docking_inputpatchdock_mpi.cc File Reference

#include <iostream>
#include <iomanip>
#include <protocols/viewer/viewers.hh>
#include <protocols/moves/Mover.fwd.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/constraint_movers/ConstraintSetMover.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/pack_rotamers.hh>
#include <protocols/simple_task_operations/RestrictToInterface.hh>
#include <core/pack/task/operation/NoRepackDisulfides.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <utility/tools/make_vector1.hh>
#include <basic/options/util.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <core/import_pose/import_pose.hh>
#include <mpi.h>
#include <utility/mpi_util.hh>
#include <protocols/docking/DockingProtocol.hh>
#include <protocols/docking/metrics.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/conformation/Conformation.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/angle.functions.hh>
#include <numeric/random/random.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/ProteinSilentStruct.hh>
#include <core/io/silent/silent.fwd.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <basic/options/option_macros.hh>
#include <protocols/scoring/Interface.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <protocols/forge/methods/pose_mod.hh>
#include <protocols/docking/DockingLowRes.hh>
#include <protocols/docking/DockingInitialPerturbation.hh>
#include <boost/timer.hpp>
#include <protocols/docking/util.hh>

Functions
void	read_patchdock_entry (utility::vector1< utility::vector1< double > > &saved_transformations_, string patchdock_fname_)
	work/shilei/rosetta/rosetta_source/src/apps/pilot/wendao/test_bbmc.cc More...
void	transform_pose (core::pose::Pose &pose, core::Size const chain, utility::vector1< double > const &t)
void	run_parallel_docking ()
int	main (int argc, char *argv[])

Function Documentation

main()

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

References argv, basic::init(), NEW_OPT, local::nstruct, and run_parallel_docking().

read_patchdock_entry()

void read_patchdock_entry	(	utility::vector1< utility::vector1< double > > &	saved_transformations_,
		string	patchdock_fname_
	)

work/shilei/rosetta/rosetta_source/src/apps/pilot/wendao/test_bbmc.cc

References compute_difference::alpha, basic::options::OptionKeys::corrections::beta, data, loops::gamma, getline(), line, utility_exit_with_message, x, predPRE::y, and predPRE::z.

Referenced by run_parallel_docking().

run_parallel_docking()

void run_parallel_docking

(

)

References val2thr::atom, CREATE_EXCEPTION, pyrosetta::create_score_function, basic::options::OptionKeys::constraints::cst_file, basic::options::OptionKeys::constraints::cst_weight, lactamize::filename, create_a3b_hbs::i, min(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::in::file::native, docking::native_pose, create_a3b_hbs::nres, local::nstruct, basic::options::OptionKeys::out::file::o, basic::options::option, predPRE::pdbname, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, numeric::random::random_range(), basic::options::OptionKeys::antibody::design::random_start, read_patchdock_entry(), utility::receive_doubles_from_node(), loops_kic::rms, basic::options::OptionKeys::in::file::s, utility::send_doubles_to_node(), basic::options::OptionKeys::loops::timer, utility::to_string(), transform_pose(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

transform_pose()

void transform_pose	(	core::pose::Pose &	pose,
		core::Size const	chain,
		utility::vector1< double > const &	t
	)

References val2thr::atom, predPRE::chain, chain_begin(), chain_end(), in::detect_disulf(), option, beta_nonlocal::pose, residue, 3d_histogram::rotation, predPRE::t, basic::options::OptionKeys::rigid::translation, and basic::options::OptionKeys::inout::dbms::user.

Referenced by run_parallel_docking().