hotspot_hash.cc File Reference

app to find potential hotspot residue placements on the surface of a protein target Method: make a disembodied residue, with option to make residue backbone invisible to the scorefxn centroid dock residue to the target, then full-atom dock and repack the residue only (must use -norepack1) write out all docked residues that contact the target with even a somewhat reasonable energy More...

#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <devel/init.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <basic/options/option_macros.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <protocols/scoring/Interface.hh>
#include <protocols/hotspot_hashing/HotspotStubSet.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <core/kinematics/MoveMap.hh>
#include <basic/Tracer.hh>
#include <utility/exit.hh>
#include <core/types.hh>
#include <utility/file/file_sys_util.hh>
#include <sstream>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/hotspot.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/docking.OptionKeys.gen.hh>
#include <basic/options/keys/chemical.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/variant_util.hh>
#include <utility/vector1.hh>

Functions
void	benchmark_contacts (pose::Pose const &start_pose, scoring::ScoreFunctionOP scorefxn)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("pilot_apps.jcorn.hotspot_hash")

Detailed Description

app to find potential hotspot residue placements on the surface of a protein target Method: make a disembodied residue, with option to make residue backbone invisible to the scorefxn centroid dock residue to the target, then full-atom dock and repack the residue only (must use -norepack1) write out all docked residues that contact the target with even a somewhat reasonable energy

app to find potential hotspot residue placements on the surface of a protein target Method: make a disembodied residue, with option to make residue backbone invisible to the scorefxn (default) centroid dock residue to the target, then full-atom dock and repack

Author

Jacob Corn @created May 2008 @usage hotspot_hash -randomize1 -randomize2 -norepack1 [-score_interface] -prefix <Rosetta Residue name> -run::n_cycles <# lowres docks> -ntrials <# hires docks> [-sc_only] -user_tag <output suffix>

Jacob Corn @created May 2008 @usage hotspot_hash [-benchmark] <benchmark an existing 2-chain complex> -residue <list of Rosetta Residue name3s || ALL (default)> -run:n_cycles <# stubs to find> (default 10) -hotspot:target <target PDB to hash> -hotspot:target_res <interesting residue on the target> (default none) -hotspot:target_dist <max distance in A from target_res> (default any) -hotspot:angle <Maximum allowed angle between stubCA, target CoM, and stubCB (default off) -hotspot:angle_res <Residue to use for angle calculation from stubCA, <this option>, and stubCB. Used to determine if stub is pointing towards target. 0 uses the default, which is the targets center of mass> -hotspot:length <length of helix as host for hotspot> (default 1) -hotspot:sc_only <Use sidechain only, or also count backbone?> (default T) -hashfile <input existing hash file> -o <output hash file> (default hash.hsh) -scorecut <absolute score or percentage cut> (default off) -score:weights <weights to use for hashing> (default standard, environmental dependence off) -hotspot:envhb <use environmental dependent hbonds? default off) -score:patch <score patch to use for hashing>

Function Documentation

benchmark_contacts()

void benchmark_contacts	(	pose::Pose const &	start_pose,
		scoring::ScoreFunctionOP	scorefxn
	)

References test.T009_Exceptions::e, basic::Tracer::flush(), create_a3b_hbs::i, create_a3b_hbs::ii, interface, vancomycin::min_mover, beta_nonlocal::mm, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, beta_nonlocal::pose, residue, hotspot::sc_only(), oop_conformations::scorefxn, and TR.

Referenced by main().

main()

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

References hotspot::angle(), hotspot::angle_res(), argv, hotspot::batch_size(), hotspot::benchmark(), benchmark_contacts(), basic::Tracer::Debug, test.T009_Exceptions::e, hotspot::envhb(), packing::ex1::ex1(), packing::ex2::ex2(), packing::extrachi_cutoff(), in::file::fail_on_bad_hbond(), utility::file::file_delete(), utility::file::file_exists(), detail::find(), hotspot::hashfile(), create_a3b_hbs::i, basic::init(), in::file::l(), oop_conformations::length, hotspot::length(), run::n_cycles(), basic::options::OptionKeys::run::n_cycles, out::file::o(), OPT, basic::options::option, option, options, out::overwrite(), score::patch(), basic::options::OptionKeys::chemical::patch_selectors, predPRE::pdbname, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, docking::randomize1, docking::randomize2, hotspot::residue(), in::file::s(), hotspot::sc_only(), basic::options::OptionKeys::ddg::score_cutoff, out::scorecut(), basic::options::OptionKeys::out::scorecut, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), basic::options::start_files(), in::file::sucker_params(), hotspot::target(), hotspot::target_dist(), hotspot::target_res(), hotspot::threshold(), revert_app::threshold, TR, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and score::weights().

Variable Documentation

TR

basic::Tracer TR("pilot_apps.jcorn.hotspot_hash") ( "pilot_apps.jcorn.hotspot_hash"  )

static

Referenced by benchmark_contacts(), and main().