Rosetta  2019.47
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GlycanClashCheckMover Class Reference

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:
Inheritance graph
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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, boolis_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

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

Constructor & Destructor Documentation

GlycanClashCheckMover::GlycanClashCheckMover ( )
inline

Default constructor.

References basic::init().

GlycanClashCheckMover::GlycanClashCheckMover ( GlycanClashCheckMover const &  )
default

Copy constructor.

GlycanClashCheckMover::~GlycanClashCheckMover ( )
overridedefault

Member Function Documentation

void GlycanClashCheckMover::apply ( core::pose::Pose pose)
inlineoverride
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(), ObjexxFCL::index(), basic::options::OptionKeys::carbohydrates::clash_check::soft_clash, and basic::options::TR.

protocols::moves::MoverOP GlycanClashCheckMover::clone ( ) const
inlineoverride
protocols::moves::MoverOP GlycanClashCheckMover::fresh_instance ( ) const
inlineoverride
std::string GlycanClashCheckMover::get_name ( ) const
inlineoverride

Return the name of the Mover.

References DRRAFTER::type.

void GlycanClashCheckMover::init ( )
inlineprivate
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 numeric::xyzVector< typename >::distance(), and basic::options::OptionKeys::carbohydrates::clash_check::soft_clash.

core::Real GlycanClashCheckMover::lj_radius_to_zero_e_radius ( core::Real  num) const
inlineprivate
bool GlycanClashCheckMover::reinitialize_for_each_job ( ) const
inlineoverride
void GlycanClashCheckMover::report_data ( core::pose::Pose pose)
inlineprivate

References basic::options::TR.

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

Generate string representation of DockGlycansProtocol for debugging purposes.

References basic::options::OptionKeys::cp::output, and show().

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

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

Member Data Documentation

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

Branching residue numbers for each branch start.

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

Starting glycan branches. Strings set from command line.

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

Rosetta chain numberings.

utility::vector1< core::Size > GlycanClashCheckMover::chain_resnums_
private
utility::vector1< std::string > GlycanClashCheckMover::chains_
private

Chains we are getting info on.

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

Glycan to chain atomic clashes.

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

Glycan to chain 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.

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.

utility::vector1< core::Size > GlycanClashCheckMover::glycan_resnums_
private
bool GlycanClashCheckMover::ignore_full_res_output_
private
bool GlycanClashCheckMover::ignore_hydrogens_
private
core::Real GlycanClashCheckMover::lj_n_
private
bool GlycanClashCheckMover::output_per_glycan_data_
private
std::map< std::string, utility::vector1< std::string > > GlycanClashCheckMover::pymol_print_
private
std::map< std::string, core::Real > GlycanClashCheckMover::res_data_
private
std::map< std::string, core::Real > GlycanClashCheckMover::score_data_
private
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: