Class to print out info specific to glycan poses. Will be expanded as needed. Hope to eventually add it as both a mover and a features reporter. Needs to be completely rewritten. More...

Inheritance diagram for GlycanClashCheckMover:

[legend]

Public Member Functions
	GlycanClashCheckMover ()
	Default constructor. More...

	GlycanClashCheckMover (GlycanClashCheckMover const &)=default
	Copy constructor. More...

	~GlycanClashCheckMover () override=default

void	show (std::ostream &output=std::cout) const override
	Generate string representation of DockGlycansProtocol for debugging purposes. More...

std::string	get_name () const override
	Return the name of the Mover. More...

protocols::moves::MoverOP	clone () const override

protocols::moves::MoverOP	fresh_instance () const override

bool	reinitialize_for_each_job () const override

void	apply (core::pose::Pose &pose) override
	Apply the corresponding protocol to <pose>. More...

Private Types
typedef std::map< std::string, utility::vector1< core::Size > >::const_iterator	branch_it_type

Private Member Functions
void	init ()

core::Real	lj_radius_to_zero_e_radius (core::Real num) const

std::pair< bool, bool >	is_clashing (core::pose::Pose const &pose, core::Size const glycan_resnum, core::Size const other_resnum, core::Size const gx)
	Return a pair of booleans denoting a clash and a soft clash. gx is the glycan atom num. More...

void	calculate_atom_clashes (std::string const &clash_type, const core::pose::Pose &pose, std::string branch, core::Size const &glycan_resnum, utility::vector1< core::Size > other_resnums, std::map< std::string, utility::vector1< core::Size > > &atom_clashes, std::map< std::string, utility::vector1< core::Size > > &soft_atom_clashes)
	Calculate regular and soft clashes. Again, this could be made better. Expecially in regard to pre-computing the soft cutoffs, lj_radius at zero, etc. More...

void	tabulate_individual_data (std::string const &clash_type, std::string const &data_type, core::pose::Pose const &pose, std::map< std::string, utility::vector1< core::Size > > const &data)

core::Size	total_residue_clashes (utility::vector1< core::Size > const &clashes, core::Size at_least_x)

core::Size	total_atom_clashes (utility::vector1< core::Size > const &clashes)

void	report_data (core::pose::Pose &pose)

Private Attributes
utility::vector1< std::string >	branches_
	Starting glycan branches. Strings set from command line. More...

utility::vector1< core::Size >	branch_point_resnums_

utility::vector1< std::string >	chains_
	Chains we are getting info on. More...

utility::vector1< core::Size >	chain_nums_
	Rosetta chain numberings. More...

std::map< std::string, utility::vector1< core::Size > >	branch_residues_
	Branching residue numbers for each branch start. More...

std::map< std::string, utility::vector1< core::Size > >	glycan_glycan_res_atomic_clashes_
	Glycan to Glycan total number of clashes defined by atom-atom fa_rep radii. More...

std::map< std::string, utility::vector1< core::Size > >	glycan_chain_res_atomic_clashes_
	Glycan to chain atomic clashes. More...

std::map< std::string, utility::vector1< core::Size > >	glycan_glycan_res_soft_atomic_clashes_
	Glycan to Glycan total number of clashes defined by atom-atom fa_rep radii. More...

std::map< std::string, utility::vector1< core::Size > >	glycan_chain_res_soft_atomic_clashes_
	Glycan to chain atomic clashes. More...

core::Real	soft_clash_percent_
	When we calculate atom-atom distances using VDW, clash is softly if distance < (atomI_vdw + atomJ_vdw)*(1 - soft_clash) More...

bool	ignore_hydrogens_

bool	ignore_full_res_output_

bool	output_per_glycan_data_

utility::vector1< core::Size >	glycan_resnums_

utility::vector1< core::Size >	chain_resnums_

std::map< std::string, core::Real >	score_data_

std::map< std::string, core::Real >	res_data_

std::map< std::string, utility::vector1< std::string > >	pymol_print_

core::Real	lj_n_

Detailed Description

Class to print out info specific to glycan poses. Will be expanded as needed. Hope to eventually add it as both a mover and a features reporter. Needs to be completely rewritten.

Member Typedef Documentation

◆ branch_it_type

typedef std::map< std::string, utility::vector1< core::Size > >::const_iterator GlycanClashCheckMover::branch_it_type

private

Constructor & Destructor Documentation

◆ GlycanClashCheckMover() [1/2]

GlycanClashCheckMover::GlycanClashCheckMover ( )

inline

Default constructor.

References basic::init().

◆ GlycanClashCheckMover() [2/2]

GlycanClashCheckMover::GlycanClashCheckMover ( GlycanClashCheckMover const & )

default

Copy constructor.

◆ ~GlycanClashCheckMover()

GlycanClashCheckMover::~GlycanClashCheckMover ( )

overridedefault

Member Function Documentation

◆ apply()

void GlycanClashCheckMover::apply ( core::pose::Pose & pose )

inlineoverride

Apply the corresponding protocol to <pose>.

References basic::options::OptionKeys::carbohydrates::carbohydrates, chains, utility::io::oc::cout, create_a3b_hbs::i, beta_nonlocal::pose, myspace::report_data(), predPRE::resnum, utility::to_string(), and basic::options::TR.

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

◆ calculate_atom_clashes()

void GlycanClashCheckMover::calculate_atom_clashes	(	std::string const &	clash_type,
		const core::pose::Pose &	pose,
		std::string	branch,
		core::Size const &	glycan_resnum,
		utility::vector1< core::Size >	other_resnums,
		std::map< std::string, utility::vector1< core::Size > > &	atom_clashes,
		std::map< std::string, utility::vector1< core::Size > > &	soft_atom_clashes
	)

inlineprivate

Calculate regular and soft clashes. Again, this could be made better. Expecially in regard to pre-computing the soft cutoffs, lj_radius at zero, etc.

N Clashes: Number of atoms making at least one clash to other resnum N Bad Clashes: Number of atoms making at least one soft clash to other resnum.

References utility::json_spirit::has_value(), natoms(), beta_nonlocal::pose, basic::options::OptionKeys::carbohydrates::clash_check::soft_clash, and basic::options::TR.

◆ clone()

protocols::moves::MoverOP GlycanClashCheckMover::clone ( ) const

inlineoverride

◆ fresh_instance()

protocols::moves::MoverOP GlycanClashCheckMover::fresh_instance ( ) const

inlineoverride

◆ get_name()

std::string GlycanClashCheckMover::get_name ( ) const

inlineoverride

Return the name of the Mover.

◆ init()

void GlycanClashCheckMover::init ( )

inlineprivate

References basic::options::OptionKeys::carbohydrates::clash_check::check_chains, basic::options::OptionKeys::carbohydrates::clash_check::glycan_branches, basic::options::OptionKeys::carbohydrates::clash_check::ignore_full_res_output, basic::options::OptionKeys::carbohydrates::clash_check::ignore_hydrogens, basic::options::option, basic::options::OptionKeys::carbohydrates::clash_check::output_per_glycan_data, ObjexxFCL::pow(), and basic::options::OptionKeys::carbohydrates::clash_check::soft_clash.

◆ is_clashing()

std::pair< bool, bool > GlycanClashCheckMover::is_clashing	(	core::pose::Pose const &	pose,
		core::Size const	glycan_resnum,
		core::Size const	other_resnum,
		core::Size const	gx
	)

inlineprivate

Return a pair of booleans denoting a clash and a soft clash. gx is the glycan atom num.

References clash(), numeric::xyzVector< T >::distance(), natoms(), beta_nonlocal::pose, and basic::options::OptionKeys::carbohydrates::clash_check::soft_clash.

◆ lj_radius_to_zero_e_radius()

core::Real GlycanClashCheckMover::lj_radius_to_zero_e_radius ( core::Real num ) const

inlineprivate

◆ reinitialize_for_each_job()

bool GlycanClashCheckMover::reinitialize_for_each_job ( ) const

inlineoverride

◆ report_data()

void GlycanClashCheckMover::report_data ( core::pose::Pose & pose )

inlineprivate

References create_a3b_hbs::i, beta_nonlocal::pose, and basic::options::TR.

◆ show()

void GlycanClashCheckMover::show ( std::ostream & output = std::cout ) const

inlineoverride

Generate string representation of DockGlycansProtocol for debugging purposes.

References bin_torsions::output, and show().

Referenced by pyrosetta.distributed.viewer.core.Viewer::__call__().

◆ tabulate_individual_data()

void GlycanClashCheckMover::tabulate_individual_data	(	std::string const &	clash_type,
		std::string const &	data_type,
		core::pose::Pose const &	pose,
		std::map< std::string, utility::vector1< core::Size > > const &	data
	)

inlineprivate

References predPRE::chain, data, beta_nonlocal::pose, create_a3b_hbs::prefix, predPRE::resnum, and utility::to_string().

◆ total_atom_clashes()

core::Size GlycanClashCheckMover::total_atom_clashes ( utility::vector1< core::Size > const & clashes )

inlineprivate

References predPRE::resnum.

◆ total_residue_clashes()

core::Size GlycanClashCheckMover::total_residue_clashes	(	utility::vector1< core::Size > const &	clashes,
		core::Size	at_least_x
	)

inlineprivate

References predPRE::resnum.

Member Data Documentation

◆ branch_point_resnums_

utility::vector1< core::Size > GlycanClashCheckMover::branch_point_resnums_

private

◆ branch_residues_

std::map< std::string, utility::vector1< core::Size > > GlycanClashCheckMover::branch_residues_

private

Branching residue numbers for each branch start.

◆ branches_

utility::vector1< std::string > GlycanClashCheckMover::branches_

private

Starting glycan branches. Strings set from command line.

◆ chain_nums_

utility::vector1< core::Size > GlycanClashCheckMover::chain_nums_

private

Rosetta chain numberings.

◆ chain_resnums_

utility::vector1< core::Size > GlycanClashCheckMover::chain_resnums_

private

◆ chains_

utility::vector1< std::string > GlycanClashCheckMover::chains_

private

Chains we are getting info on.

◆ glycan_chain_res_atomic_clashes_

std::map< std::string, utility::vector1< core::Size > > GlycanClashCheckMover::glycan_chain_res_atomic_clashes_

private

Glycan to chain atomic clashes.

◆ glycan_chain_res_soft_atomic_clashes_

std::map< std::string, utility::vector1< core::Size > > GlycanClashCheckMover::glycan_chain_res_soft_atomic_clashes_

private

Glycan to chain atomic clashes.

◆ glycan_glycan_res_atomic_clashes_

std::map< std::string, utility::vector1< core::Size > > GlycanClashCheckMover::glycan_glycan_res_atomic_clashes_

private

Glycan to Glycan total number of clashes defined by atom-atom fa_rep radii.

◆ glycan_glycan_res_soft_atomic_clashes_

std::map< std::string, utility::vector1< core::Size > > GlycanClashCheckMover::glycan_glycan_res_soft_atomic_clashes_

private

Glycan to Glycan total number of clashes defined by atom-atom fa_rep radii.

◆ glycan_resnums_

utility::vector1< core::Size > GlycanClashCheckMover::glycan_resnums_

private

◆ ignore_full_res_output_

bool GlycanClashCheckMover::ignore_full_res_output_

private

◆ ignore_hydrogens_

bool GlycanClashCheckMover::ignore_hydrogens_

private

◆ lj_n_

core::Real GlycanClashCheckMover::lj_n_

private

◆ output_per_glycan_data_

bool GlycanClashCheckMover::output_per_glycan_data_

private

◆ pymol_print_

std::map< std::string, utility::vector1< std::string > > GlycanClashCheckMover::pymol_print_

private

◆ res_data_

std::map< std::string, core::Real > GlycanClashCheckMover::res_data_

private

◆ score_data_

std::map< std::string, core::Real > GlycanClashCheckMover::score_data_

private

◆ soft_clash_percent_

core::Real GlycanClashCheckMover::soft_clash_percent_

private

When we calculate atom-atom distances using VDW, clash is softly if distance < (atomI_vdw + atomJ_vdw)*(1 - soft_clash)

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

src/apps/public/carbohydrates/glycan_clash_check.cc

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ branch_it_type

Constructor & Destructor Documentation

◆ GlycanClashCheckMover() [1/2]

◆ GlycanClashCheckMover() [2/2]

◆ ~GlycanClashCheckMover()

Member Function Documentation

◆ apply()

◆ calculate_atom_clashes()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ init()

◆ is_clashing()

◆ lj_radius_to_zero_e_radius()

◆ reinitialize_for_each_job()

◆ report_data()

◆ show()

◆ tabulate_individual_data()

◆ total_atom_clashes()

◆ total_residue_clashes()

Member Data Documentation

◆ branch_point_resnums_

◆ branch_residues_

◆ branches_

◆ chain_nums_

◆ chain_resnums_

◆ chains_

◆ glycan_chain_res_atomic_clashes_

◆ glycan_chain_res_soft_atomic_clashes_

◆ glycan_glycan_res_atomic_clashes_

◆ glycan_glycan_res_soft_atomic_clashes_

◆ glycan_resnums_

◆ ignore_full_res_output_

◆ ignore_hydrogens_

◆ lj_n_

◆ output_per_glycan_data_

◆ pymol_print_

◆ res_data_

◆ score_data_

◆ soft_clash_percent_