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protocols::antibody2::AntibodyInfo Class Reference

#include <AntibodyInfo.hh>

Inheritance diagram for protocols::antibody2::AntibodyInfo:
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Collaboration diagram for protocols::antibody2::AntibodyInfo:
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Public Member Functions

 AntibodyInfo (pose::Pose const &pose, AntibodyNumberingEnum const &numbering_scheme=Aroop, bool const &cdr_pdb_numbered=true)
 
std::string get_Current_AntibodyNumberingScheme () const
 : get the current numbeirng scheme being used More...
 
loops::LoopsOP get_CDR_in_loopsop (AntibodyCDRNameEnum const &cdr_name) const
 return the loop of a certain loop type More...
 
loops::Loop get_CDR_loop (AntibodyCDRNameEnum const &cdr_name) const
 return the loop of a certain loop type More...
 
loops::LoopsOP get_AllCDRs_in_loopsop () const
 return a LoopsOP object, which saves all the CDR Loop object More...
 
vector1< char > get_CDR_Sequence_with_Stem (AntibodyCDRNameEnum const &cdr_name, Size left_stem=0, Size right_stem=0) const
 return the sequence of a particular CDR loop More...
 
vector1< char > const & get_Ab_Sequence () const
 return the antibody sequence of LH or just H for camelid More...
 
std::string get_CDR_Name (AntibodyCDRNameEnum const &cdr_name) const
 intput an enum, and get a string for it More...
 
bool is_Camelid () const
 return this antibody is camelid or not More...
 
vector1< vector1< FrameWork > > get_AntibodyFrameworkInfo () const
 return the framework numbering information More...
 
kinematics::FoldTreeCOP setup_simple_fold_tree (Size const &jumppoint1, Size const &cutpoint, Size const &jumppoint2, pose::Pose const &pose) const
 
kinematics::FoldTreeCOP get_FoldTree_AllCDRs_LHDock (pose::Pose &pose) const
 change to all CDR and VL-VH dock fold tree More...
 
kinematics::FoldTreeCOP get_FoldTree_AllCDRs (pose::Pose const &pose) const
 
kinematics::FoldTree get_FoldTree_LH_A (pose::Pose const &pose) const
 SnugDock foldtrees. More...
 
kinematics::FoldTree get_FoldTree_L_HA (pose::Pose const &pose) const
 Fold tree for LH refinement in snugdock, docks L with H + antigen chains. The function assumes that the coordinates for antigen chains in the input PDB file are right after the antibody heavy chain (which must be named H).The expected order of chains is thus L, H followed by the antigen chains. More...
 
kinematics::FoldTree get_FoldTree_LA_H (pose::Pose const &pose) const
 Fold tree for LH refinement in snugdock, docks L + antigen chains with H. The function assumes that the coordinates for antigen chains in the input PDB file are right after the antibody heavy chain (which must be named H).The expected order of chains is thus L, H followed by the antigen chains. More...
 
kinematics::MoveMap get_MoveMap_for_Loops (pose::Pose const &pose, loops::Loops const &the_loops, bool const &bb_only=false, bool const &include_nb_sc=false, Real const &nb_dist=10.0) const
 get a movemap for loops More...
 
kinematics::MoveMap get_MoveMap_for_LoopsandDock (pose::Pose const &pose, loops::Loops const &the_loops, bool const &bb_only=false, bool const &include_nb_sc=false, Real const &nb_dist=10.0) const
 get a movemap for loops and set the first jump be true More...
 
pack::task::TaskFactoryOP get_TaskFactory_AllCDRs (pose::Pose &pose) const
 TaskFactory. More...
 
pack::task::TaskFactoryOP get_TaskFactory_OneCDR (pose::Pose &pose, AntibodyCDRNameEnum const &cdr_name) const
 
AntibodyCDRNameEnum get_TotalNumCDRs () const
 return num of cdr loops, 3 (nanobody) or 6 (regular antibody) More...
 
bool get_PoseHasAntigen () const
 return whether this pose has antigen or not More...
 
H3BaseTypeEnum get_Predicted_H3BaseType () const
 get H3 cterminal kink/extended conformation (predicted by constructor) More...
 
vector1< Sizeget_PackingAngleResidues () const
 get residues used to calculate VL/VH packing angle More...
 
void show (std::ostream &out=std::cout)
 use the H3 cterm coordinates in the pose to calculate the cterminal type More...
 

Private Member Functions

void set_default ()
 
                all the setters                   ///

////////////////////////////////////////////////////////////////////////////////////// More...

 
void identify_antibody (pose::Pose const &pose)
 check the input pose is nanobody, antibody or wrong More...
 
void init (pose::Pose const &pose)
 initialization More...
 
void setup_CDRsInfo (pose::Pose const &pose)
 setup the CDR loops objects based on the input numbering scheme More...
 
void setup_FrameWorkInfo (pose::Pose const &pose)
 setup the framework information based on the input numbering scheme More...
 
void setup_VL_VH_packing_angle (pose::Pose const &pose)
 setup the residues used to calculate VL/VH packing angle More...
 
void predict_H3_base_type (pose::Pose const &pose)
 predict H3 cterminus base as Kinked or Extended More...
 
void detect_and_set_camelid_CDR_H3_stem_type (pose::Pose const &pose)
 
void detect_and_set_regular_CDR_H3_stem_type (pose::Pose const &pose)
 
void detect_and_set_regular_CDR_H3_stem_type_new_rule (pose::Pose const &pose)
 
void identify_CDR_from_a_sequence (std::string const &querychain)
 identify CDRs on L or H sequence More...
 
vector1< vector1< Size > > get_CDR_NumberingInfo (AntibodyNumberingEnum const &numbering_scheme) const
 /// More...
 

Static Private Member Functions

static vector1< std::string >
const & 
get_string_cdr_name (void)
 copy More...
 
static vector1< std::string >
const & 
get_string_h3_base_type (void)
 
static vector1< std::string >
const & 
get_string_numbering_scheme (void)
 
static
core::scoring::ScoreFunctionCOP 
get_Pack_ScoreFxn (void)
 
static
core::scoring::ScoreFunctionCOP 
get_Dock_ScoreFxn (void)
 
static
core::scoring::ScoreFunctionCOP 
get_LoopCentral_ScoreFxn (void)
 
static
core::scoring::ScoreFunctionCOP 
get_LoopHighRes_ScoreFxn (void)
 

Private Attributes

bool is_camelid_
 private members More...
 
bool InputPose_has_antigen_
 
bool cdr_pdb_numbered_
 
vector1< loops::LoopsOPvector1_loopsop_having_cdr_
 the CDR and Framework information More...
 
loops::LoopsOP loopsop_having_allcdrs_
 
vector1< vector1< FrameWork > > framework_info_
 
vector1< char > ab_sequence_
 
vector1< Sizepacking_angle_residues_
 
AntibodyNumberingEnum numbering_scheme_
 Antibody properties. More...
 
H3BaseTypeEnum predicted_H3_base_type_
 
AntibodyCDRNameEnum total_cdr_loops_
 

Friends

std::ostream & operator<< (std::ostream &out, const AntibodyInfo &ab_info)
 

Constructor & Destructor Documentation

protocols::antibody2::AntibodyInfo::AntibodyInfo ( pose::Pose const &  pose,
AntibodyNumberingEnum const &  numbering_scheme = Aroop,
bool const &  cdr_pdb_numbered = true 
)

Member Function Documentation

void protocols::antibody2::AntibodyInfo::detect_and_set_camelid_CDR_H3_stem_type ( pose::Pose const &  pose)
private
void protocols::antibody2::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type ( pose::Pose const &  pose)
private
void protocols::antibody2::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type_new_rule ( pose::Pose const &  pose)
private
vector1<char> const& protocols::antibody2::AntibodyInfo::get_Ab_Sequence ( ) const
inline

return the antibody sequence of LH or just H for camelid

loops::LoopsOP protocols::antibody2::AntibodyInfo::get_AllCDRs_in_loopsop ( ) const
inline

return a LoopsOP object, which saves all the CDR Loop object

vector1< vector1<FrameWork> > protocols::antibody2::AntibodyInfo::get_AntibodyFrameworkInfo ( ) const
inline

return the framework numbering information

loops::LoopsOP protocols::antibody2::AntibodyInfo::get_CDR_in_loopsop ( AntibodyCDRNameEnum const &  cdr_name) const
inline

return the loop of a certain loop type

Referenced by get_TaskFactory_OneCDR().

loops::Loop protocols::antibody2::AntibodyInfo::get_CDR_loop ( AntibodyCDRNameEnum const &  cdr_name) const
inline
std::string protocols::antibody2::AntibodyInfo::get_CDR_Name ( AntibodyCDRNameEnum const &  cdr_name) const
inline

intput an enum, and get a string for it

Referenced by protocols::antibody2::operator<<().

vector1< vector1< Size > > protocols::antibody2::AntibodyInfo::get_CDR_NumberingInfo ( AntibodyNumberingEnum const &  numbering_scheme) const
private
vector1< char > protocols::antibody2::AntibodyInfo::get_CDR_Sequence_with_Stem ( AntibodyCDRNameEnum const &  cdr_name,
Size  left_stem = 0,
Size  right_stem = 0 
) const

return the sequence of a particular CDR loop

References ab_sequence_, get_CDR_loop(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by protocols::antibody2::operator<<().

std::string protocols::antibody2::AntibodyInfo::get_Current_AntibodyNumberingScheme ( ) const
inline

: get the current numbeirng scheme being used

static core::scoring::ScoreFunctionCOP protocols::antibody2::AntibodyInfo::get_Dock_ScoreFxn ( void  )
staticprivate
kinematics::FoldTreeCOP protocols::antibody2::AntibodyInfo::get_FoldTree_AllCDRs ( pose::Pose const &  pose) const
kinematics::FoldTreeCOP protocols::antibody2::AntibodyInfo::get_FoldTree_AllCDRs_LHDock ( pose::Pose pose) const

change to all CDR and VL-VH dock fold tree

all_cdr_VL_VH_fold_tree

Authors
Aroop 07/13/2010
Last Modified: 07/13/2010

References loopsop_having_allcdrs_, core::pose::Pose::pdb_info(), protocols::geometry::residue_center_of_mass(), setup_simple_fold_tree(), and core::pose::Pose::total_residue().

kinematics::FoldTree protocols::antibody2::AntibodyInfo::get_FoldTree_L_HA ( pose::Pose const &  pose) const

Fold tree for LH refinement in snugdock, docks L with H + antigen chains. The function assumes that the coordinates for antigen chains in the input PDB file are right after the antibody heavy chain (which must be named H).The expected order of chains is thus L, H followed by the antigen chains.

L_HA_foldtree

Authors
Krishna Praneeth Kilambi 08/14/2012
Last Modified: 08/14/2012

References core::pose::Pose::chain(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::pdb_info(), protocols::geometry::residue_center_of_mass(), and core::pose::Pose::total_residue().

kinematics::FoldTree protocols::antibody2::AntibodyInfo::get_FoldTree_LA_H ( pose::Pose const &  pose) const

Fold tree for LH refinement in snugdock, docks L + antigen chains with H. The function assumes that the coordinates for antigen chains in the input PDB file are right after the antibody heavy chain (which must be named H).The expected order of chains is thus L, H followed by the antigen chains.

LA_H_foldtree

Authors
Krishna Praneeth Kilambi 08/14/2012
Last Modified: 08/14/2012

References core::pose::Pose::chain(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::pdb_info(), protocols::geometry::residue_center_of_mass(), and core::pose::Pose::total_residue().

kinematics::FoldTree protocols::antibody2::AntibodyInfo::get_FoldTree_LH_A ( pose::Pose const &  pose) const

SnugDock foldtrees.

Fold tree for snugdock, docks LH with the antigen chains. The function assumes that the coordinates for antigen chains in the input PDB file are right after the antibody heavy chain (which must be named H).The expected order of chains is thus L, H followed by the antigen chains.

LH_A_foldtree

Authors
Krishna Praneeth Kilambi 08/14/2012
Last Modified: 08/14/2012

References core::pose::Pose::chain(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::pdb_info(), protocols::geometry::residue_center_of_mass(), and core::pose::Pose::total_residue().

static core::scoring::ScoreFunctionCOP protocols::antibody2::AntibodyInfo::get_LoopCentral_ScoreFxn ( void  )
staticprivate
static core::scoring::ScoreFunctionCOP protocols::antibody2::AntibodyInfo::get_LoopHighRes_ScoreFxn ( void  )
staticprivate
kinematics::MoveMap protocols::antibody2::AntibodyInfo::get_MoveMap_for_Loops ( pose::Pose const &  pose,
loops::Loops const &  the_loops,
bool const &  bb_only = false,
bool const &  include_nb_sc = false,
Real const &  nb_dist = 10.0 
) const
kinematics::MoveMap protocols::antibody2::AntibodyInfo::get_MoveMap_for_LoopsandDock ( pose::Pose const &  pose,
loops::Loops const &  the_loops,
bool const &  bb_only = false,
bool const &  include_nb_sc = false,
Real const &  nb_dist = 10.0 
) const

get a movemap for loops and set the first jump be true

References get_MoveMap_for_Loops(), protocols::loops::Loops::num_loop(), and core::kinematics::MoveMap::set_jump().

static core::scoring::ScoreFunctionCOP protocols::antibody2::AntibodyInfo::get_Pack_ScoreFxn ( void  )
staticprivate
vector1< Size > protocols::antibody2::AntibodyInfo::get_PackingAngleResidues ( ) const
inline

get residues used to calculate VL/VH packing angle

bool protocols::antibody2::AntibodyInfo::get_PoseHasAntigen ( ) const
inline

return whether this pose has antigen or not

H3BaseTypeEnum protocols::antibody2::AntibodyInfo::get_Predicted_H3BaseType ( ) const
inline

get H3 cterminal kink/extended conformation (predicted by constructor)

Referenced by protocols::antibody2::operator<<().

vector1< std::string > const & protocols::antibody2::AntibodyInfo::get_string_cdr_name ( void  )
staticprivate

copy

all the static functions

vector1< std::string > const & protocols::antibody2::AntibodyInfo::get_string_h3_base_type ( void  )
staticprivate
vector1< std::string > const & protocols::antibody2::AntibodyInfo::get_string_numbering_scheme ( void  )
staticprivate
pack::task::TaskFactoryOP protocols::antibody2::AntibodyInfo::get_TaskFactory_AllCDRs ( pose::Pose pose) const
pack::task::TaskFactoryOP protocols::antibody2::AntibodyInfo::get_TaskFactory_OneCDR ( pose::Pose pose,
AntibodyCDRNameEnum const &  cdr_name 
) const
AntibodyCDRNameEnum protocols::antibody2::AntibodyInfo::get_TotalNumCDRs ( ) const
inline

return num of cdr loops, 3 (nanobody) or 6 (regular antibody)

void protocols::antibody2::AntibodyInfo::identify_antibody ( pose::Pose const &  pose)
private
void protocols::antibody2::AntibodyInfo::identify_CDR_from_a_sequence ( std::string const &  querychain)
private

identify CDRs on L or H sequence

TODO:

Author
: Daisuke Kuroda (dkuro.nosp@m.da19.nosp@m.81@gm.nosp@m.ail..nosp@m.com) 06/18/2012

: Identify 3 CDRs from a sequence. Automatically judge heavy or light chains (I hope!). The input can be either a light chain, a heavy chain or another sequence.

Last Modified: 08/28/2012 by DK

References protocols::TR().

void protocols::antibody2::AntibodyInfo::init ( pose::Pose const &  pose)
private
bool protocols::antibody2::AntibodyInfo::is_Camelid ( ) const
inline

return this antibody is camelid or not

Referenced by protocols::antibody2::operator<<(), and setup_FrameWorkInfo().

void protocols::antibody2::AntibodyInfo::predict_H3_base_type ( pose::Pose const &  pose)
private

predict H3 cterminus base as Kinked or Extended

                                                                     ///

predicit H3 cterminus base type (Kinked or Extended) based on sequence /// ///

References detect_and_set_camelid_CDR_H3_stem_type(), detect_and_set_regular_CDR_H3_stem_type_new_rule(), and is_camelid_.

Referenced by init().

void protocols::antibody2::AntibodyInfo::set_default ( )
private

                all the setters                   ///

//////////////////////////////////////////////////////////////////////////////////////

References protocols::antibody2::Aroop, InputPose_has_antigen_, is_camelid_, protocols::antibody2::Kinked, loopsop_having_allcdrs_, numbering_scheme_, and predicted_H3_base_type_.

Referenced by AntibodyInfo().

void protocols::antibody2::AntibodyInfo::setup_CDRsInfo ( pose::Pose const &  pose)
private
void protocols::antibody2::AntibodyInfo::setup_FrameWorkInfo ( pose::Pose const &  pose)
private
kinematics::FoldTreeCOP protocols::antibody2::AntibodyInfo::setup_simple_fold_tree ( Size const &  jumppoint1,
Size const &  cutpoint,
Size const &  jumppoint2,
pose::Pose const &  pose 
) const
                                                               ///

provide fold tree utilities for various purpose /// ///

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

Referenced by get_FoldTree_AllCDRs_LHDock().

void protocols::antibody2::AntibodyInfo::setup_VL_VH_packing_angle ( pose::Pose const &  pose)
private
void protocols::antibody2::AntibodyInfo::show ( std::ostream &  out = std::cout)

use the H3 cterm coordinates in the pose to calculate the cterminal type

Show the complete setup of the docking protocol

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
const AntibodyInfo ab_info 
)
friend

Member Data Documentation

vector1<char> protocols::antibody2::AntibodyInfo::ab_sequence_
private
bool protocols::antibody2::AntibodyInfo::cdr_pdb_numbered_
private

Referenced by AntibodyInfo().

vector1< vector1<FrameWork> > protocols::antibody2::AntibodyInfo::framework_info_
private

Referenced by setup_FrameWorkInfo().

bool protocols::antibody2::AntibodyInfo::InputPose_has_antigen_
private

Referenced by identify_antibody(), and set_default().

bool protocols::antibody2::AntibodyInfo::is_camelid_
private

private members

the information of the antibody pose

Referenced by identify_antibody(), init(), predict_H3_base_type(), set_default(), and setup_FrameWorkInfo().

loops::LoopsOP protocols::antibody2::AntibodyInfo::loopsop_having_allcdrs_
private
AntibodyNumberingEnum protocols::antibody2::AntibodyInfo::numbering_scheme_
private
vector1< Size > protocols::antibody2::AntibodyInfo::packing_angle_residues_
private
H3BaseTypeEnum protocols::antibody2::AntibodyInfo::predicted_H3_base_type_
private
AntibodyCDRNameEnum protocols::antibody2::AntibodyInfo::total_cdr_loops_
private
vector1<loops::LoopsOP> protocols::antibody2::AntibodyInfo::vector1_loopsop_having_cdr_
private

the CDR and Framework information

Referenced by setup_CDRsInfo().


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