Holds flags, options, and pose variables for the Glycosylation Protocol. More...

#include <GlycopeptideDockingFlags.hh>

Inheritance diagram for protocols::glycopeptide_docking::GlycopeptideDockingFlags:

Public Member Functions
	GlycopeptideDockingFlags ()
	Constructor sets user options. More...

GlycopeptideDockingFlagsOP	clone () const

core::Size	first_residue_substrate () const
	Get index (internal numbering) of the first residue of the substrate. More...

core::Size	last_residue_substrate () const
	Get index (internal numbering) of the last residue of the substrate. More...

core::Size	anchor_residue_substrate () const
	Get index (internal numbering) of the fold tree anchor (fold tree goes out in all direction from this residue). Only important when fold tree is specified as 'outward'. More...

core::Size	glycosylation_residue_substrate () const

core::Size	jump_num_substrate () const
	Get jump number of the substrate. More...

core::Size	first_residue_enzyme () const
	Get first residue of the enzyme. More...

core::Size	last_residue_enzyme () const
	Get last residue of the enzyme. More...

void	setup_from_options ()
	Set variables from specified command line options. More...

void	set_enzyme_chain (core::pose::Pose const &pose)
	Set enzyme chain. More...

void	set_anchor_residue (core::pose::Pose const &pose, std::string const &special_residue)
	Set anchor residue. Residue from which the foldtree emnates outwards when fold tree type is set as "outward". More...

void	set_anchor_residue (core::Size in)
	Set anchor residue with internal numbering. More...

core::Size	get_anchor_residue ()
	Get anchor residue with internal numbering. More...

void	set_glycosylation_residue (core::pose::Pose const &pose, std::string const &special_residue)
	Set glycosylation residue from pose and pdb numbering. More...

void	set_glycosylation_residue (core::Size in)
	Set glycosylation residue with internal numbering. More...

core::Size	get_glycosylation_residue ()
	Get glycosylation residue with internal numbering. More...

void	set_substrate_chain (core::pose::Pose const &pose)
	Set substrate chain. More...

void	show () const
	Show set options. More...

void	set_score_only (bool in)
	Set whether to run in score_only mode. Protocol is not run. Only score is evaluated with distance, rmsd and interaction energy metrics. More...

bool	score_only ()
	Get whether to run in sampling or score-only mode. More...

bool	debug_pdbs ()
	Get whether to output interim debug pdbs during low and high resolution cycles. More...

void	set_debug_pdbs (bool in)
	Set whether to output interim debug pdbs during low and high resolution cycles. More...

void	set_interface_distance (core::Real distance)
	Set interface distance. More...

core::Real	get_interface_distance ()
	Get interface distance. More...

void	set_glycosylation_refinement (bool low, bool high)
	Set low and high res refinement options. More...

bool	low_res_refinement ()
	Get whether low refinement is on. More...

bool	high_res_refinement ()
	Get whether high refinement is on. More...

core::Size	high_res_outer_cycles ()
	Get how many outer MC cycles to run for high-res refinement. More...

core::Size	low_res_outer_cycles ()
	Get how many outer MC cycles to run for low-res refinement. More...

core::Size	low_res_inner_cycles ()
	Get how many inner MC cycles to run for low-res refinement. More...

core::Size	get_sugar_donor ()
	Get residue index of sugar donor. More...

void	set_sugar_donor (core::Size in)
	Set residue index of sugar donor. More...

std::string	substrate_type ()
	Get substrate type: Only 'peptide' type is supported for now. More...

void	set_substrate_type (std::string const &in)
	Set substrate type: Only 'peptide' type is supported for now TODO: lipids - if there are interesting applications. More...

std::string	get_upstream_chain ()
	Get upstream chain for 'outward' fold tree. More...

std::string	get_downstream_chain ()
	Get downstream chain for 'outward' fold tree. More...

void	set_upstream_chain (std::string const &chain)
	Set upstream chain for 'outward' fold tree. More...

void	set_downstream_chain (std::string const &chain)
	Set downstream chain for 'outward' fold tree. More...

void	set_fold_tree_type (std::string const &in)
	Set fold tree type: outward OR docking. More...

std::string	tree_type ()
	Get fold tree type. More...

void	set_interface_moves (core::Size n)
	Set how frequently the interface must be sampled: Eg. every 3rd cycle. More...

core::Size	get_interface_moves ()
	Get how frequently the interface is sampled. More...

void	set_backbone_moves (core::Size n)
	Set cycles for backbone moves in high resolution. More...

core::Size	get_backbone_moves ()
	Get cycles for backbone moves in high resolution. More...

void	set_anchor_repacking (bool in)
	On anchor residue sidechain repacking on or off. More...

bool	pack_anchor ()
	Get whether anchor repacking on or off. More...

void	set_allow_glycan_torsion_moves (bool in)
	Set whether to sample glycan torsional dofs with glycan sampler. More...

bool	get_allow_glycan_torsion_moves ()
	Get whether to sample glycan torsional dofs with glycan sampler. More...

void	set_constraints_file (std::string const &filename)
	Set name of constraints file Useful for setting constraints to preserve any catalytic motifs. More...

std::string	get_constraints_file ()
	Get name of constraints file. More...

void	set_randomize_substrate_torsions (bool in)
	Set whether to randomize initial torsions. More...

bool	randomize_substrate_torsions ()
	Get whether to randomize initial torsions. More...

bool	enable_backbone_moves_substrate ()
	Get whether to sample substrate backbone TODO: Add similar option for enzyme. More...

void	set_backbone_moves_substrate (bool in)
	Set whether to sample substrate backbone. More...

bool	additional_metrics ()
	Get whether to output additional distance metrics to scorefile. More...

void	enable_additional_metrics (bool in)
	Enable writing of additional metrics to scorefile. More...

void	set_residues_to_preglycosylate (utility::vector1< core::Size > in)
	Set residue indices (int numbering) to pre-glycosylate before starting sampling. More...

utility::vector1< core::Size >	get_residues_to_preglycosylate ()
	Get residue indices (int numbering) to pre-glycosylate before starting sampling. More...

void	set_sugars_to_preglycosylate (utility::vector1< std::string > in)
	Set names of sugars for pre-glycosylate before starting sampling #sugar names must match #residue indices for preglycosylation. More...

utility::vector1< std::string >	get_sugars_to_preglycosylate ()
	Get names of sugars for pre-glycosylate before starting sampling #sugar names must match #residue indices for preglycosylation. More...

Private Member Functions
core::Size	get_resnum (core::pose::Pose const &pose, std::string const &special_residue)
	Function to get index of anchor, donor and glycosylation residues from specified string. More...

Private Attributes
core::Size	first_residue_substrate_

core::Size	last_residue_substrate_

core::Size	anchor_residue_substrate_

core::Size	residue_to_glycosylate_

core::Size	jump_num_substrate_

core::Size	first_residue_enzyme_

core::Size	last_residue_enzyme_

bool	glycosylation_high_res_refinement_ =true

bool	glycosylation_low_res_refinement_ =true

std::string	constraints_ =""

core::Size	high_res_outer_cycles_ =10

core::Size	low_res_outer_cycles_ =30

core::Size	low_res_inner_cycles_ =50

std::string	substrate_type_ ="peptide"

std::string	tree_type_ ="docking"

bool	randomize_substrate_torsions_ =false

bool	enable_backbone_moves_pp_ =true

std::string	downstream_chains_ =""

std::string	upstream_chains_ =""

bool	prevent_anchor_repacking_ =true

core::Size	donor_ =1

bool	debug_pdbs_ =false

core::Size	nevery_interface_moves_ =3

core::Size	ntotal_backbone_moves_ =30

bool	allow_glycan_torsion_moves_ =false

core::Real	interface_distance_ =8.0

bool	score_only_ =false

bool	additional_metrics_ =false

utility::vector1< core::Size >	preglycosylate_residues_

utility::vector1< std::string >	preglycosylate_sugars_

Detailed Description

Holds flags, options, and pose variables for the Glycosylation Protocol.

Constructor & Destructor Documentation

◆ GlycopeptideDockingFlags()

protocols::glycopeptide_docking::GlycopeptideDockingFlags::GlycopeptideDockingFlags ( )

Constructor sets user options.

Member Function Documentation

◆ additional_metrics()

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::additional_metrics ( )

inline

Get whether to output additional distance metrics to scorefile.

Get the same output as publication Mahajan et. al. 2020 Biorxiv

References additional_metrics_.

◆ anchor_residue_substrate()

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::anchor_residue_substrate ( ) const

Get index (internal numbering) of the fold tree anchor (fold tree goes out in all direction from this residue). Only important when fold tree is specified as 'outward'.

◆ clone()

GlycopeptideDockingFlagsOP protocols::glycopeptide_docking::GlycopeptideDockingFlags::clone ( ) const

◆ debug_pdbs()

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::debug_pdbs ( )

inline

Get whether to output interim debug pdbs during low and high resolution cycles.

References debug_pdbs_.

◆ enable_additional_metrics()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::enable_additional_metrics ( bool in )

inline

Enable writing of additional metrics to scorefile.

References additional_metrics_, and core::conformation::membrane::in.

◆ enable_backbone_moves_substrate()

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::enable_backbone_moves_substrate ( )

inline

Get whether to sample substrate backbone TODO: Add similar option for enzyme.

References enable_backbone_moves_pp_.

◆ first_residue_enzyme()

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::first_residue_enzyme ( ) const

Get first residue of the enzyme.

◆ first_residue_substrate()

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::first_residue_substrate ( ) const

Get index (internal numbering) of the first residue of the substrate.

◆ get_allow_glycan_torsion_moves()

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_allow_glycan_torsion_moves ( )

inline

Get whether to sample glycan torsional dofs with glycan sampler.

References allow_glycan_torsion_moves_.

◆ get_anchor_residue()

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_anchor_residue ( )

inline

Get anchor residue with internal numbering.

References anchor_residue_substrate_.

◆ get_backbone_moves()

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_backbone_moves ( )

inline

Get cycles for backbone moves in high resolution.

References ntotal_backbone_moves_.

◆ get_constraints_file()

std::string protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_constraints_file ( )

inline

Get name of constraints file.

References constraints_.

◆ get_downstream_chain()

std::string protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_downstream_chain ( )

inline

Get downstream chain for 'outward' fold tree.

References downstream_chains_.

◆ get_glycosylation_residue()

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_glycosylation_residue ( )

inline

Get glycosylation residue with internal numbering.

References residue_to_glycosylate_.

◆ get_interface_distance()

core::Real protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_interface_distance ( )

inline

Get interface distance.

References interface_distance_.

◆ get_interface_moves()

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_interface_moves ( )

inline

Get how frequently the interface is sampled.

References nevery_interface_moves_.

◆ get_residues_to_preglycosylate()

utility::vector1<core::Size> protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_residues_to_preglycosylate ( )

inline

Get residue indices (int numbering) to pre-glycosylate before starting sampling.

References preglycosylate_residues_.

◆ get_resnum()

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_resnum	(	core::pose::Pose const &	pose,
		std::string const &	special_residue
	)

private

Function to get index of anchor, donor and glycosylation residues from specified string.

@Get residue from pose

References core::pose::Pose::pdb_info().

◆ get_sugar_donor()

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_sugar_donor ( )

inline

Get residue index of sugar donor.

References donor_.

◆ get_sugars_to_preglycosylate()

utility::vector1<std::string> protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_sugars_to_preglycosylate ( )

inline

Get names of sugars for pre-glycosylate before starting sampling #sugar names must match #residue indices for preglycosylation.

References preglycosylate_sugars_.

◆ get_upstream_chain()

std::string protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_upstream_chain ( )

inline

Get upstream chain for 'outward' fold tree.

References upstream_chains_.

◆ glycosylation_residue_substrate()

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::glycosylation_residue_substrate ( ) const

Get index (internal numbering) of the site of glycosylation under investigation. (There may be other glycosylated residues on the peptide)

◆ high_res_outer_cycles()

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::high_res_outer_cycles ( )

inline

Get how many outer MC cycles to run for high-res refinement.

References high_res_outer_cycles_.

◆ high_res_refinement()

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::high_res_refinement ( )

inline

Get whether high refinement is on.

References glycosylation_high_res_refinement_.

◆ jump_num_substrate()

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::jump_num_substrate ( ) const

Get jump number of the substrate.

◆ last_residue_enzyme()

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::last_residue_enzyme ( ) const

Get last residue of the enzyme.

◆ last_residue_substrate()

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::last_residue_substrate ( ) const

Get index (internal numbering) of the last residue of the substrate.

◆ low_res_inner_cycles()

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::low_res_inner_cycles ( )

inline

Get how many inner MC cycles to run for low-res refinement.

References low_res_inner_cycles_.

◆ low_res_outer_cycles()

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::low_res_outer_cycles ( )

inline

Get how many outer MC cycles to run for low-res refinement.

References low_res_outer_cycles_.

◆ low_res_refinement()

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::low_res_refinement ( )

inline

Get whether low refinement is on.

References glycosylation_low_res_refinement_.

◆ pack_anchor()

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::pack_anchor ( )

inline

Get whether anchor repacking on or off.

References prevent_anchor_repacking_.

◆ randomize_substrate_torsions()

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::randomize_substrate_torsions ( )

inline

Get whether to randomize initial torsions.

References randomize_substrate_torsions_.

◆ score_only()

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::score_only ( )

inline

Get whether to run in sampling or score-only mode.

References score_only_.

◆ set_allow_glycan_torsion_moves()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_allow_glycan_torsion_moves ( bool in )

inline

Set whether to sample glycan torsional dofs with glycan sampler.

References allow_glycan_torsion_moves_, and core::conformation::membrane::in.

◆ set_anchor_repacking()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_anchor_repacking ( bool in )

inline

On anchor residue sidechain repacking on or off.

References core::conformation::membrane::in, and prevent_anchor_repacking_.

◆ set_anchor_residue() [1/2]

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_anchor_residue	(	core::pose::Pose const &	pose,
		std::string const &	special_residue
	)

Set anchor residue. Residue from which the foldtree emnates outwards when fold tree type is set as "outward".

@Set anchor or residue_to_glycosylate residue/s from command line or script options.

◆ set_anchor_residue() [2/2]

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_anchor_residue ( core::Size in )

inline

Set anchor residue with internal numbering.

References anchor_residue_substrate_, and core::conformation::membrane::in.

◆ set_backbone_moves()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_backbone_moves ( core::Size n )

inline

Set cycles for backbone moves in high resolution.

References ntotal_backbone_moves_.

◆ set_backbone_moves_substrate()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_backbone_moves_substrate ( bool in )

inline

Set whether to sample substrate backbone.

References enable_backbone_moves_pp_, and core::conformation::membrane::in.

◆ set_constraints_file()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_constraints_file ( std::string const & filename )

inline

Set name of constraints file Useful for setting constraints to preserve any catalytic motifs.

References constraints_, and protocols::abinitio::filename().

◆ set_debug_pdbs()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_debug_pdbs ( bool in )

inline

Set whether to output interim debug pdbs during low and high resolution cycles.

References debug_pdbs_, and core::conformation::membrane::in.

◆ set_downstream_chain()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_downstream_chain ( std::string const & chain )

inline

Set downstream chain for 'outward' fold tree.

References downstream_chains_.

◆ set_enzyme_chain()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_enzyme_chain ( core::pose::Pose const & pose )

Set enzyme chain.

Specify the enzyme chain from pose information.

References core::conformation::Conformation::chain_endings(), and core::pose::Pose::conformation().

◆ set_fold_tree_type()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_fold_tree_type ( std::string const & in )

inline

Set fold tree type: outward OR docking.

References core::conformation::membrane::in, and tree_type_.

◆ set_glycosylation_refinement()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_glycosylation_refinement	(	bool	low,
		bool	high
	)

inline

Set low and high res refinement options.

References glycosylation_high_res_refinement_.

◆ set_glycosylation_residue() [1/2]

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_glycosylation_residue	(	core::pose::Pose const &	pose,
		std::string const &	special_residue
	)

Set glycosylation residue from pose and pdb numbering.

@Set anchor or residue_to_glycosylate residue/s from command line or script options.

◆ set_glycosylation_residue() [2/2]

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_glycosylation_residue ( core::Size in )

inline

Set glycosylation residue with internal numbering.

References core::conformation::membrane::in, and residue_to_glycosylate_.

◆ set_interface_distance()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_interface_distance ( core::Real distance )

inline

Set interface distance.

References core::kinematics::distance(), and interface_distance_.

◆ set_interface_moves()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_interface_moves ( core::Size n )

inline

Set how frequently the interface must be sampled: Eg. every 3rd cycle.

References nevery_interface_moves_.

◆ set_randomize_substrate_torsions()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_randomize_substrate_torsions ( bool in )

inline

Set whether to randomize initial torsions.

References core::conformation::membrane::in, and randomize_substrate_torsions_.

◆ set_residues_to_preglycosylate()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_residues_to_preglycosylate ( utility::vector1< core::Size > in )

inline

Set residue indices (int numbering) to pre-glycosylate before starting sampling.

References core::conformation::membrane::in, and preglycosylate_residues_.

◆ set_score_only()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_score_only ( bool in )

inline

Set whether to run in score_only mode. Protocol is not run. Only score is evaluated with distance, rmsd and interaction energy metrics.

References core::conformation::membrane::in, and score_only_.

◆ set_substrate_chain()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_substrate_chain ( core::pose::Pose const & pose )

Set substrate chain.

@ brief Specify the substrate chain from pose information

References core::conformation::Residue::chain(), core::pose::chain_end_res(), core::conformation::Conformation::chain_endings(), core::pose::Pose::conformation(), core::conformation::Residue::connected_residue_at_lower(), protocols::loops::cut_point, core::pose::get_resnum_list_ordered(), core::conformation::Residue::has_lower_connect(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and TR().

◆ set_substrate_type()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_substrate_type ( std::string const & in )

inline

Set substrate type: Only 'peptide' type is supported for now TODO: lipids - if there are interesting applications.

References core::conformation::membrane::in, and substrate_type_.

◆ set_sugar_donor()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_sugar_donor ( core::Size in )

inline

Set residue index of sugar donor.

References donor_, and core::conformation::membrane::in.

◆ set_sugars_to_preglycosylate()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_sugars_to_preglycosylate ( utility::vector1< std::string > in )

inline

Set names of sugars for pre-glycosylate before starting sampling #sugar names must match #residue indices for preglycosylation.

References core::conformation::membrane::in, and preglycosylate_sugars_.

◆ set_upstream_chain()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_upstream_chain ( std::string const & chain )

inline

Set upstream chain for 'outward' fold tree.

References upstream_chains_.

◆ setup_from_options()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::setup_from_options ( )

Set variables from specified command line options.

◆ show()

void protocols::glycopeptide_docking::GlycopeptideDockingFlags::show ( ) const

Show set options.

References TR().

◆ substrate_type()

std::string protocols::glycopeptide_docking::GlycopeptideDockingFlags::substrate_type ( )

inline

Get substrate type: Only 'peptide' type is supported for now.

References substrate_type_.

◆ tree_type()

std::string protocols::glycopeptide_docking::GlycopeptideDockingFlags::tree_type ( )

inline

Get fold tree type.

References tree_type_.

Member Data Documentation

◆ additional_metrics_

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::additional_metrics_ =false

private

Referenced by additional_metrics(), and enable_additional_metrics().

◆ allow_glycan_torsion_moves_

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::allow_glycan_torsion_moves_ =false

private

Referenced by get_allow_glycan_torsion_moves(), and set_allow_glycan_torsion_moves().

◆ anchor_residue_substrate_

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::anchor_residue_substrate_

private

Referenced by get_anchor_residue(), and set_anchor_residue().

◆ constraints_

std::string protocols::glycopeptide_docking::GlycopeptideDockingFlags::constraints_ =""

private

Referenced by get_constraints_file(), and set_constraints_file().

◆ debug_pdbs_

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::debug_pdbs_ =false

private

Referenced by debug_pdbs(), and set_debug_pdbs().

◆ donor_

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::donor_ =1

private

Referenced by get_sugar_donor(), and set_sugar_donor().

◆ downstream_chains_

std::string protocols::glycopeptide_docking::GlycopeptideDockingFlags::downstream_chains_ =""

private

Referenced by get_downstream_chain(), and set_downstream_chain().

◆ enable_backbone_moves_pp_

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::enable_backbone_moves_pp_ =true

private

Referenced by enable_backbone_moves_substrate(), and set_backbone_moves_substrate().

◆ first_residue_enzyme_

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::first_residue_enzyme_

private

◆ first_residue_substrate_

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::first_residue_substrate_

private

◆ glycosylation_high_res_refinement_

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::glycosylation_high_res_refinement_ =true

private

Referenced by high_res_refinement(), and set_glycosylation_refinement().

◆ glycosylation_low_res_refinement_

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::glycosylation_low_res_refinement_ =true

private

Referenced by low_res_refinement().

◆ high_res_outer_cycles_

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::high_res_outer_cycles_ =10

private

Referenced by high_res_outer_cycles().

◆ interface_distance_

core::Real protocols::glycopeptide_docking::GlycopeptideDockingFlags::interface_distance_ =8.0

private

Referenced by get_interface_distance(), and set_interface_distance().

◆ jump_num_substrate_

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::jump_num_substrate_

private

◆ last_residue_enzyme_

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::last_residue_enzyme_

private

◆ last_residue_substrate_

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::last_residue_substrate_

private

◆ low_res_inner_cycles_

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::low_res_inner_cycles_ =50

private

Referenced by low_res_inner_cycles().

◆ low_res_outer_cycles_

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::low_res_outer_cycles_ =30

private

Referenced by low_res_outer_cycles().

◆ nevery_interface_moves_

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::nevery_interface_moves_ =3

private

Referenced by get_interface_moves(), and set_interface_moves().

◆ ntotal_backbone_moves_

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::ntotal_backbone_moves_ =30

private

Referenced by get_backbone_moves(), and set_backbone_moves().

◆ preglycosylate_residues_

utility::vector1<core::Size> protocols::glycopeptide_docking::GlycopeptideDockingFlags::preglycosylate_residues_

private

Referenced by get_residues_to_preglycosylate(), and set_residues_to_preglycosylate().

◆ preglycosylate_sugars_

utility::vector1<std::string> protocols::glycopeptide_docking::GlycopeptideDockingFlags::preglycosylate_sugars_

private

Referenced by get_sugars_to_preglycosylate(), and set_sugars_to_preglycosylate().

◆ prevent_anchor_repacking_

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::prevent_anchor_repacking_ =true

private

Referenced by pack_anchor(), and set_anchor_repacking().

◆ randomize_substrate_torsions_

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::randomize_substrate_torsions_ =false

private

Referenced by randomize_substrate_torsions(), and set_randomize_substrate_torsions().

◆ residue_to_glycosylate_

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::residue_to_glycosylate_

private

Referenced by get_glycosylation_residue(), and set_glycosylation_residue().

◆ score_only_

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::score_only_ =false

private

Referenced by score_only(), and set_score_only().

◆ substrate_type_

std::string protocols::glycopeptide_docking::GlycopeptideDockingFlags::substrate_type_ ="peptide"

private

Referenced by set_substrate_type(), and substrate_type().

◆ tree_type_

std::string protocols::glycopeptide_docking::GlycopeptideDockingFlags::tree_type_ ="docking"

private

Referenced by set_fold_tree_type(), and tree_type().

◆ upstream_chains_

std::string protocols::glycopeptide_docking::GlycopeptideDockingFlags::upstream_chains_ =""

private

Referenced by get_upstream_chain(), and set_upstream_chain().

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

src/protocols/glycopeptide_docking/GlycopeptideDockingFlags.hh
src/protocols/glycopeptide_docking/GlycopeptideDockingFlags.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ GlycopeptideDockingFlags()

Member Function Documentation

◆ additional_metrics()

◆ anchor_residue_substrate()

◆ clone()

◆ debug_pdbs()

◆ enable_additional_metrics()

◆ enable_backbone_moves_substrate()

◆ first_residue_enzyme()

◆ first_residue_substrate()

◆ get_allow_glycan_torsion_moves()

◆ get_anchor_residue()

◆ get_backbone_moves()

◆ get_constraints_file()

◆ get_downstream_chain()

◆ get_glycosylation_residue()

◆ get_interface_distance()

◆ get_interface_moves()

◆ get_residues_to_preglycosylate()

◆ get_resnum()

◆ get_sugar_donor()

◆ get_sugars_to_preglycosylate()

◆ get_upstream_chain()

◆ glycosylation_residue_substrate()

◆ high_res_outer_cycles()

◆ high_res_refinement()

◆ jump_num_substrate()

◆ last_residue_enzyme()

◆ last_residue_substrate()

◆ low_res_inner_cycles()

◆ low_res_outer_cycles()

◆ low_res_refinement()

◆ pack_anchor()

◆ randomize_substrate_torsions()

◆ score_only()

◆ set_allow_glycan_torsion_moves()

◆ set_anchor_repacking()

◆ set_anchor_residue() [1/2]

◆ set_anchor_residue() [2/2]

◆ set_backbone_moves()

◆ set_backbone_moves_substrate()

◆ set_constraints_file()

◆ set_debug_pdbs()

◆ set_downstream_chain()

◆ set_enzyme_chain()

◆ set_fold_tree_type()

◆ set_glycosylation_refinement()

◆ set_glycosylation_residue() [1/2]

◆ set_glycosylation_residue() [2/2]

◆ set_interface_distance()

◆ set_interface_moves()

◆ set_randomize_substrate_torsions()

◆ set_residues_to_preglycosylate()

◆ set_score_only()

◆ set_substrate_chain()

◆ set_substrate_type()

◆ set_sugar_donor()

◆ set_sugars_to_preglycosylate()

◆ set_upstream_chain()

◆ setup_from_options()

◆ show()

◆ substrate_type()

◆ tree_type()

Member Data Documentation

◆ additional_metrics_

◆ allow_glycan_torsion_moves_

◆ anchor_residue_substrate_

◆ constraints_

◆ debug_pdbs_

◆ donor_

◆ downstream_chains_

◆ enable_backbone_moves_pp_

◆ first_residue_enzyme_

◆ first_residue_substrate_

◆ glycosylation_high_res_refinement_