CrystFFTDock Class Reference

Inheritance diagram for CrystFFTDock:

Public Member Functions
	CrystFFTDock ()
std::string	get_name () const override
void	writeMRC (FArray3D< Real > density, std::string mapfilename, bool is_oversampled=false, bool fftshift=false)
void	setup_maps (Pose &pose, FArray3D< Real > &rho_ca, FArray3D< Real > &rho_cb, Real trans_step)
core::Real	resample_maps_and_get_self (FArray3D< Real > const &rho_ca, FArray3D< Real > const &rho_cb, numeric::xyzMatrix< Real > R, protocols::cryst::Spacegroup const &sg, FArray3D< Real > &r_rho_ca, FArray3D< Real > &r_rho_cb, utility::vector1< SingleInterface > &p1_interface_map)
void	dump_transformed_pdb (Pose pose, InterfaceHit ih, numeric::UniformRotationSampler const &urs, std::string outname)
Pose	transform_pdb (Pose const &pose, InterfaceHit ih, numeric::UniformRotationSampler const &urs)
void	transform_map (FArray3D< Real > const &rho, numeric::xyzMatrix< Real > S, numeric::xyzVector< Real > T, FArray3D< Real > &Srho)
void	transform_map_offset0 (FArray3D< Real > const &rho, numeric::xyzMatrix< Real > S, FArray3D< Real > &Srho)
Real	get_radius_of_pose (Pose &pose)
Real	get_transform_distance (InterfaceHit ih_vec, InterfaceHit ih_vec_clustered, numeric::UniformRotationSampler const &urs, Real radius)
void	fft2dslice (FArray3D< Real > const &rho, FArray3D< std::complex< Real > > &Frho, int axisSlice)
void	ifft2dslice (FArray3D< std::complex< Real > > const &Frho, FArray3D< Real > &rho, int axisSlice)
void	project_along_axis (FArray3D< Real > &rho, numeric::xyzVector< Real > axis)
void	do_convolution (FArray3D< Real > const &rho, FArray3D< Real > const &Srho, numeric::xyzMatrix< Real > S, FArray3D< Real > &conv_out)
void	get_interfaces_allatom (Pose pose, utility::vector1< core::kinematics::RT > const &rts, numeric::xyzMatrix< Real > R, numeric::xyzVector< Real > xyz_grid, utility::vector1< SingleInterface > &allInterfaces)
core::Real	get_clash_score_exact (numeric::xyzVector< int > xyz_grid, numeric::xyzMatrix< Real > R, numeric::xyzVector< Real > T, FArray3D< Real > const &r_rho_ca)
void	apply (Pose &pose) override

Private Attributes
core::Real	ca_clashdist_
core::Real	cb_clashdist_
core::Real	n_clashdist_
core::Real	c_clashdist_
core::Real	o_clashdist_
core::Real	interfacedist_
core::Real	cluster_cutoff_
numeric::xyzVector< int >	grid_
numeric::xyzVector< int >	oversamplegrid_
numeric::xyzMatrix< Real >	i2c_
numeric::xyzMatrix< Real >	c2i_
protocols::cryst::Spacegroup	sg_
core::Real	maxclash_
core::Real	mininterface_
core::Real	mininterface_sum_
core::Real	trans_step_
core::Real	rot_step_
Size	nmodels_
Size	rotnum_
bool	ss_only_
bool	eval_native_
bool	debug_
bool	debug_exact_

Constructor & Destructor Documentation

CrystFFTDock()

CrystFFTDock::CrystFFTDock ( )

inline

References basic::options::OptionKeys::corrections::water::cluster_cutoff, basic::options::OptionKeys::msd::debug, basic::options::OptionKeys::mp::mutate_relax::nmodels, and option.

Member Function Documentation

apply()

void CrystFFTDock::apply ( Pose &  pose )

override

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::A, InterfaceHitDatabase::add_interface(), compute_difference::alpha, utility::file::FileName::base(), base_name(), basic::options::OptionKeys::corrections::beta, C, center_pose_at_origin(), basic::options::OptionKeys::corrections::water::cluster_cutoff, utility::file::combine_names(), ObjexxFCL::FArray3D< T >::dimension(), basic::options::OptionKeys::in::file::dssp, loops::gamma, numeric::UniformRotationSampler::get(), get_interface_score(), create_a3b_hbs::i, enumerate_junctions::int, numeric::inverse(), create_a3b_hbs::j, max(), min(), numeric::UniformRotationSampler::nrots(), option, test.T008_Serialization::oss, erraser_single_res_analysis::out, InterfaceHitDatabase::pop(), beta_nonlocal::pose, out::prefix(), numeric::UniformRotationSampler::remove_redundant(), reverse(), numeric::xyzMatrix< T >::rows(), beta_nonlocal::rts, docking::s, InterfaceHit::score, InterfaceHitDatabase::size(), utility::split(), out::suffix(), InterfaceHit::to_string(), InterfaceHitDatabase::top(), basic::TR, basic::options::OptionKeys::inout::dbms::user, x, test.T110_numeric::xy, basic::options::OptionKeys::in::file::xyz, predPRE::y, y2, and predPRE::z.

Referenced by pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

do_convolution()

void CrystFFTDock::do_convolution	(	FArray3D< Real > const &	rho,
		FArray3D< Real > const &	Srho,
		numeric::xyzMatrix< Real >	S,
		FArray3D< Real > &	conv_out
	)

References ObjexxFCL::FArray3D< T >::dimension(), create_a3b_hbs::i, enumerate_junctions::int, numeric::inverse(), docking::Q, docking::R, kmeans_adaptive_kernel_density_bb_dependent_rotlib::rho, numeric::xyzMatrix< T >::row_x(), numeric::xyzMatrix< T >::row_y(), numeric::xyzMatrix< T >::row_z(), numeric::xyzMatrix< T >::rows(), basic::TR, numeric::urs_Quat::x_, numeric::xyzMatrix< T >::xx(), numeric::xyzMatrix< T >::xy(), numeric::xyzMatrix< T >::xz(), numeric::urs_Quat::y_, numeric::xyzMatrix< T >::yx(), numeric::xyzMatrix< T >::yy(), numeric::xyzMatrix< T >::yz(), numeric::urs_Quat::z_, numeric::xyzMatrix< T >::zx(), numeric::xyzMatrix< T >::zy(), and numeric::xyzMatrix< T >::zz().

dump_transformed_pdb()

void CrystFFTDock::dump_transformed_pdb	(	Pose	pose,
		InterfaceHit	ih,
		numeric::UniformRotationSampler const &	urs,
		std::string	outname
	)

References numeric::UniformRotationSampler::get(), test.T008_Serialization::oss, beta_nonlocal::pose, docking::R, InterfaceHit::rot_index, InterfaceHit::score, pyrosetta.distributed.cluster.exceptions::T, InterfaceHit::x, InterfaceHit::y, and InterfaceHit::z.

fft2dslice()

void CrystFFTDock::fft2dslice	(	FArray3D< Real > const &	rho,
		FArray3D< std::complex< Real > > &	Frho,
		int	axisSlice
	)

References ObjexxFCL::FArray2D< T >::dimension(), numeric::fourier::fft2(), create_a3b_hbs::ii, beta_nonlocal::jj, kk, kmeans_adaptive_kernel_density_bb_dependent_rotlib::rho, and utility_exit_with_message.

get_clash_score_exact()

core::Real CrystFFTDock::get_clash_score_exact	(	numeric::xyzVector< int >	xyz_grid,
		numeric::xyzMatrix< Real >	R,
		numeric::xyzVector< Real >	T,
		FArray3D< Real > const &	r_rho_ca
	)

References ObjexxFCL::FArray3D< T >::dimension(), create_a3b_hbs::i, enumerate_junctions::int, pos_mod(), docking::R, pyrosetta.distributed.cluster.exceptions::T, x, predPRE::y, and predPRE::z.

get_interfaces_allatom()

void CrystFFTDock::get_interfaces_allatom	(	Pose	pose,
		utility::vector1< core::kinematics::RT > const &	rts,
		numeric::xyzMatrix< Real >	R,
		numeric::xyzVector< Real >	xyz_grid,
		utility::vector1< SingleInterface > &	allInterfaces
	)

References basic::options::OptionKeys::matdes::design::contact_dist, dist(), numeric::xyzVector< T >::distance_squared(), create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, beta_nonlocal::jj, create_a3b_hbs::k, kk, numeric::xyzVector< T >::length(), max(), min_mod(), create_a3b_hbs::nres, beta_nonlocal::pose, docking::R, basic::options::OptionKeys::cluster::radius, docking::s, and Xi.

get_name()

std::string CrystFFTDock::get_name ( ) const

inlineoverride

get_radius_of_pose()

Real CrystFFTDock::get_radius_of_pose

(

Pose &

pose

)

References create_a3b_hbs::i, enumerate_junctions::int, beta_nonlocal::pose, create_a3b_hbs::r, and basic::options::OptionKeys::cluster::radius.

get_transform_distance()

Real CrystFFTDock::get_transform_distance	(	InterfaceHit	ih_vec,
		InterfaceHit	ih_vec_clustered,
		numeric::UniformRotationSampler const &	urs,
		Real	radius
	)

References basic::options::OptionKeys::hotspot::angle, DEG2RAD, dist(), numeric::UniformRotationSampler::get(), numeric::inverse(), oop_conformations::length, predPRE::R2, basic::options::OptionKeys::cluster::radius, InterfaceHit::rot_index, numeric::urs_R2ang(), InterfaceHit::x, InterfaceHit::y, y1, y2, InterfaceHit::z, basic::options::OptionKeys::motifs::z1, and basic::options::OptionKeys::motifs::z2.

ifft2dslice()

void CrystFFTDock::ifft2dslice	(	FArray3D< std::complex< Real > > const &	Frho,
		FArray3D< Real > &	rho,
		int	axisSlice
	)

References ObjexxFCL::FArray2D< T >::dimension(), numeric::fourier::ifft2(), create_a3b_hbs::ii, beta_nonlocal::jj, kk, kmeans_adaptive_kernel_density_bb_dependent_rotlib::rho, ObjexxFCL::FArray2D< T >::u1(), and utility_exit_with_message.

project_along_axis()

void CrystFFTDock::project_along_axis	(	FArray3D< Real > &	rho,
		numeric::xyzVector< Real >	axis
	)

References max(), P, pos_mod(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::rho, x, predPRE::y, and predPRE::z.

resample_maps_and_get_self()

core::Real CrystFFTDock::resample_maps_and_get_self	(	FArray3D< Real > const &	rho_ca,
		FArray3D< Real > const &	rho_cb,
		numeric::xyzMatrix< Real >	R,
		protocols::cryst::Spacegroup const &	sg,
		FArray3D< Real > &	r_rho_ca,
		FArray3D< Real > &	r_rho_cb,
		utility::vector1< SingleInterface > &	p1_interface_map
	)

References a, ObjexxFCL::abs(), compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, ObjexxFCL::FArray3D< T >::dimension(), enumerate_junctions::int, interp_linear(), numeric::inverse(), max(), docking::R, rx, x, predPRE::y, subloop_histogram::ymax, and predPRE::z.

setup_maps()

void CrystFFTDock::setup_maps	(	Pose &	pose,
		FArray3D< Real > &	rho_ca,
		FArray3D< Real > &	rho_cb,
		Real	trans_step
	)

References ObjexxFCL::abs(), CB, ObjexxFCL::FArray3D< T >::dimension(), create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, create_a3b_hbs::k, max(), min_mod(), option, beta_nonlocal::pose, numeric::xyzMatrix< T >::rows(), basic::TR, x, predPRE::y, and predPRE::z.

transform_map()

void CrystFFTDock::transform_map	(	FArray3D< Real > const &	rho,
		numeric::xyzMatrix< Real >	S,
		numeric::xyzVector< Real >	T,
		FArray3D< Real > &	Srho
	)

References ObjexxFCL::FArray3D< T >::dimension(), pos_mod(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::rho, rx, pyrosetta.distributed.cluster.exceptions::T, x, predPRE::y, and predPRE::z.

transform_map_offset0()

void CrystFFTDock::transform_map_offset0	(	FArray3D< Real > const &	rho,
		numeric::xyzMatrix< Real >	S,
		FArray3D< Real > &	Srho
	)

References ObjexxFCL::FArray3D< T >::dimension(), pos_mod(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::rho, rx, x, predPRE::y, and predPRE::z.

transform_pdb()

Pose CrystFFTDock::transform_pdb	(	Pose const &	pose,
		InterfaceHit	ih,
		numeric::UniformRotationSampler const &	urs
	)

References numeric::UniformRotationSampler::get(), beta_nonlocal::pose, docking::R, InterfaceHit::rot_index, pyrosetta.distributed.cluster.exceptions::T, InterfaceHit::x, InterfaceHit::y, and InterfaceHit::z.

writeMRC()

void CrystFFTDock::writeMRC	(	FArray3D< Real >	density,
		std::string	mapfilename,
		bool	is_oversampled = false,
		bool	fftshift = false
	)

References score_vs_rmsd::density, run_backbone::float, basic::options::OptionKeys::docking::ligand::grid::grid, create_a3b_hbs::i, enumerate_junctions::int, erraser_single_res_analysis::out, pos_mod(), and basic::TR.

Member Data Documentation

c2i_

numeric::xyzMatrix<Real> CrystFFTDock::c2i_

private

c_clashdist_

core::Real CrystFFTDock::c_clashdist_

private

ca_clashdist_

core::Real CrystFFTDock::ca_clashdist_

private

cb_clashdist_

core::Real CrystFFTDock::cb_clashdist_

private

cluster_cutoff_

core::Real CrystFFTDock::cluster_cutoff_

private

debug_

bool CrystFFTDock::debug_

private

debug_exact_

bool CrystFFTDock::debug_exact_

private

eval_native_

bool CrystFFTDock::eval_native_

private

grid_

numeric::xyzVector<int> CrystFFTDock::grid_

private

i2c_

numeric::xyzMatrix<Real> CrystFFTDock::i2c_

private

interfacedist_

core::Real CrystFFTDock::interfacedist_

private

maxclash_

core::Real CrystFFTDock::maxclash_

private

mininterface_

core::Real CrystFFTDock::mininterface_

private

mininterface_sum_

core::Real CrystFFTDock::mininterface_sum_

private

n_clashdist_

core::Real CrystFFTDock::n_clashdist_

private

nmodels_

Size CrystFFTDock::nmodels_

private

o_clashdist_

core::Real CrystFFTDock::o_clashdist_

private

oversamplegrid_

numeric::xyzVector<int> CrystFFTDock::oversamplegrid_

private

rot_step_

core::Real CrystFFTDock::rot_step_

private

rotnum_

Size CrystFFTDock::rotnum_

private

sg_

protocols::cryst::Spacegroup CrystFFTDock::sg_

private

ss_only_

bool CrystFFTDock::ss_only_

private

trans_step_

core::Real CrystFFTDock::trans_step_

private

---

The documentation for this class was generated from the following file:

• src/apps/pilot/frank/cryst_design.cc