Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::glycopeptide_docking::GlycopeptideDockingFlags Class Reference

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

#include <GlycopeptideDockingFlags.hh>

Inheritance diagram for protocols::glycopeptide_docking::GlycopeptideDockingFlags:
Inheritance graph
[legend]

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::Sizeget_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::Sizepreglycosylate_residues_
 
utility::vector1< std::string > preglycosylate_sugars_
 

Detailed Description

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

Constructor & Destructor Documentation

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

Constructor sets user options.

Member Function Documentation

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_.

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'.

GlycopeptideDockingFlagsOP protocols::glycopeptide_docking::GlycopeptideDockingFlags::clone ( ) const
bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::debug_pdbs ( )
inline

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

References debug_pdbs_.

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.

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_.

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

Get first residue of the enzyme.

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

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

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_.

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

Get anchor residue with internal numbering.

References anchor_residue_substrate_.

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

Get cycles for backbone moves in high resolution.

References ntotal_backbone_moves_.

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

Get name of constraints file.

References constraints_.

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

Get downstream chain for 'outward' fold tree.

References downstream_chains_.

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

Get glycosylation residue with internal numbering.

References residue_to_glycosylate_.

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

Get interface distance.

References interface_distance_.

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

Get how frequently the interface is sampled.

References nevery_interface_moves_.

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_.

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.

residue from pose

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

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

Get residue index of sugar donor.

References donor_.

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_.

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

Get upstream chain for 'outward' fold tree.

References upstream_chains_.

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)

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_.

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

Get whether high refinement is on.

References glycosylation_high_res_refinement_.

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

Get jump number of the substrate.

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

Get last residue of the enzyme.

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

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

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_.

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_.

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

Get whether low refinement is on.

References glycosylation_low_res_refinement_.

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

Get whether anchor repacking on or off.

References prevent_anchor_repacking_.

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

Get whether to randomize initial torsions.

References randomize_substrate_torsions_.

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

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

References score_only_.

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.

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_.

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".

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

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.

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

Set cycles for backbone moves in high resolution.

References ntotal_backbone_moves_.

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.

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().

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.

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

Set downstream chain for 'outward' fold tree.

References downstream_chains_.

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().

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_.

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_.

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.

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

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_.

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

Set interface distance.

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

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_.

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_.

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_.

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_.

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

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.

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_.

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

Set upstream chain for 'outward' fold tree.

References upstream_chains_.

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

Set variables from specified command line options.

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

Show set options.

References TR().

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

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

References substrate_type_.

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

Get fold tree type.

References tree_type_.

Member Data Documentation

bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::additional_metrics_ =false
private
bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::allow_glycan_torsion_moves_ =false
private
core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::anchor_residue_substrate_
private
std::string protocols::glycopeptide_docking::GlycopeptideDockingFlags::constraints_ =""
private
bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::debug_pdbs_ =false
private

Referenced by debug_pdbs(), and set_debug_pdbs().

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

Referenced by get_sugar_donor(), and set_sugar_donor().

std::string protocols::glycopeptide_docking::GlycopeptideDockingFlags::downstream_chains_ =""
private
bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::enable_backbone_moves_pp_ =true
private
core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::first_residue_enzyme_
private
core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::first_residue_substrate_
private
bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::glycosylation_high_res_refinement_ =true
private
bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::glycosylation_low_res_refinement_ =true
private

Referenced by low_res_refinement().

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

Referenced by high_res_outer_cycles().

core::Real protocols::glycopeptide_docking::GlycopeptideDockingFlags::interface_distance_ =8.0
private
core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::jump_num_substrate_
private
core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::last_residue_enzyme_
private
core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::last_residue_substrate_
private
core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::low_res_inner_cycles_ =50
private

Referenced by low_res_inner_cycles().

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

Referenced by low_res_outer_cycles().

core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::nevery_interface_moves_ =3
private
core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::ntotal_backbone_moves_ =30
private
utility::vector1<core::Size> protocols::glycopeptide_docking::GlycopeptideDockingFlags::preglycosylate_residues_
private
utility::vector1<std::string> protocols::glycopeptide_docking::GlycopeptideDockingFlags::preglycosylate_sugars_
private
bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::prevent_anchor_repacking_ =true
private
bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::randomize_substrate_torsions_ =false
private
core::Size protocols::glycopeptide_docking::GlycopeptideDockingFlags::residue_to_glycosylate_
private
bool protocols::glycopeptide_docking::GlycopeptideDockingFlags::score_only_ =false
private

Referenced by score_only(), and set_score_only().

std::string protocols::glycopeptide_docking::GlycopeptideDockingFlags::substrate_type_ ="peptide"
private
std::string protocols::glycopeptide_docking::GlycopeptideDockingFlags::tree_type_ ="docking"
private

Referenced by set_fold_tree_type(), and tree_type().

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

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