src/apps/public/backrub.cc File Reference

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")

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Detailed Description

run backrub Monte Carlo

Author:

Colin A. Smith (colin.smith@ucsf.edu)

Detailed:

Currently a work in progress. The goal is to match the features of rosetta++ -backrub_mc

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Function Documentation

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().

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

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().

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Variable Documentation

numeric::random::RandomGenerator RG(222578262) [static]

basic::Tracer TR("apps.backrub")