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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>

Inheritance diagram for protocols::antibody::AntibodyInfo:
Inheritance graph
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Public Member Functions

 AntibodyInfo (core::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 (core::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...
 
 AntibodyInfo (core::pose::Pose const &pose, CDRDefinitionEnum const cdr_definition, bool const cdr_pdb_numbered=true)
 Constructor using just the cdr definition. More...
 
 AntibodyInfo (AntibodyInfo const &src)
 Copy Constructor. More...
 
AntibodyInfoOP clone () const
 Clone the pointer. More...
 
 ~AntibodyInfo () override
 
std::string get_current_AntibodyNumberingScheme () const
 : get the current numbering scheme being used More...
 
std::string get_current_CDRDefinition () const
 
AntibodyEnumManagerCOP get_antibody_enum_manager () const
 Get a const OP to the antibody enum manager. More...
 
clusters::CDRClusterEnumManagerCOP get_cdr_cluster_enum_manager () const
 Get a const OP to the cluster enum manager. More...
 
core::Size get_CDR_length (CDRNameEnum const cdr_name) const
 get the length of the cdr upon construction of AntibodyInfo More...
 
core::Size get_CDR_length (CDRNameEnum const cdr_name, core::pose::Pose const &pose) const
 On-the-fly CDR length. More...
 
core::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...
 
std::string get_light_chain_type () const
 Return if antibody is lambda, kappa or unknown. Type set via cmd-line option for now. More...
 
LightChainTypeEnum get_light_chain_type_enum () const
 Return if antibody is lambda, kappa or unknown. Type set via cmd-line option for now. More...
 
void set_light_chain_type (LightChainTypeEnum light_chain)
 Set the light chain type via enum. More...
 
bool antigen_present () const
 return whether this pose has antigen or not More...
 
core::Size get_total_num_CDRs (bool include_proto_cdr4=false) const
 return whether a cdr contacts antigen. If no antigen is present, returns false. More...
 
utility::vector1< CDRNameEnum >
const & 
get_all_cdrs_present (bool include_proto_cdr4=false) const
 Get a vector of all the CDRs in this antibody. Easy to iterate on. More...
 
utility::vector1< CDRNameEnum >
const & 
get_all_cdrs (bool include_proto_cdr4=false) const
 Get a vector of all CDRs. Easy to iterate on. More...
 
bool has_CDR (CDRNameEnum const cdr_name) const
 Does the antibody have this CDR? See also: is_camelid()) get_total_num_CDRs()) More...
 
core::Size get_CDR_start_PDB_num (CDRNameEnum const cdr_name) const
 Return PDB residue number of CDR start residue. More...
 
core::Size get_CDR_end_PDB_num (CDRNameEnum const cdr_name) const
 Return PDB residue number of CDR end residue. More...
 
core::Size get_CDR_start (CDRNameEnum const cdr_name, core::pose::Pose const &pose) const
 Return pose number of CDR start residue. More...
 
core::Size get_CDR_start (CDRNameEnum const cdr_name, core::pose::Pose const &pose, CDRDefinitionEnum const &transform) const
 
core::Size get_CDR_end (CDRNameEnum const cdr_name, core::pose::Pose const &pose) const
 Return pose number of CDR end residue in the definition of the numbering scheme of transform. More...
 
core::Size get_CDR_end (CDRNameEnum const cdr_name, core::pose::Pose const &pose, CDRDefinitionEnum const &transform) const
 
CDRNameEnum get_CDRNameEnum_of_residue (core::pose::Pose const &pose, core::Size resnum, bool de_as_framework=true) const
 Get the CDRNameEnum for region, if not in a CDR throw exception – CDR can be id'ed with the "get_region_of_residue" function. More...
 
AntibodyRegionEnum get_region_of_residue (core::pose::Pose const &pose, core::Size resnum, bool de_as_framework=true) const
 Get the region of the resnum - aka - antigen_region, cdr_region, or framework_region By default, count the DE region (CDR4) as framework. More...
 
utility::vector1
< utility::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
 
utility::vector1< core::Sizeget_PackingAngleResidues () const
 get residues used to calculate VL/VH packing angle More...
 
utility::vector1< char > get_antigen_chains () const
 gets all non-LH chains. Empty vector if no antigen present. More...
 
utility::vector1< core::Sizeget_antigen_chain_ids (const core::pose::Pose &pose) const
 
std::string get_antigen_chain_string () const
 Return the antigen chains as a string. More...
 
utility::vector1< char > get_antibody_chains () const
 
utility::vector1< core::Sizeget_antibody_chain_ids (const core::pose::Pose &pose) const
 
std::string get_antibody_chain_string () const
 Returns H or LH depeding on camelid. More...
 
core::Size kink_begin (core::pose::Pose const &pose) const
 return pose residue number of the first residue of the H3 kink More...
 
core::Size kink_end (core::pose::Pose const &pose) const
 return pose residue number of the last residue of the H3 kink More...
 
core::Size kink_trp (core::pose::Pose const &pose) const
 return pose residue number of the last residue of the H3 kink More...
 
core::Size kink_anion_residue (core::pose::Pose const &pose) const
 return pose residue number of the kink 'anion' (typically Asp/Glu) residue in the kink bulge HBond More...
 
core::Size kink_cation_residue (core::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< core::Vectorkink_anion_atoms (const core::pose::Pose &pose) const
 return side chain anion atoms (typically Asp/Glu oxygens) in the kink bulge HBond More...
 
std::vector< core::Vectorkink_cation_atoms (const core::pose::Pose &pose) const
 return side chain cation atoms (typically Lys/His nitrogens) in the kink bulge HBond More...
 
core::Size qq_light_residue (const core::pose::Pose &pose) const
 get pose number for light chain residue that is part of the qq constraint More...
 
core::Size qq_heavy_residue (const core::pose::Pose &pose) const
 get pose number for heavy chain residue that is part of the qq constraint More...
 
core::Size get_landmark_resnum (core::pose::Pose const &pose, AntibodyNumberingSchemeEnum const scheme, char const chain, core::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...
 
AntibodyNumbering const & get_antibody_numbering_info () const
 Get the full antibody numbering struct for use in anything. More...
 
void setup_CDR_clusters (core::pose::Pose const &pose, bool attempt_set_from_pose=false)
 setup the clustering information for each CDR to totalCDRLoops Optionally, attempt to set the CDR cluster from the Pose data cache if any data is there. More...
 
void setup_CDR_clusters (core::pose::Pose const &pose, utility::vector1< bool > const &cdrs, bool attempt_set_from_pose=false)
 setup the clustering information for each CDR according to boolean vector. Optionally, attempt to set the CDR cluster from the Pose data cache if any data is there. More...
 
void setup_CDR_cluster (core::pose::Pose const &pose, CDRNameEnum cdr, bool attempt_set_from_pose=false)
 setup the clustering information for a particular CDR. Optionally, attempt to set the CDR cluster from the Pose data cache if any data is there. More...
 
void set_CDR_cluster (CDRNameEnum cdr, clusters::CDRClusterCOP cluster)
 Manually set the CDR cluster for a particular CDR. More...
 
clusters::CDRClusterCOP 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...
 
clusters::CDRClusterSetOP get_CDR_cluster_set () const
 
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 (clusters::CDRClusterEnum const cluster) const
 
clusters::CDRClusterEnum get_cluster_enum (std::string const &cluster) const
 
CDRNameEnum get_cdr_enum_for_cluster (clusters::CDRClusterEnum const cluster) const
 
core::Size get_cluster_length (clusters::CDRClusterEnum const cluster) const
 
std::string get_CDR_sequence_with_stem (CDRNameEnum const cdr_name, core::Size left_stem=0, core::Size right_stem=0) const
 return the sequence of a particular CDR loop Deprecated in favor of on the fly sequence. More...
 
std::string get_CDR_sequence_with_stem (CDRNameEnum const cdr_name, core::pose::Pose const &pose, core::Size left_stem=0, core::Size right_stem=0) const
 On-The-Fly CDR sequence. More...
 
std::string get_CDR_sequence_with_stem (CDRNameEnum const cdr_name, core::pose::Pose const &pose, core::Size left_stem, core::Size right_stem, CDRDefinitionEnum const &transform) const
 On-The-Fly CDR sequence. More...
 
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, core::pose::Pose const &pose, core::Size overhang=0) const
 return the loop of a certain loop type on the fly More...
 
loops::Loop get_CDR_loop (CDRNameEnum const cdr_name, core::pose::Pose const &pose, CDRDefinitionEnum const transform, core::Size overhang=0) 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 (core::pose::Pose const &pose, core::Size overhang=0) const
 On-the-fly CDR LoopsOP. More...
 
loops::LoopsOP get_CDR_loops (core::pose::Pose const &pose, const utility::vector1< bool > &cdrs, core::Size overhang=0) const
 
core::kinematics::FoldTreeCOP setup_simple_fold_tree (core::Size const &jumppoint1, core::Size const &cutpoint, core::Size const &jumppoint2, core::pose::Pose const &pose) const
 
core::kinematics::FoldTreeCOP get_FoldTree_AllCDRs_LHDock (core::pose::Pose const &pose) const
 change to all CDR and VL-VH dock fold tree More...
 
core::kinematics::FoldTreeCOP get_FoldTree_AllCDRs (core::pose::Pose const &pose) const
 
core::kinematics::FoldTree get_FoldTree_LH_A (core::pose::Pose const &pose) const
 SnugDock foldtrees. More...
 
core::kinematics::FoldTree get_FoldTree_L_HA (core::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...
 
core::kinematics::FoldTree get_FoldTree_LA_H (core::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...
 
core::kinematics::MoveMap get_MoveMap_for_Loops (core::pose::Pose const &pose, loops::Loops const &the_loops, bool const &bb_only=false, bool const &include_nb_sc=false, core::Real const &nb_dist=10.0) const
 get a movemap for loops. More...
 
core::kinematics::MoveMap get_MoveMap_for_AllCDRsSideChains_and_H3backbone (core::pose::Pose const &pose, bool const &include_nb_sc=false, core::Real const &nb_dist=10.0) const
 
void add_CDR_to_MoveMap (core::pose::Pose const &pose, core::kinematics::MoveMapOP movemap, CDRNameEnum const cdr_name, bool const &bb_only=false, bool const &include_nb_sc=false, core::Real const &nb_dist=10.0) const
 Add CDR flexibility to a movemap. Uses pose for numbering. More...
 
core::kinematics::MoveMap get_MoveMap_for_LoopsandDock (core::pose::Pose const &pose, loops::Loops const &the_loops, bool const &bb_only=false, bool const &include_nb_sc=false, core::Real const &nb_dist=10.0) const
 get a movemap for loops and set the first jump be true More...
 
core::pack::task::TaskFactoryOP get_TaskFactory_AllCDRs (core::pose::Pose &pose) const
 TaskFactory. More...
 
core::pack::task::TaskFactoryOP get_TaskFactory_OneCDR (core::pose::Pose &pose, CDRNameEnum const cdr_name) const
 
void show (std::ostream &out=std::cout) const
 

Private Member Functions

void set_default ()
 Setters for private AntibodyInfo variables /// //////////////////////////////////////////////////////////////////////////////////////. More...
 
void identify_antibody (core::pose::Pose const &pose)
 check the input pose is nanobody, antibody or wrong. Sets sequence. Sets Antigen chains. More...
 
void identify_light_chain (core::pose::Pose const &pose)
 place-holder for identification of light chain type: lambda/kappa/unknown. More...
 
void init (core::pose::Pose const &pose)
 
void setup_CDRsInfo (core::pose::Pose const &pose)
 setup the CDR loops objects based on the input numbering scheme More...
 
void setup_FrameWorkInfo (core::pose::Pose const &pose)
 setup the framework information based on the input numbering scheme More...
 
void setup_VL_VH_packing_angle (core::pose::Pose const &pose)
 setup the residues used to calculate VL/VH packing angle More...
 
void predict_H3_base_type (core::pose::Pose const &pose)
 predict H3 cterminus base as Kinked or Extended More...
 
void detect_and_set_camelid_CDR_H3_stem_type (core::pose::Pose const &pose)
 
void detect_and_set_regular_CDR_H3_stem_type (core::pose::Pose const &pose)
 
void detect_and_set_regular_CDR_H3_stem_type_new_rule (core::pose::Pose const &pose)
 
void identify_CDR_from_a_sequence (std::string const &querychain)
 identify CDRs on L or H sequence More...
 
void setup_numbering_info_for_scheme (AntibodyNumberingSchemeEnum const &numbering_scheme, CDRDefinitionEnum const cdr_definition)
 Setup the Internal AntibodyNumbering variables. More...
 
utility::vector1
< utility::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...
 
utility::vector1< PDBLandmarkOPget_numbering_scheme_landmarks (AntibodyNumberingSchemeEnum const numbering_scheme) const
 
bool numbering_scheme_transform_present (AntibodyNumberingSchemeEnum const numbering_scheme) const
 
void check_cdr_quality (core::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 has_antigen_
 
bool cdr_pdb_numbered_
 
utility::vector1< loops::LoopsOPvector1_loopsop_having_cdr_
 the CDR and Framework information More...
 
loops::LoopsOP loopsop_having_allcdrs_
 
utility::vector1
< utility::vector1< FrameWork > > 
framework_info_
 
utility::vector1< char > ab_sequence_
 
std::map< core::Size, char > sequence_map_
 
utility::vector1< core::Sizepacking_angle_residues_
 
utility::vector1
< utility::vector1< core::Size > > 
packing_angle_numbering_
 
H3BaseTypeEnum predicted_H3_base_type_
 Antibody properties. More...
 
CDRNameEnum total_cdr_loops_
 
utility::vector1< char > chains_for_cdrs_
 
utility::vector1< char > chains_for_antigen_
 
core::Size L_chain_
 
core::Size H_chain_
 
LightChainTypeEnum light_chain_type_
 
clusters::CDRClusterSetOP cdr_cluster_set_
 
AntibodyNumbering numbering_info_
 Internal Per-Scheme Numbering. More...
 
utility::vector1
< utility::vector1< core::Size > > 
current_transform_
 
AntibodyEnumManagerOP enum_manager_
 
clusters::CDRClusterEnumManagerOP cdr_cluster_manager_
 
AntibodyNumberingParserOP numbering_parser_
 
utility::vector1< CDRNameEnumall_cdrs_present_
 
utility::vector1< CDRNameEnumall_cdrs_present_and_proto_
 

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 ( core::pose::Pose const &  pose,
bool const  cdr_pdb_numbered = true 
)

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

References cdr_pdb_numbered_, enum_manager_, identify_antibody(), init(), and set_default().

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

Member Function Documentation

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

return whether this pose has antigen or not

References has_antigen_.

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?

References protocols::antibody::AntibodyNumbering::cdr_definition_transform, and numbering_info_.

Referenced by get_cdr_definition_transform().

void protocols::antibody::AntibodyInfo::check_cdr_quality ( core::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 get_CDR_loop(), get_CDR_name(), protocols::loops::has_severe_pep_bond_geom_issues(), core::pose::Pose::pdb_info(), and total_cdr_loops_.

Referenced by init().

AntibodyInfoOP protocols::antibody::AntibodyInfo::clone ( ) const

Clone the pointer.

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

void protocols::antibody::AntibodyInfo::detect_and_set_camelid_CDR_H3_stem_type ( core::pose::Pose const &  pose)
private
void protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type ( core::pose::Pose const &  pose)
private
void protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type_new_rule ( core::pose::Pose const &  pose)
private
utility::vector1< CDRNameEnum > const & protocols::antibody::AntibodyInfo::get_all_cdrs ( bool  include_proto_cdr4 = false) const

Get a vector of all CDRs. Easy to iterate on.

References enum_manager_.

utility::vector1< CDRNameEnum > const & protocols::antibody::AntibodyInfo::get_all_cdrs_present ( bool  include_proto_cdr4 = false) const
loops::LoopsOP protocols::antibody::AntibodyInfo::get_AllCDRs_in_loopsop ( ) const

return a LoopsOP object, initialized upon class construction.

References loopsop_having_allcdrs_.

Referenced by get_FoldTree_AllCDRs(), get_FoldTree_AllCDRs_LHDock(), get_MoveMap_for_AllCDRsSideChains_and_H3backbone(), and get_TaskFactory_AllCDRs().

vector1< core::Size > protocols::antibody::AntibodyInfo::get_antibody_chain_ids ( const core::pose::Pose pose) const
std::string protocols::antibody::AntibodyInfo::get_antibody_chain_string ( ) const

Returns H or LH depeding on camelid.

References is_camelid_.

vector1< char > protocols::antibody::AntibodyInfo::get_antibody_chains ( ) const

References is_camelid_.

AntibodyEnumManagerCOP protocols::antibody::AntibodyInfo::get_antibody_enum_manager ( ) const

Get a const OP to the antibody enum manager.

References enum_manager_.

AntibodyNumbering const& protocols::antibody::AntibodyInfo::get_antibody_numbering_info ( ) const
inline

Get the full antibody numbering struct for use in anything.

References numbering_info_.

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

return the antibody sequence of LH or just H for camelid

References ab_sequence_.

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

return the framework numbering information

References framework_info_.

vector1< core::Size > protocols::antibody::AntibodyInfo::get_antigen_chain_ids ( const core::pose::Pose pose) const
std::string protocols::antibody::AntibodyInfo::get_antigen_chain_string ( ) const

Return the antigen chains as a string.

References chains_for_antigen_.

utility::vector1< char > protocols::antibody::AntibodyInfo::get_antigen_chains ( ) const
inline

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

References chains_for_antigen_.

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

References chains_for_cdrs_.

CDRClusterCOP 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 cdr_cluster_set_.

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

CDRClusterEnumManagerCOP protocols::antibody::AntibodyInfo::get_cdr_cluster_enum_manager ( ) const

Get a const OP to the cluster enum manager.

References cdr_cluster_manager_.

CDRClusterSetOP protocols::antibody::AntibodyInfo::get_CDR_cluster_set ( ) const

References cdr_cluster_set_.

vector1< vector1< PDBLandmarkOP > > protocols::antibody::AntibodyInfo::get_cdr_definition_transform ( CDRDefinitionEnum const  cdr_definition) const
private
Size protocols::antibody::AntibodyInfo::get_CDR_end ( CDRNameEnum const  cdr_name,
core::pose::Pose const &  pose 
) const
Size protocols::antibody::AntibodyInfo::get_CDR_end ( CDRNameEnum const  cdr_name,
core::pose::Pose const &  pose,
CDRDefinitionEnum const &  transform 
) const
core::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, protocols::antibody::AntibodyNumbering::cdr_numbering, and numbering_info_.

CDRNameEnum protocols::antibody::AntibodyInfo::get_cdr_enum_for_cluster ( clusters::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

References vector1_loopsop_having_cdr_.

Referenced by get_TaskFactory_OneCDR().

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 
) 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,
core::pose::Pose const &  pose,
core::Size  overhang = 0 
) const

return the loop of a certain loop type on the fly

References get_CDR_end(), get_CDR_start(), protocols::loops::start, and protocols::loops::stop.

loops::Loop protocols::antibody::AntibodyInfo::get_CDR_loop ( CDRNameEnum const  cdr_name,
core::pose::Pose const &  pose,
CDRDefinitionEnum const  transform,
core::Size  overhang = 0 
) const

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

References protocols::antibody::AntibodyNumbering::cdr_definition, get_CDR_end(), get_CDR_loop(), get_CDR_start(), numbering_info_, protocols::loops::start, and protocols::loops::stop.

loops::LoopsOP protocols::antibody::AntibodyInfo::get_CDR_loops ( core::pose::Pose const &  pose,
core::Size  overhang = 0 
) const

On-the-fly CDR LoopsOP.

References get_CDR_loop(), and total_cdr_loops_.

loops::LoopsOP protocols::antibody::AntibodyInfo::get_CDR_loops ( core::pose::Pose const &  pose,
const utility::vector1< bool > &  cdrs,
core::Size  overhang = 0 
) const
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

References enum_manager_.

std::string protocols::antibody::AntibodyInfo::get_CDR_sequence_with_stem ( CDRNameEnum const  cdr_name,
core::Size  left_stem = 0,
core::Size  right_stem = 0 
) const

return the sequence of a particular CDR loop Deprecated in favor of on the fly sequence.

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

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

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

On-The-Fly CDR sequence.

References get_CDR_end(), get_CDR_start(), and core::pose::Pose::sequence().

Size protocols::antibody::AntibodyInfo::get_CDR_start ( CDRNameEnum const  cdr_name,
core::pose::Pose const &  pose 
) const
Size protocols::antibody::AntibodyInfo::get_CDR_start ( CDRNameEnum const  cdr_name,
core::pose::Pose const &  pose,
CDRDefinitionEnum const &  transform 
) const
core::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::AntibodyNumbering::cdr_numbering, protocols::antibody::cdr_start, and numbering_info_.

CDRNameEnum protocols::antibody::AntibodyInfo::get_CDRNameEnum_of_residue ( core::pose::Pose const &  pose,
core::Size  resnum,
bool  de_as_framework = true 
) const

Get the CDRNameEnum for region, if not in a CDR throw exception – CDR can be id'ed with the "get_region_of_residue" function.

References core::pose::Pose::chain(), core::sequence::end, get_all_cdrs_present(), get_CDR_end(), get_CDR_start(), core::pose::get_chain_from_chain_id(), and protocols::loops::start.

CDRClusterEnum protocols::antibody::AntibodyInfo::get_cluster_enum ( std::string const &  cluster) const

References cdr_cluster_manager_.

core::Size protocols::antibody::AntibodyInfo::get_cluster_length ( clusters::CDRClusterEnum const  cluster) const

References cdr_cluster_manager_.

std::string protocols::antibody::AntibodyInfo::get_cluster_name ( clusters::CDRClusterEnum const  cluster) const

References cdr_cluster_manager_.

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

: get the current numbering scheme being used

References enum_manager_, numbering_info_, and protocols::antibody::AntibodyNumbering::numbering_scheme.

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 ( core::pose::Pose const &  pose) const
kinematics::FoldTreeCOP protocols::antibody::AntibodyInfo::get_FoldTree_AllCDRs_LHDock ( core::pose::Pose const &  pose) const
kinematics::FoldTree protocols::antibody::AntibodyInfo::get_FoldTree_L_HA ( core::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.

Author
Krishna Praneeth Kilambi 08/14/2012

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

kinematics::FoldTree protocols::antibody::AntibodyInfo::get_FoldTree_LA_H ( core::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.

Author
Krishna Praneeth Kilambi 08/14/2012

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

kinematics::FoldTree protocols::antibody::AntibodyInfo::get_FoldTree_LH_A ( core::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.

Author
Krishna Praneeth Kilambi 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(), core::pose::residue_center_of_mass(), and core::pose::Pose::size().

H3BaseTypeEnum protocols::antibody::AntibodyInfo::get_H3_kink_type ( ) const

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

References predicted_H3_base_type_.

std::string protocols::antibody::AntibodyInfo::get_H3_kink_type_name ( ) const
core::Size protocols::antibody::AntibodyInfo::get_landmark_resnum ( core::pose::Pose const &  pose,
AntibodyNumberingSchemeEnum const  scheme,
char const  chain,
core::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 enum_manager_, get_numbering_scheme_landmarks(), numbering_info_, protocols::antibody::AntibodyNumbering::numbering_scheme, numbering_scheme_transform_present(), core::pose::Pose::pdb_info(), core::id::to_string(), and protocols::antibody::TR().

Referenced by detect_and_set_regular_CDR_H3_stem_type(), detect_and_set_regular_CDR_H3_stem_type_new_rule(), get_CDR_end(), get_CDR_start(), qq_heavy_residue(), qq_light_residue(), setup_FrameWorkInfo(), and setup_VL_VH_packing_angle().

std::string protocols::antibody::AntibodyInfo::get_light_chain_type ( ) const
inline

Return if antibody is lambda, kappa or unknown. Type set via cmd-line option for now.

References enum_manager_, and light_chain_type_.

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

LightChainTypeEnum protocols::antibody::AntibodyInfo::get_light_chain_type_enum ( ) const
inline

Return if antibody is lambda, kappa or unknown. Type set via cmd-line option for now.

References light_chain_type_.

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 ( core::pose::Pose const &  pose,
bool const &  include_nb_sc = false,
core::Real const &  nb_dist = 10.0 
) const
kinematics::MoveMap protocols::antibody::AntibodyInfo::get_MoveMap_for_Loops ( core::pose::Pose const &  pose,
loops::Loops const &  the_loops,
bool const &  bb_only = false,
bool const &  include_nb_sc = false,
core::Real const &  nb_dist = 10.0 
) const
kinematics::MoveMap protocols::antibody::AntibodyInfo::get_MoveMap_for_LoopsandDock ( core::pose::Pose const &  pose,
loops::Loops const &  the_loops,
bool const &  bb_only = false,
bool const &  include_nb_sc = false,
core::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().

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

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

get residues used to calculate VL/VH packing angle

References packing_angle_residues_.

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

AntibodyRegionEnum protocols::antibody::AntibodyInfo::get_region_of_residue ( core::pose::Pose const &  pose,
core::Size  resnum,
bool  de_as_framework = true 
) const
pack::task::TaskFactoryOP protocols::antibody::AntibodyInfo::get_TaskFactory_AllCDRs ( core::pose::Pose pose) const
pack::task::TaskFactoryOP protocols::antibody::AntibodyInfo::get_TaskFactory_OneCDR ( core::pose::Pose pose,
CDRNameEnum const  cdr_name 
) const
core::Size protocols::antibody::AntibodyInfo::get_total_num_CDRs ( bool  include_proto_cdr4 = false) const

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) Do not use for enum-based for loop if including cdr4. Use get_all_cdrs_present instead!

References all_cdrs_present_, and all_cdrs_present_and_proto_.

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

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

Does the antibody have this CDR? See also: is_camelid()) get_total_num_CDRs())

References protocols::antibody::h4, is_camelid_, protocols::antibody::l4, and total_cdr_loops_.

Referenced by setup_CDR_cluster().

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.

References cdr_cluster_set_.

void protocols::antibody::AntibodyInfo::identify_antibody ( core::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.

References protocols::antibody::TR().

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

place-holder for identification of light chain type: lambda/kappa/unknown.

References enum_manager_, is_camelid(), light_chain_type_, and protocols::antibody::unknown.

Referenced by init().

void protocols::antibody::AntibodyInfo::init ( core::pose::Pose const &  pose)
private
bool protocols::antibody::AntibodyInfo::is_camelid ( ) const
inline
std::vector< Vector > protocols::antibody::AntibodyInfo::kink_anion_atoms ( const core::pose::Pose pose) const
core::Size protocols::antibody::AntibodyInfo::kink_anion_residue ( core::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, get_CDR_loop(), protocols::antibody::h3, and protocols::loops::Loop::stop().

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

core::Size protocols::antibody::AntibodyInfo::kink_begin ( core::pose::Pose const &  pose) const
inline
std::vector< Vector > protocols::antibody::AntibodyInfo::kink_cation_atoms ( const core::pose::Pose pose) const
core::Size protocols::antibody::AntibodyInfo::kink_cation_residue ( core::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, get_CDR_loop(), protocols::antibody::h3, and protocols::loops::Loop::start().

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

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

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

References protocols::antibody::Aroop, get_CDR_loop(), protocols::antibody::h3, and protocols::loops::Loop::stop().

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

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

References protocols::antibody::Aroop, get_CDR_loop(), protocols::antibody::h3, and protocols::loops::Loop::stop().

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 ( core::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().

core::Size protocols::antibody::AntibodyInfo::qq_heavy_residue ( const core::pose::Pose pose) const

get pose number for heavy chain residue that is part of the qq constraint

References protocols::antibody::Chothia_Scheme, get_landmark_resnum(), core::pose::Pose::residue(), and protocols::antibody::TR().

core::Size protocols::antibody::AntibodyInfo::qq_light_residue ( const core::pose::Pose pose) const

get pose number for light chain residue that is part of the qq constraint

References protocols::antibody::Chothia_Scheme, get_landmark_resnum(), core::pose::Pose::residue(), and protocols::antibody::TR().

void protocols::antibody::AntibodyInfo::set_CDR_cluster ( CDRNameEnum  cdr,
clusters::CDRClusterCOP  cluster 
)

Manually set the CDR cluster for a particular CDR.

References cdr_cluster_set_.

void protocols::antibody::AntibodyInfo::set_default ( )
private
void protocols::antibody::AntibodyInfo::set_light_chain_type ( LightChainTypeEnum  light_chain)

Set the light chain type via enum.

References is_camelid(), light_chain_type_, protocols::antibody::TR(), and protocols::antibody::unknown.

void protocols::antibody::AntibodyInfo::setup_CDR_cluster ( core::pose::Pose const &  pose,
CDRNameEnum  cdr,
bool  attempt_set_from_pose = false 
)
void protocols::antibody::AntibodyInfo::setup_CDR_clusters ( core::pose::Pose const &  pose,
bool  attempt_set_from_pose = false 
)

setup the clustering information for each CDR to totalCDRLoops Optionally, attempt to set the CDR cluster from the Pose data cache if any data is there.

References total_cdr_loops_.

Referenced by init().

void protocols::antibody::AntibodyInfo::setup_CDR_clusters ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  cdrs,
bool  attempt_set_from_pose = false 
)

setup the clustering information for each CDR according to boolean vector. Optionally, attempt to set the CDR cluster from the Pose data cache if any data is there.

References protocols::antibody::CDRNameEnum_proto_total, and setup_CDR_cluster().

void protocols::antibody::AntibodyInfo::setup_CDRsInfo ( core::pose::Pose const &  pose)
private
void protocols::antibody::AntibodyInfo::setup_FrameWorkInfo ( core::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 ( core::Size const &  jumppoint1,
core::Size const &  cutpoint,
core::Size const &  jumppoint2,
core::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().

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

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

utility::vector1<char> protocols::antibody::AntibodyInfo::ab_sequence_
private
utility::vector1< CDRNameEnum > protocols::antibody::AntibodyInfo::all_cdrs_present_
private
utility::vector1< CDRNameEnum > protocols::antibody::AntibodyInfo::all_cdrs_present_and_proto_
private
clusters::CDRClusterEnumManagerOP protocols::antibody::AntibodyInfo::cdr_cluster_manager_
private
clusters::CDRClusterSetOP protocols::antibody::AntibodyInfo::cdr_cluster_set_
private
bool protocols::antibody::AntibodyInfo::cdr_pdb_numbered_
private

Referenced by AntibodyInfo().

utility::vector1<char> protocols::antibody::AntibodyInfo::chains_for_antigen_
private
utility::vector1<char> protocols::antibody::AntibodyInfo::chains_for_cdrs_
private
utility::vector1< utility::vector1< core::Size> > protocols::antibody::AntibodyInfo::current_transform_
private
AntibodyEnumManagerOP protocols::antibody::AntibodyInfo::enum_manager_
private
utility::vector1< utility::vector1<FrameWork> > protocols::antibody::AntibodyInfo::framework_info_
private
core::Size protocols::antibody::AntibodyInfo::H_chain_
private
bool protocols::antibody::AntibodyInfo::has_antigen_
private
bool protocols::antibody::AntibodyInfo::is_camelid_
private
core::Size protocols::antibody::AntibodyInfo::L_chain_
private
LightChainTypeEnum protocols::antibody::AntibodyInfo::light_chain_type_
private
loops::LoopsOP protocols::antibody::AntibodyInfo::loopsop_having_allcdrs_
private
AntibodyNumbering protocols::antibody::AntibodyInfo::numbering_info_
private
AntibodyNumberingParserOP protocols::antibody::AntibodyInfo::numbering_parser_
private
utility::vector1<utility::vector1< core::Size > > protocols::antibody::AntibodyInfo::packing_angle_numbering_
private
utility::vector1< core::Size > protocols::antibody::AntibodyInfo::packing_angle_residues_
private
H3BaseTypeEnum protocols::antibody::AntibodyInfo::predicted_H3_base_type_
private
std::map<core::Size, char> protocols::antibody::AntibodyInfo::sequence_map_
private
CDRNameEnum protocols::antibody::AntibodyInfo::total_cdr_loops_
private
utility::vector1<loops::LoopsOP> protocols::antibody::AntibodyInfo::vector1_loopsop_having_cdr_
private

the CDR and Framework information

Referenced by AntibodyInfo(), get_CDR_in_loopsop(), get_CDR_loop(), and setup_CDRsInfo().


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