protocols::protein_grid::ProteinGrid Class Reference

#include <ProteinGrid.hh>

Public Types
typedef utility::vector1< utility::vector1< utility::vector1< core::Size > > >	ProteinMatrix
	condensing the data type name for the main 3D vector (or matrix) that represents the protein More...

Public Member Functions
	ProteinGrid (core::pose::PoseOP in_pose)
	ProteinGrid (core::pose::PoseOP in_pose, core::Real resolution)
	ProteinGrid (core::pose::PoseOP in_pose, numeric::xyzVector< int > sub_area_center, utility::vector1< core::Size > sub_region_dimensions)
	ProteinGrid (core::pose::PoseOP in_pose, core::Real resolution, numeric::xyzVector< int > sub_area_center, utility::vector1< core::Size > sub_region_dimensions)
	ProteinGrid (ProteinGrid const &)=default
ProteinGrid &	operator= (ProteinGrid const &)=default
	~ProteinGrid ()
core::Size	get_grid_volume ()
core::Size	get_sub_area_grid_volume ()
core::Real	get_grid_occupied_cell_ratio ()
core::Real	get_sub_grid_occupied_cell_ratio ()
core::Real	get_grid_occupied_cell_count ()
core::Real	get_sub_grid_occupied_cell_count ()
void	set_sub_regions (numeric::xyzVector< int > sub_area_center, utility::vector1< core::Size > sub_region_dimensions)
void	ignore_sub_area ()
void	ignore_lj_radii ()
void	project_lj_radii ()
void	placed_ligand_space_fill_analysis (core::conformation::ResidueOP ligresOP)
bool	placed_ligand_clash_analysis (core::conformation::ResidueOP ligresOP)
core::pose::Pose	export_protein_matrix_to_pose ()
void	export_protein_matrix_to_pdb (std::string pdb_name_prefix)
void	set_print_whole_matrix (bool setter)
void	set_print_empty_space (bool setter)

Private Member Functions
	ProteinGrid ()
void	wrap_matrix_around_pose ()
void	validate_resolution ()
void	reset_xyz_vectors ()
void	reset_sub_region_vectors ()
void	define_sub_regions ()
bool	is_coordinate_in_sub_area (core::Size x, core::Size y, core::Size z)
void	initialize_from_options ()
std::string	base_10_to_base_62 (core::Size starting_num)

Private Attributes
ProteinMatrix	protein_matrix_
core::pose::PoseOP	working_pose_
utility::vector1< int >	xyz_shift_
utility::vector1< core::Size >	xyz_bound_
core::Size	matrix_volume_ = 0
core::Size	sub_matrix_volume_ = 0
core::Real	resolution_ = 1
bool	using_sub_area_ = false
bool	using_lj_radii_ = false
numeric::xyzVector< int >	true_sub_area_center_
numeric::xyzVector< core::Size >	adjusted_sub_area_center_
utility::vector1< core::Size >	true_sub_region_dimensions_
utility::vector1< core::Size >	adjusted_sub_region_dimensions_
utility::vector1< core::Size >	sub_region_max_
utility::vector1< core::Size >	sub_region_min_
core::Size	matrix_fullness_ = 0
core::Real	fullness_ratio_ = 0
core::Size	sub_matrix_fullness_ = 0
core::Real	sub_fullness_ratio_ = 0
bool	print_whole_matrix_ = false
bool	print_empty_space_ = false

Member Typedef Documentation

ProteinMatrix

typedef utility::vector1<utility::vector1<utility::vector1<core::Size> > > protocols::protein_grid::ProteinGrid::ProteinMatrix

condensing the data type name for the main 3D vector (or matrix) that represents the protein

Constructor & Destructor Documentation

ProteinGrid() [1/6]

protocols::protein_grid::ProteinGrid::ProteinGrid

(

core::pose::PoseOP

in_pose

)

References initialize_from_options(), reset_sub_region_vectors(), working_pose_, and wrap_matrix_around_pose().

ProteinGrid() [2/6]

protocols::protein_grid::ProteinGrid::ProteinGrid	(	core::pose::PoseOP	in_pose,
		core::Real	resolution
	)

References initialize_from_options(), reset_sub_region_vectors(), resolution_, validate_resolution(), working_pose_, and wrap_matrix_around_pose().

ProteinGrid() [3/6]

protocols::protein_grid::ProteinGrid::ProteinGrid	(	core::pose::PoseOP	in_pose,
		numeric::xyzVector< int >	sub_area_center,
		utility::vector1< core::Size >	sub_region_dimensions
	)

References initialize_from_options(), protocols::protein_grid::ms_tr(), reset_sub_region_vectors(), true_sub_area_center_, true_sub_region_dimensions_, using_sub_area_, protocols::hybridization::val, working_pose_, and wrap_matrix_around_pose().

ProteinGrid() [4/6]

protocols::protein_grid::ProteinGrid::ProteinGrid	(	core::pose::PoseOP	in_pose,
		core::Real	resolution,
		numeric::xyzVector< int >	sub_area_center,
		utility::vector1< core::Size >	sub_region_dimensions
	)

References initialize_from_options(), protocols::protein_grid::ms_tr(), reset_sub_region_vectors(), resolution_, true_sub_area_center_, true_sub_region_dimensions_, using_sub_area_, protocols::hybridization::val, validate_resolution(), working_pose_, and wrap_matrix_around_pose().

ProteinGrid() [5/6]

protocols::protein_grid::ProteinGrid::ProteinGrid ( ProteinGrid const &  )

default

~ProteinGrid()

protocols::protein_grid::ProteinGrid::~ProteinGrid ( )

default

ProteinGrid() [6/6]

protocols::protein_grid::ProteinGrid::ProteinGrid ( )

private

Member Function Documentation

base_10_to_base_62()

std::string protocols::protein_grid::ProteinGrid::base_10_to_base_62 ( core::Size  starting_num )

private

Referenced by export_protein_matrix_to_pose().

define_sub_regions()

void protocols::protein_grid::ProteinGrid::define_sub_regions ( )

private

References adjusted_sub_area_center_, adjusted_sub_region_dimensions_, get_sub_area_grid_volume(), protocols::protein_grid::ms_tr(), protein_matrix_, resolution_, sub_matrix_volume_, sub_region_max_, sub_region_min_, true_sub_area_center_, true_sub_region_dimensions_, xyz_bound_, and xyz_shift_.

Referenced by wrap_matrix_around_pose().

export_protein_matrix_to_pdb()

void protocols::protein_grid::ProteinGrid::export_protein_matrix_to_pdb

(

std::string

pdb_name_prefix

)

References core::pose::add_comment(), core::pose::Pose::dump_pdb(), export_protein_matrix_to_pose(), fullness_ratio_, protocols::protein_grid::ms_tr(), sub_fullness_ratio_, core::id::to_string(), using_sub_area_, and working_pose_.

export_protein_matrix_to_pose()

core::pose::Pose protocols::protein_grid::ProteinGrid::export_protein_matrix_to_pose

(

)

References core::chemical::MutableResidueType::add_atom(), core::chemical::MutableResidueType::add_bond(), core::pose::Pose::append_residue_by_jump(), core::chemical::MutableResidueType::assign_internal_coordinates(), base_10_to_base_62(), core::conformation::ResidueFactory::create_residue(), core::chemical::ResidueType::make(), protocols::protein_grid::ms_tr(), core::chemical::MutableResidueType::natoms(), print_empty_space_, print_whole_matrix_, protein_matrix_, resolution_, core::chemical::MutableResidueType::set_icoor(), core::chemical::MutableResidueType::set_ideal_xyz(), core::conformation::Residue::type(), using_sub_area_, working_pose_, xyz_bound_, and xyz_shift_.

Referenced by export_protein_matrix_to_pdb().

get_grid_occupied_cell_count()

core::Real protocols::protein_grid::ProteinGrid::get_grid_occupied_cell_count

(

)

References matrix_fullness_.

get_grid_occupied_cell_ratio()

core::Real protocols::protein_grid::ProteinGrid::get_grid_occupied_cell_ratio

(

)

References fullness_ratio_.

get_grid_volume()

core::Size protocols::protein_grid::ProteinGrid::get_grid_volume

(

)

References xyz_bound_.

Referenced by wrap_matrix_around_pose().

get_sub_area_grid_volume()

core::Size protocols::protein_grid::ProteinGrid::get_sub_area_grid_volume

(

)

References sub_region_max_, and sub_region_min_.

Referenced by define_sub_regions().

get_sub_grid_occupied_cell_count()

core::Real protocols::protein_grid::ProteinGrid::get_sub_grid_occupied_cell_count

(

)

References sub_matrix_fullness_.

get_sub_grid_occupied_cell_ratio()

core::Real protocols::protein_grid::ProteinGrid::get_sub_grid_occupied_cell_ratio

(

)

References sub_fullness_ratio_.

ignore_lj_radii()

void protocols::protein_grid::ProteinGrid::ignore_lj_radii

(

)

References protocols::protein_grid::ms_tr(), using_lj_radii_, and wrap_matrix_around_pose().

ignore_sub_area()

void protocols::protein_grid::ProteinGrid::ignore_sub_area

(

)

References protocols::protein_grid::ms_tr(), project_lj_radii(), using_lj_radii_, using_sub_area_, and wrap_matrix_around_pose().

initialize_from_options()

void protocols::protein_grid::ProteinGrid::initialize_from_options ( )

private

References print_empty_space_, and print_whole_matrix_.

Referenced by ProteinGrid().

is_coordinate_in_sub_area()

bool protocols::protein_grid::ProteinGrid::is_coordinate_in_sub_area ( core::Size  x, core::Size  y, core::Size  z  )

private

References sub_region_max_, sub_region_min_, and using_sub_area_.

Referenced by placed_ligand_space_fill_analysis(), project_lj_radii(), and wrap_matrix_around_pose().

operator=()

ProteinGrid& protocols::protein_grid::ProteinGrid::operator= ( ProteinGrid const &  )

default

placed_ligand_clash_analysis()

bool protocols::protein_grid::ProteinGrid::placed_ligand_clash_analysis

(

core::conformation::ResidueOP

ligresOP

)

References protein_matrix_, resolution_, and xyz_shift_.

placed_ligand_space_fill_analysis()

void protocols::protein_grid::ProteinGrid::placed_ligand_space_fill_analysis

(

core::conformation::ResidueOP

ligresOP

)

References fullness_ratio_, is_coordinate_in_sub_area(), matrix_fullness_, matrix_volume_, project_lj_radii(), protein_matrix_, resolution_, sub_fullness_ratio_, sub_matrix_fullness_, sub_matrix_volume_, using_lj_radii_, using_sub_area_, xyz_bound_, and xyz_shift_.

project_lj_radii()

void protocols::protein_grid::ProteinGrid::project_lj_radii

(

)

References fullness_ratio_, is_coordinate_in_sub_area(), matrix_fullness_, matrix_volume_, protocols::protein_grid::ms_tr(), protein_matrix_, resolution_, sub_fullness_ratio_, sub_matrix_fullness_, sub_matrix_volume_, using_lj_radii_, using_sub_area_, working_pose_, xyz_bound_, and xyz_shift_.

Referenced by ignore_sub_area(), and placed_ligand_space_fill_analysis().

reset_sub_region_vectors()

void protocols::protein_grid::ProteinGrid::reset_sub_region_vectors ( )

private

References adjusted_sub_area_center_, adjusted_sub_region_dimensions_, sub_region_max_, sub_region_min_, true_sub_area_center_, and true_sub_region_dimensions_.

Referenced by ProteinGrid().

reset_xyz_vectors()

void protocols::protein_grid::ProteinGrid::reset_xyz_vectors ( )

private

References xyz_bound_, and xyz_shift_.

Referenced by wrap_matrix_around_pose().

set_print_empty_space()

void protocols::protein_grid::ProteinGrid::set_print_empty_space

(

bool

setter

)

References print_empty_space_.

set_print_whole_matrix()

void protocols::protein_grid::ProteinGrid::set_print_whole_matrix

(

bool

setter

)

References print_whole_matrix_.

set_sub_regions()

void protocols::protein_grid::ProteinGrid::set_sub_regions	(	numeric::xyzVector< int >	sub_area_center,
		utility::vector1< core::Size >	sub_region_dimensions
	)

References protocols::protein_grid::ms_tr(), true_sub_area_center_, true_sub_region_dimensions_, using_sub_area_, protocols::hybridization::val, and wrap_matrix_around_pose().

validate_resolution()

void protocols::protein_grid::ProteinGrid::validate_resolution ( )

private

References protocols::protein_grid::ms_tr(), and resolution_.

Referenced by ProteinGrid().

wrap_matrix_around_pose()

void protocols::protein_grid::ProteinGrid::wrap_matrix_around_pose ( )

private

References define_sub_regions(), fullness_ratio_, get_grid_volume(), is_coordinate_in_sub_area(), matrix_fullness_, matrix_volume_, protocols::protein_grid::ms_tr(), protein_matrix_, reset_xyz_vectors(), resolution_, sub_fullness_ratio_, sub_matrix_fullness_, sub_matrix_volume_, using_sub_area_, working_pose_, xyz_bound_, and xyz_shift_.

Referenced by ignore_lj_radii(), ignore_sub_area(), ProteinGrid(), and set_sub_regions().

Member Data Documentation

adjusted_sub_area_center_

numeric::xyzVector<core::Size> protocols::protein_grid::ProteinGrid::adjusted_sub_area_center_

private

Referenced by define_sub_regions(), and reset_sub_region_vectors().

adjusted_sub_region_dimensions_

utility::vector1<core::Size> protocols::protein_grid::ProteinGrid::adjusted_sub_region_dimensions_

private

Referenced by define_sub_regions(), and reset_sub_region_vectors().

fullness_ratio_

core::Real protocols::protein_grid::ProteinGrid::fullness_ratio_ = 0

private

Referenced by export_protein_matrix_to_pdb(), get_grid_occupied_cell_ratio(), placed_ligand_space_fill_analysis(), project_lj_radii(), and wrap_matrix_around_pose().

matrix_fullness_

core::Size protocols::protein_grid::ProteinGrid::matrix_fullness_ = 0

private

Referenced by get_grid_occupied_cell_count(), placed_ligand_space_fill_analysis(), project_lj_radii(), and wrap_matrix_around_pose().

matrix_volume_

core::Size protocols::protein_grid::ProteinGrid::matrix_volume_ = 0

private

Referenced by placed_ligand_space_fill_analysis(), project_lj_radii(), and wrap_matrix_around_pose().

print_empty_space_

bool protocols::protein_grid::ProteinGrid::print_empty_space_ = false

private

Referenced by export_protein_matrix_to_pose(), initialize_from_options(), and set_print_empty_space().

print_whole_matrix_

bool protocols::protein_grid::ProteinGrid::print_whole_matrix_ = false

private

Referenced by export_protein_matrix_to_pose(), initialize_from_options(), and set_print_whole_matrix().

protein_matrix_

ProteinMatrix protocols::protein_grid::ProteinGrid::protein_matrix_

private

Referenced by define_sub_regions(), export_protein_matrix_to_pose(), placed_ligand_clash_analysis(), placed_ligand_space_fill_analysis(), project_lj_radii(), and wrap_matrix_around_pose().

resolution_

core::Real protocols::protein_grid::ProteinGrid::resolution_ = 1

private

Referenced by define_sub_regions(), export_protein_matrix_to_pose(), placed_ligand_clash_analysis(), placed_ligand_space_fill_analysis(), project_lj_radii(), ProteinGrid(), validate_resolution(), and wrap_matrix_around_pose().

sub_fullness_ratio_

core::Real protocols::protein_grid::ProteinGrid::sub_fullness_ratio_ = 0

private

Referenced by export_protein_matrix_to_pdb(), get_sub_grid_occupied_cell_ratio(), placed_ligand_space_fill_analysis(), project_lj_radii(), and wrap_matrix_around_pose().

sub_matrix_fullness_

core::Size protocols::protein_grid::ProteinGrid::sub_matrix_fullness_ = 0

private

Referenced by get_sub_grid_occupied_cell_count(), placed_ligand_space_fill_analysis(), project_lj_radii(), and wrap_matrix_around_pose().

sub_matrix_volume_

core::Size protocols::protein_grid::ProteinGrid::sub_matrix_volume_ = 0

private

Referenced by define_sub_regions(), placed_ligand_space_fill_analysis(), project_lj_radii(), and wrap_matrix_around_pose().

sub_region_max_

utility::vector1<core::Size> protocols::protein_grid::ProteinGrid::sub_region_max_

private

Referenced by define_sub_regions(), get_sub_area_grid_volume(), is_coordinate_in_sub_area(), and reset_sub_region_vectors().

sub_region_min_

utility::vector1<core::Size> protocols::protein_grid::ProteinGrid::sub_region_min_

private

Referenced by define_sub_regions(), get_sub_area_grid_volume(), is_coordinate_in_sub_area(), and reset_sub_region_vectors().

true_sub_area_center_

numeric::xyzVector<int> protocols::protein_grid::ProteinGrid::true_sub_area_center_

private

Referenced by define_sub_regions(), ProteinGrid(), reset_sub_region_vectors(), and set_sub_regions().

true_sub_region_dimensions_

utility::vector1<core::Size> protocols::protein_grid::ProteinGrid::true_sub_region_dimensions_

private

Referenced by define_sub_regions(), ProteinGrid(), reset_sub_region_vectors(), and set_sub_regions().

using_lj_radii_

bool protocols::protein_grid::ProteinGrid::using_lj_radii_ = false

private

Referenced by ignore_lj_radii(), ignore_sub_area(), placed_ligand_space_fill_analysis(), and project_lj_radii().

using_sub_area_

bool protocols::protein_grid::ProteinGrid::using_sub_area_ = false

private

Referenced by export_protein_matrix_to_pdb(), export_protein_matrix_to_pose(), ignore_sub_area(), is_coordinate_in_sub_area(), placed_ligand_space_fill_analysis(), project_lj_radii(), ProteinGrid(), set_sub_regions(), and wrap_matrix_around_pose().

working_pose_

core::pose::PoseOP protocols::protein_grid::ProteinGrid::working_pose_

private

Referenced by export_protein_matrix_to_pdb(), export_protein_matrix_to_pose(), project_lj_radii(), ProteinGrid(), and wrap_matrix_around_pose().

xyz_bound_

utility::vector1<core::Size> protocols::protein_grid::ProteinGrid::xyz_bound_

private

Referenced by define_sub_regions(), export_protein_matrix_to_pose(), get_grid_volume(), placed_ligand_space_fill_analysis(), project_lj_radii(), reset_xyz_vectors(), and wrap_matrix_around_pose().

xyz_shift_

utility::vector1<int> protocols::protein_grid::ProteinGrid::xyz_shift_

private

Referenced by define_sub_regions(), export_protein_matrix_to_pose(), placed_ligand_clash_analysis(), placed_ligand_space_fill_analysis(), project_lj_radii(), reset_xyz_vectors(), and wrap_matrix_around_pose().

---

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

• src/protocols/protein_grid/ProteinGrid.hh
• src/protocols/protein_grid/ProteinGrid.cc