Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Static Private Member Functions | Private Attributes | Friends | List of all members
protocols::antibody::AntibodyInfo Class Reference

This class is used to get all relevant information you would need when dealing with an antibody. More...

#include <AntibodyInfo.hh>

Public Member Functions

 AntibodyInfo (pose::Pose const &pose, bool const &cdr_pdb_numbered=true)
 Constructor that Loads default numbering scheme and cdr definition from options (Chothia/Aroop) More...
 
 AntibodyInfo (pose::Pose const &pose, AntibodyNumberingSchemeEnum const &numbering_scheme, CDRDefinitionEnum const &cdr_definition, bool const &cdr_pdb_numbered=true)
 Constructor that uses the numbering scheme and cdr_definition given. More...
 
virtual ~AntibodyInfo ()
 
std::string get_current_AntibodyNumberingScheme () const
 : get the current numbering scheme being used More...
 
std::string get_current_CDRDefinition () const
 
Size get_CDR_length (CDRNameEnum const &cdr_name) const
 get the length of the cdr More...
 
Size get_CDR_length (CDRNameEnum const &cdr_name, core::pose::Pose const &pose, CDRDefinitionEnum const &transform) const
 
std::string get_CDR_name (CDRNameEnum const &cdr_name) const
 
CDRNameEnum get_CDR_name_enum (std::string const &cdr_name) const
 
char get_CDR_chain (CDRNameEnum const &cdr_name) const
 
bool is_camelid () const
 return this antibody is camelid or not More...
 
bool antigen_present () const
 return whether this pose has antigen or not More...
 
CDRNameEnum get_total_num_CDRs () const
 return whether a cdr contacts antigen. If no antigen is present, returns false. More...
 
Size get_CDR_start_PDB_num (CDRNameEnum const &cdr_name) const
 Return PDB residue number of CDR start residue. More...
 
Size get_CDR_end_PDB_num (CDRNameEnum const &cdr_name) const
 Return PDB residue number of CDR end residue. More...
 
Size get_CDR_start (CDRNameEnum const &cdr_name, pose::Pose const &pose) const
 Return pose number of CDR start residue. More...
 
Size get_CDR_start (CDRNameEnum const &cdr_name, pose::Pose const &pose, CDRDefinitionEnum const &transform) const
 
Size get_CDR_end (CDRNameEnum const &cdr_name, pose::Pose const &pose) const
 Return pose number of CDR end residue in the definition of the numbering scheme of transform. More...
 
Size get_CDR_end (CDRNameEnum const &cdr_name, pose::Pose const &pose, CDRDefinitionEnum const &transform) const
 
vector1< vector1< FrameWork > > get_AntibodyFrameworkInfo () const
 return the framework numbering information More...
 
H3BaseTypeEnum get_H3_kink_type () const
 get H3 cterminal kink/extended conformation (predicted by constructor) More...
 
std::string get_H3_kink_type_name () const
 
vector1< Sizeget_PackingAngleResidues () const
 get residues used to calculate VL/VH packing angle More...
 
vector1< char > get_antigen_chains () const
 gets all non-LH chains. Empty vector if no antigen present. More...
 
vector1< core::Sizeget_antigen_chain_ids (const core::pose::Pose &pose) const
 
Size kink_begin (pose::Pose const &pose) const
 return pose residue number of the first residue of the H3 kink More...
 
Size kink_end (pose::Pose const &pose) const
 return pose residue number of the last residue of the H3 kink More...
 
Size kink_trp (pose::Pose const &pose) const
 return pose residue number of the last residue of the H3 kink More...
 
Size kink_anion_residue (pose::Pose const &pose) const
 return pose residue number of the kink 'anion' (typically Asp/Glu) residue in the kink bulge HBond More...
 
Size kink_cation_residue (pose::Pose const &pose) const
 return pose residue number of the kink 'cation' (typically Arg/Lys) residue in the kink bulge HBond More...
 
std::vector< Vectorkink_anion_atoms (const pose::Pose &pose) const
 return side chain anion atoms (typically Asp/Glu oxygens) in the kink bulge HBond More...
 
std::vector< Vectorkink_cation_atoms (const pose::Pose &pose) const
 return side chain cation atoms (typically Lys/His nitrogens) in the kink bulge HBond More...
 
core::Size get_landmark_resnum (pose::Pose const &pose, AntibodyNumberingSchemeEnum const scheme, char const chain, Size const pdb_resnum, char const insertion_code=' ', bool fail_on_missing_resnum=true) const
 Used to get a residue number of a particular place in the framework or conserved residue in the CDR. Use this instead of PDBInfo. More...
 
void setup_CDR_clusters (pose::Pose const &pose)
 setup the clustering information for each CDR to totalCDRLoops More...
 
CDRClusterOP get_CDR_cluster (CDRNameEnum const cdr_name) const
 get the cdr's cluster identity and distance to cluster using it's structure as a CDRCluster object. More...
 
bool has_cluster_for_cdr (CDRNameEnum const cdr_name) const
 Check to make sure AbInfo has a cluster object for this CDR. In that all 6 CDRs not nessessarily present for each antibody. More...
 
std::string get_cluster_name (CDRClusterEnum const cluster) const
 
CDRClusterEnum get_cluster_enum (std::string const cluster) const
 
CDRNameEnum get_cdr_enum_for_cluster (CDRClusterEnum const cluster) const
 
core::Size get_cluster_length (CDRClusterEnum const cluster) const
 
std::string get_CDR_sequence_with_stem (CDRNameEnum const &cdr_name, Size left_stem=0, Size right_stem=0) const
 return the sequence of a particular CDR loop More...
 
std::string get_CDR_sequence_with_stem (CDRNameEnum const &cdr_name, core::pose::Pose const &pose, CDRDefinitionEnum const &transform, Size left_stem=0, Size right_stem=0) const
 
std::string get_antibody_sequence () const
 return the antibody sequence of LH or just H for camelid More...
 
loops::Loop get_CDR_loop (CDRNameEnum const cdr_name) const
 return the loop of a certain loop type More...
 
loops::Loop get_CDR_loop (CDRNameEnum const cdr_name, pose::Pose const &pose) const
 return the loop of a certain loop type on the fly More...
 
loops::Loop get_CDR_loop (CDRNameEnum const cdr_name, pose::Pose const &pose, CDRDefinitionEnum const transform) const
 return the loop of a certain loop type in definitions of the numbering scheme transform. More...
 
loops::LoopsOP get_CDR_in_loopsop (CDRNameEnum const cdr_name) const
 return the loop of a certain loop type More...
 
loops::LoopsOP get_AllCDRs_in_loopsop () const
 return a LoopsOP object, initialized upon class construction. More...
 
loops::LoopsOP get_CDR_loops (pose::Pose const &pose) const
 On-the-fly CDR LoopsOP. 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 const &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_AllCDRsSideChains_and_H3backbone (pose::Pose const &pose, bool const &include_nb_sc=false, Real const &nb_dist=10.0) const
 
void add_CDR_to_MoveMap (pose::Pose const &pose, kinematics::MoveMapOP movemap, CDRNameEnum const &cdr_name, bool const &bb_only=false, bool const &include_nb_sc=false, Real const &nb_dist=10.0) const
 Add CDR flexibility to a movemap. Uses pose for numbering. 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, CDRNameEnum const &cdr_name) const
 
AntibodyEnumManagerOP get_antibody_enum_manager () const
 use the H3 cterm coordinates in the pose to calculate the cterminal type More...
 
CDRClusterEnumManagerOP get_cdr_cluster_enum_manager () const
 
void show (std::ostream &out=std::cout)
 

Private Member Functions

void set_default ()
 Setters for private AntibodyInfo variables /// //////////////////////////////////////////////////////////////////////////////////////. More...
 
void identify_antibody (pose::Pose const &pose)
 check the input pose is nanobody, antibody or wrong. Sets sequence. Sets Antigen chains. More...
 
void init (pose::Pose const &pose)
 
void setup_numbering_info_for_scheme (AntibodyNumberingSchemeEnum const &numbering_scheme, CDRDefinitionEnum const &cdr_definition)
 Setup the Internal AntibodyNumbering variables. More...
 
vector1< vector1< PDBLandmarkOP > > get_cdr_definition_transform (CDRDefinitionEnum const cdr_definition) const
 Gets transform for numbering scheme. Allows const qualification for other functions. More...
 
bool cdr_definition_transform_present (CDRDefinitionEnum const cdr_definition) const
 Is the transform from our numbering scheme to cdr_definition defined? More...
 
vector1< PDBLandmarkOPget_numbering_scheme_landmarks (AntibodyNumberingSchemeEnum const numbering_scheme) const
 
bool numbering_scheme_transform_present (AntibodyNumberingSchemeEnum const numbering_scheme) const
 
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...
 
void check_cdr_quality (pose::Pose const &pose) const
 Make sure there are no large chainbreaks - aka missing residues - in the CDR loops or really bad peptide bonds Controlled via cmd-line flags. More...
 

Static Private Member Functions

static
core::scoring::ScoreFunctionCOP 
get_Pack_ScoreFxn (void)
 /// More...
 
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 data 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_
 
std::map< Size, char > sequence_map_
 
vector1< Sizepacking_angle_residues_
 
vector1< vector1< Size > > packing_angle_numbering_
 
H3BaseTypeEnum predicted_H3_base_type_
 Antibody properties. More...
 
CDRNameEnum total_cdr_loops_
 
vector1< char > chains_for_cdrs_
 
vector1< char > chains_for_antigen_
 
Size L_chain_
 
Size H_chain_
 
CDRClusterSetOP cdr_cluster_set_
 
AntibodyNumbering numbering_info_
 Internal Per-Scheme Numbering. More...
 
vector1< vector1< core::Size > > current_transform_
 
AntibodyEnumManagerOP enum_manager_
 
CDRClusterEnumManagerOP cdr_cluster_manager_
 
AntibodyNumberingParserOP numbering_parser_
 

Friends

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

Detailed Description

This class is used to get all relevant information you would need when dealing with an antibody.

It mainly holds numbering information, but passes out a variety of Rosetta specific objects like movemaps, Loops, taskfactories, etc. as well as other information such as CDR cluster type, camelid, H3 types, etc.

Constructor & Destructor Documentation

protocols::antibody::AntibodyInfo::AntibodyInfo ( pose::Pose const &  pose,
bool const &  cdr_pdb_numbered = true 
)

Constructor that Loads default numbering scheme and cdr definition from options (Chothia/Aroop)

References protocols::init::init().

protocols::antibody::AntibodyInfo::AntibodyInfo ( pose::Pose const &  pose,
AntibodyNumberingSchemeEnum const &  numbering_scheme,
CDRDefinitionEnum const &  cdr_definition,
bool const &  cdr_pdb_numbered = true 
)

Constructor that uses the numbering scheme and cdr_definition given.

References protocols::init::init().

protocols::antibody::AntibodyInfo::~AntibodyInfo ( )
virtual

Member Function Documentation

void protocols::antibody::AntibodyInfo::add_CDR_to_MoveMap ( pose::Pose const &  pose,
kinematics::MoveMapOP  movemap,
CDRNameEnum const &  cdr_name,
bool const &  bb_only = false,
bool const &  include_nb_sc = false,
Real const &  nb_dist = 10.0 
) const

Add CDR flexibility to a movemap. Uses pose for numbering.

References protocols::loops::select_loop_residues(), protocols::loops::start, protocols::loops::stop, and core::pose::Pose::total_residue().

bool protocols::antibody::AntibodyInfo::antigen_present ( ) const
inline

return whether this pose has antigen or not

bool protocols::antibody::AntibodyInfo::cdr_definition_transform_present ( CDRDefinitionEnum const  cdr_definition) const
private

Is the transform from our numbering scheme to cdr_definition defined?

void protocols::antibody::AntibodyInfo::check_cdr_quality ( pose::Pose const &  pose) const
private

Make sure there are no large chainbreaks - aka missing residues - in the CDR loops or really bad peptide bonds Controlled via cmd-line flags.

References protocols::loops::has_severe_pep_bond_geom_issues(), option, and core::pose::Pose::pdb_info().

void protocols::antibody::AntibodyInfo::detect_and_set_camelid_CDR_H3_stem_type ( pose::Pose const &  pose)
private
void protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type ( pose::Pose const &  pose)
private
void protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type_new_rule ( pose::Pose const &  pose)
private
loops::LoopsOP protocols::antibody::AntibodyInfo::get_AllCDRs_in_loopsop ( ) const
AntibodyEnumManagerOP protocols::antibody::AntibodyInfo::get_antibody_enum_manager ( ) const

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

std::string protocols::antibody::AntibodyInfo::get_antibody_sequence ( ) const

return the antibody sequence of LH or just H for camelid

References seq.

vector1< vector1< FrameWork > > protocols::antibody::AntibodyInfo::get_AntibodyFrameworkInfo ( ) const

return the framework numbering information

References utility_exit_with_message.

vector1< core::Size > protocols::antibody::AntibodyInfo::get_antigen_chain_ids ( const core::pose::Pose pose) const
vector1< char > protocols::antibody::AntibodyInfo::get_antigen_chains ( ) const
inline

gets all non-LH chains. Empty vector if no antigen present.

Referenced by protocols::antibody::design::AntibodyGraftDesignMover::graft_cdr().

char protocols::antibody::AntibodyInfo::get_CDR_chain ( CDRNameEnum const &  cdr_name) const
inline
CDRClusterOP protocols::antibody::AntibodyInfo::get_CDR_cluster ( CDRNameEnum const  cdr_name) const

get the cdr's cluster identity and distance to cluster using it's structure as a CDRCluster object.

See North, B., A. Lehmann, et al. (2011). JMB 406(2): 228-256. Must use setup_CDR_clusters first.

Note
If this AbInfo does not have all 6 chains, CDRClusterOP may be NULL if the CDR is not present to begin with.

References utility_exit_with_message.

Referenced by protocols::antibody::design::AntibodyDesignMover::add_cluster_comments_to_pose(), protocols::antibody::operator<<(), protocols::antibody::clusters::CDRClusterFeatures::report_features(), and protocols::antibody::design::AntibodyGraftDesignMover::setup_native_clusters().

CDRClusterEnumManagerOP protocols::antibody::AntibodyInfo::get_cdr_cluster_enum_manager ( ) const
vector1< vector1< PDBLandmarkOP > > protocols::antibody::AntibodyInfo::get_cdr_definition_transform ( CDRDefinitionEnum const  cdr_definition) const
private

Gets transform for numbering scheme. Allows const qualification for other functions.

References utility_exit_with_message.

Size protocols::antibody::AntibodyInfo::get_CDR_end ( CDRNameEnum const &  cdr_name,
pose::Pose const &  pose 
) const
Size protocols::antibody::AntibodyInfo::get_CDR_end ( CDRNameEnum const &  cdr_name,
pose::Pose const &  pose,
CDRDefinitionEnum const &  transform 
) const
Size protocols::antibody::AntibodyInfo::get_CDR_end_PDB_num ( CDRNameEnum const &  cdr_name) const
inline

Return PDB residue number of CDR end residue.

References protocols::antibody::cdr_end.

CDRNameEnum protocols::antibody::AntibodyInfo::get_cdr_enum_for_cluster ( CDRClusterEnum const  cluster) const
loops::LoopsOP protocols::antibody::AntibodyInfo::get_CDR_in_loopsop ( CDRNameEnum const  cdr_name) const

return the loop of a certain loop type

Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2().

Size protocols::antibody::AntibodyInfo::get_CDR_length ( CDRNameEnum const &  cdr_name) const
Size protocols::antibody::AntibodyInfo::get_CDR_length ( CDRNameEnum const &  cdr_name,
core::pose::Pose const &  pose,
CDRDefinitionEnum const &  transform 
) const
loops::Loop protocols::antibody::AntibodyInfo::get_CDR_loop ( CDRNameEnum const  cdr_name) const
loops::Loop protocols::antibody::AntibodyInfo::get_CDR_loop ( CDRNameEnum const  cdr_name,
pose::Pose const &  pose 
) const

return the loop of a certain loop type on the fly

References protocols::loops::start, and protocols::loops::stop.

loops::Loop protocols::antibody::AntibodyInfo::get_CDR_loop ( CDRNameEnum const  cdr_name,
pose::Pose const &  pose,
CDRDefinitionEnum const  transform 
) const

return the loop of a certain loop type in definitions of the numbering scheme transform.

References protocols::loops::start, and protocols::loops::stop.

loops::LoopsOP protocols::antibody::AntibodyInfo::get_CDR_loops ( pose::Pose const &  pose) const

On-the-fly CDR LoopsOP.

std::string protocols::antibody::AntibodyInfo::get_CDR_name ( CDRNameEnum const &  cdr_name) const
CDRNameEnum protocols::antibody::AntibodyInfo::get_CDR_name_enum ( std::string const &  cdr_name) const
std::string protocols::antibody::AntibodyInfo::get_CDR_sequence_with_stem ( CDRNameEnum const &  cdr_name,
Size  left_stem = 0,
Size  right_stem = 0 
) const
std::string protocols::antibody::AntibodyInfo::get_CDR_sequence_with_stem ( CDRNameEnum const &  cdr_name,
core::pose::Pose const &  pose,
CDRDefinitionEnum const &  transform,
Size  left_stem = 0,
Size  right_stem = 0 
) const
Size protocols::antibody::AntibodyInfo::get_CDR_start ( CDRNameEnum const &  cdr_name,
pose::Pose const &  pose 
) const
Size protocols::antibody::AntibodyInfo::get_CDR_start ( CDRNameEnum const &  cdr_name,
pose::Pose const &  pose,
CDRDefinitionEnum const &  transform 
) const
Size protocols::antibody::AntibodyInfo::get_CDR_start_PDB_num ( CDRNameEnum const &  cdr_name) const
inline

Return PDB residue number of CDR start residue.

References protocols::antibody::cdr_start.

CDRClusterEnum protocols::antibody::AntibodyInfo::get_cluster_enum ( std::string const  cluster) const
core::Size protocols::antibody::AntibodyInfo::get_cluster_length ( CDRClusterEnum const  cluster) const
std::string protocols::antibody::AntibodyInfo::get_cluster_name ( CDRClusterEnum const  cluster) const
std::string protocols::antibody::AntibodyInfo::get_current_AntibodyNumberingScheme ( ) const
std::string protocols::antibody::AntibodyInfo::get_current_CDRDefinition ( ) const
static core::scoring::ScoreFunctionCOP protocols::antibody::AntibodyInfo::get_Dock_ScoreFxn ( void  )
staticprivate
kinematics::FoldTreeCOP protocols::antibody::AntibodyInfo::get_FoldTree_AllCDRs ( pose::Pose const &  pose) const
kinematics::FoldTreeCOP protocols::antibody::AntibodyInfo::get_FoldTree_AllCDRs_LHDock ( pose::Pose const &  pose) const

change to all CDR and VL-VH dock fold tree

all_cdr_VL_VH_fold_tree

Author
Aroop 07/13/2010
Brian D. Weitzner
Last Modified: 06/25/2013

References begin, core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), end, core::kinematics::Edge::PEPTIDE, core::pose::residue_center_of_mass(), core::kinematics::Edge::stop(), and core::pose::Pose::total_residue().

Referenced by protocols::antibody::RefineBetaBarrel::finalize_setup().

kinematics::FoldTree protocols::antibody::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(), nres, core::pose::Pose::pdb_info(), core::pose::residue_center_of_mass(), and core::pose::Pose::total_residue().

Referenced by protocols::antibody::SnugDock::setup_objects().

kinematics::FoldTree protocols::antibody::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(), nres, core::pose::Pose::pdb_info(), core::pose::residue_center_of_mass(), and core::pose::Pose::total_residue().

kinematics::FoldTree protocols::antibody::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(), nres, core::pose::Pose::pdb_info(), core::pose::residue_center_of_mass(), and core::pose::Pose::total_residue().

Referenced by protocols::antibody::SnugDockProtocol::apply(), protocols::antibody::SnugDock::apply(), and protocols::antibody::SnugDock::setup_objects().

H3BaseTypeEnum protocols::antibody::AntibodyInfo::get_H3_kink_type ( ) const
std::string protocols::antibody::AntibodyInfo::get_H3_kink_type_name ( ) const
core::Size protocols::antibody::AntibodyInfo::get_landmark_resnum ( pose::Pose const &  pose,
AntibodyNumberingSchemeEnum const  scheme,
char const  chain,
Size const  pdb_resnum,
char const  insertion_code = ' ',
bool  fail_on_missing_resnum = true 
) const

Used to get a residue number of a particular place in the framework or conserved residue in the CDR. Use this instead of PDBInfo.

If the current numbering scheme is not 'scheme', will return the equivalent position of the current numbering scheme using the transform scheme file in the database. Should not be used for residues within CDRs since numbering schemes vary greatly in their within cdr alignments and numbering. Use get_CDR_start/end/loop functions with relative positions for this purpose. Returns 0 if residue is not found in pose

References core::pose::Pose::pdb_info(), utility::to_string(), protocols::antibody::TR, and utility_exit_with_message.

static core::scoring::ScoreFunctionCOP protocols::antibody::AntibodyInfo::get_LoopCentral_ScoreFxn ( void  )
staticprivate
static core::scoring::ScoreFunctionCOP protocols::antibody::AntibodyInfo::get_LoopHighRes_ScoreFxn ( void  )
staticprivate
kinematics::MoveMap protocols::antibody::AntibodyInfo::get_MoveMap_for_AllCDRsSideChains_and_H3backbone ( pose::Pose const &  pose,
bool const &  include_nb_sc = false,
Real const &  nb_dist = 10.0 
) const
kinematics::MoveMap protocols::antibody::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::antibody::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
vector1< PDBLandmarkOP > protocols::antibody::AntibodyInfo::get_numbering_scheme_landmarks ( AntibodyNumberingSchemeEnum const  numbering_scheme) const
private
static core::scoring::ScoreFunctionCOP protocols::antibody::AntibodyInfo::get_Pack_ScoreFxn ( void  )
staticprivate

///

copy all the static functions

vector1< Size > protocols::antibody::AntibodyInfo::get_PackingAngleResidues ( ) const
inline

get residues used to calculate VL/VH packing angle

Referenced by protocols::antibody::vl_vh_orientation_coords().

pack::task::TaskFactoryOP protocols::antibody::AntibodyInfo::get_TaskFactory_AllCDRs ( pose::Pose pose) const
pack::task::TaskFactoryOP protocols::antibody::AntibodyInfo::get_TaskFactory_OneCDR ( pose::Pose pose,
CDRNameEnum const &  cdr_name 
) const
CDRNameEnum protocols::antibody::AntibodyInfo::get_total_num_CDRs ( ) const
inline

return whether a cdr contacts antigen. If no antigen is present, returns false.

Considered 'in_contact' if > 5 atoms of antigen are within 5 A of any atom of the CDR. return num of cdr loops, 3 (nanobody) or 6 (regular antibody)

Referenced by protocols::antibody::GraftCDRLoopsProtocol::finalize_setup(), protocols::antibody::paratope_charge(), and protocols::antibody::paratope_sasa().

bool protocols::antibody::AntibodyInfo::has_cluster_for_cdr ( CDRNameEnum const  cdr_name) const

Check to make sure AbInfo has a cluster object for this CDR. In that all 6 CDRs not nessessarily present for each antibody.

Referenced by protocols::antibody::clusters::CDRClusterFeatures::report_features().

void protocols::antibody::AntibodyInfo::identify_antibody ( pose::Pose const &  pose)
private
void protocols::antibody::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 l, and protocols::antibody::TR.

void protocols::antibody::AntibodyInfo::init ( pose::Pose const &  pose)
private
bool protocols::antibody::AntibodyInfo::is_camelid ( ) const
inline

return this antibody is camelid or not

Referenced by protocols::antibody::operator<<(), and protocols::antibody::H3CterInsert::read_H3_cter_fragment().

std::vector< Vector > protocols::antibody::AntibodyInfo::kink_anion_atoms ( const pose::Pose pose) const

return side chain anion atoms (typically Asp/Glu oxygens) in the kink bulge HBond

References protocols::antibody::Aroop, protocols::antibody::h3, core::conformation::Residue::name1(), resi, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::antibody::kink_RD_Hbond().

Size protocols::antibody::AntibodyInfo::kink_anion_residue ( pose::Pose const &  pose) const
inline

return pose residue number of the kink 'anion' (typically Asp/Glu) residue in the kink bulge HBond

References protocols::antibody::Aroop, and protocols::antibody::h3.

Referenced by protocols::antibody::kink_bb_Hbond().

Size protocols::antibody::AntibodyInfo::kink_begin ( pose::Pose const &  pose) const
inline

return pose residue number of the first residue of the H3 kink

References protocols::antibody::Aroop, and protocols::antibody::h3.

Referenced by protocols::antibody::kink_dihedral(), and protocols::antibody::kink_Trp_Hbond().

std::vector< Vector > protocols::antibody::AntibodyInfo::kink_cation_atoms ( const pose::Pose pose) const

return side chain cation atoms (typically Lys/His nitrogens) in the kink bulge HBond

References protocols::antibody::Aroop, protocols::antibody::h3, core::conformation::Residue::name1(), resi, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::antibody::kink_RD_Hbond().

Size protocols::antibody::AntibodyInfo::kink_cation_residue ( pose::Pose const &  pose) const
inline

return pose residue number of the kink 'cation' (typically Arg/Lys) residue in the kink bulge HBond

References protocols::antibody::Aroop, and protocols::antibody::h3.

Referenced by protocols::antibody::kink_bb_Hbond().

Size protocols::antibody::AntibodyInfo::kink_end ( pose::Pose const &  pose) const
inline

return pose residue number of the last residue of the H3 kink

References protocols::antibody::Aroop, and protocols::antibody::h3.

Size protocols::antibody::AntibodyInfo::kink_trp ( pose::Pose const &  pose) const
inline

return pose residue number of the last residue of the H3 kink

References protocols::antibody::Aroop, and protocols::antibody::h3.

Referenced by protocols::antibody::kink_Trp_Hbond().

bool protocols::antibody::AntibodyInfo::numbering_scheme_transform_present ( AntibodyNumberingSchemeEnum const  numbering_scheme) const
private
void protocols::antibody::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 /// ///

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

Setters for private AntibodyInfo variables /// //////////////////////////////////////////////////////////////////////////////////////.

References cdr_definition, protocols::antibody::Kinked, numbering_scheme, option, protocols::antibody::TR, and utility_exit_with_message.

void protocols::antibody::AntibodyInfo::setup_CDR_clusters ( pose::Pose const &  pose)
void protocols::antibody::AntibodyInfo::setup_CDRsInfo ( pose::Pose const &  pose)
private
void protocols::antibody::AntibodyInfo::setup_FrameWorkInfo ( pose::Pose const &  pose)
private
void protocols::antibody::AntibodyInfo::setup_numbering_info_for_scheme ( AntibodyNumberingSchemeEnum const &  numbering_scheme,
CDRDefinitionEnum const &  cdr_definition 
)
private
kinematics::FoldTreeCOP protocols::antibody::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 protocols::loops::Loops::add_loop(), and protocols::loops::fold_tree_from_loops().

Referenced by protocols::antibody::H3CterInsert::apply().

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

Show the complete setup of the docking protocol

Referenced by protocols::antibody::design::AntibodyDesignMover::apply().

Friends And Related Function Documentation

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

Member Data Documentation

vector1<char> protocols::antibody::AntibodyInfo::ab_sequence_
private
CDRClusterEnumManagerOP protocols::antibody::AntibodyInfo::cdr_cluster_manager_
private
CDRClusterSetOP protocols::antibody::AntibodyInfo::cdr_cluster_set_
private
bool protocols::antibody::AntibodyInfo::cdr_pdb_numbered_
private
vector1<char> protocols::antibody::AntibodyInfo::chains_for_antigen_
private
vector1<char> protocols::antibody::AntibodyInfo::chains_for_cdrs_
private
vector1< vector1< core::Size> > protocols::antibody::AntibodyInfo::current_transform_
private
AntibodyEnumManagerOP protocols::antibody::AntibodyInfo::enum_manager_
private
vector1< vector1<FrameWork> > protocols::antibody::AntibodyInfo::framework_info_
private
Size protocols::antibody::AntibodyInfo::H_chain_
private
bool protocols::antibody::AntibodyInfo::InputPose_has_antigen_
private
bool protocols::antibody::AntibodyInfo::is_camelid_
private

private data

the information of the antibody pose

Size protocols::antibody::AntibodyInfo::L_chain_
private
loops::LoopsOP protocols::antibody::AntibodyInfo::loopsop_having_allcdrs_
private
AntibodyNumbering protocols::antibody::AntibodyInfo::numbering_info_
private

Internal Per-Scheme Numbering.

AntibodyNumberingParserOP protocols::antibody::AntibodyInfo::numbering_parser_
private
vector1<vector1< Size > > protocols::antibody::AntibodyInfo::packing_angle_numbering_
private
vector1< Size > protocols::antibody::AntibodyInfo::packing_angle_residues_
private
H3BaseTypeEnum protocols::antibody::AntibodyInfo::predicted_H3_base_type_
private

Antibody properties.

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

std::map<Size, char> protocols::antibody::AntibodyInfo::sequence_map_
private
CDRNameEnum protocols::antibody::AntibodyInfo::total_cdr_loops_
private
vector1<loops::LoopsOP> protocols::antibody::AntibodyInfo::vector1_loopsop_having_cdr_
private

the CDR and Framework information


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