
utility::vector1< core::Size > | positions_incompatible_with_task (core::pose::Pose &pose, core::pack::task::PackerTask &packertask) |
Variables | |
static numeric::random::RandomGenerator | RG (222578262) |
basic::Tracer | TR ("apps.backrub") |
run backrub Monte Carlo
void append_fold_tree_to_file | ( | core::kinematics::FoldTree const & | foldtree, |
std::string | file_path | ||
) |
References basic::options::OptionKeys::canonical_sampling::out::out, and TR.
Referenced by my_main().
References constraints::cst_fa_file(), constraints::cst_fa_weight(), in::path::database(), in::ignore_unrecognized_res(), src::init(), in::file::l(), backrub::max_atoms(), basic::options::OptionKeys::canonical_sampling::sampling::mc_kt, backrub::min_atoms(), in::file::movemap(), my_main(), NEW_OPT, out::nstruct(), basic::options::OptionKeys::canonical_sampling::sampling::ntrials, OPT, backrub::pivot_atoms(), backrub::pivot_residues(), packing::resfile(), in::file::s(), basic::options::OptionKeys::canonical_sampling::probabilities::sc_prob_uniform, basic::options::OptionKeys::canonical_sampling::probabilities::sc_prob_withinrot, and basic::options::OptionKeys::run::trajectory.
void * my_main | ( | void * | ) |
References append_fold_tree_to_file(), backrub::backrubmover, in::file::centroid_input(), backrub::custom_fold_tree, backrub::energymethodoptions, color_pdb::i, backrub::input_jobs, backrub::input_pose, backrub::main_task_factory, basic::options::OptionKeys::mc::mc, basic::options::OptionKeys::canonical_sampling::sampling::mc_kt, test::T400_Refinement::minmover, basic::options::OptionKeys::MonteCarlo::MonteCarlo, in::file::movemap(), basic::options::OptionKeys::in::file::movemap, basic::options::OptionKeys::canonical_sampling::sampling::ntrials, basic::options::option, options, basic::options::OptionKeys::out::output_tag, backrub::packrotamersmover, backrub::pivot_atoms(), PyMOL_demo::pose, positions_incompatible_with_task(), read_fold_tree_from_file(), packing::resfile(), basic::RG, basic::options::OptionKeys::canonical_sampling::probabilities::sc_prob_uniform, basic::options::OptionKeys::canonical_sampling::probabilities::sc_prob_withinrot, backrub::score_fxn, backrub::sidechainmover, backrub::smallmover, TR, basic::options::OptionKeys::run::trajectory, basic::options::OptionKeys::mysql::user, and basic::Tracer::Warning.
Referenced by main().
utility::vector1<core::Size> positions_incompatible_with_task | ( | core::pose::Pose & | pose, |
core::pack::task::PackerTask & | packertask | ||
) |
References color_pdb::i.
Referenced by my_main().
bool read_fold_tree_from_file | ( | core::pose::Pose & | pose, |
std::string | filepath | ||
) |
References read_fold_tree_from_file(), and TR.
bool read_fold_tree_from_file | ( | core::kinematics::FoldTree & | foldtree, |
std::string | filepath | ||
) |
References ObjexxFCL::getline(), key, get_pdb::line, and TR.
Referenced by my_main(), and read_fold_tree_from_file().
numeric::random::RandomGenerator RG(222578262) [static] |
basic::Tracer TR("apps.backrub") |