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protocols::antibody Namespace Reference

Namespaces

 clusters
 
 constraints
 
 design
 
 grafting
 
 residue_selector
 
 snugdock
 
 task_operations
 

Classes

class  Ab_TemplateInfo
 Specifically for AntibodyModeling protocol templates. Not for general use. More...
 
class  AntibodyCDRGrafter
 Class to graft CDR loops from an antibody to a new antibody or from a CDR pose into a different antibody. Independant of antibody and CDR modeling. Results in 100 percent loop closure if using both graft algorithms. More...
 
class  AntibodyCDRGrafterCreator
 
class  AntibodyDatabaseManager
 Class responsible for loading information from the AntibodyDatabase. More...
 
class  AntibodyEnumManager
 Interface to this class is in AntibodyInfo. More...
 
class  AntibodyFeatures
 Collects data on an antibody including CDRs, interfaces of L_H, L_A, H_A, and LH_A (this can be set), and other metrics. More...
 
class  AntibodyFeaturesCreator
 creator for the HBondParameterFeatures class More...
 
class  AntibodyInfo
 This class is used to get all relevant information you would need when dealing with an antibody. More...
 
class  AntibodyModelerProtocol
 
struct  AntibodyNumbering
 
class  AntibodyNumberingConverterMover
 Converts numbering schemes of an antibody, independant of AntibodyInfo. By default, works on a SINGLE antibody FAB with chains L and H, as in the rest of Rosetta. More...
 
class  AntibodyNumberingConverterMoverCreator
 
class  AntibodyNumberingParser
 Class responsible for reading database Numbering Scheme definitions and their transforms from the database. More...
 
struct  CDRDBPose
 
struct  CDRDBSequence
 
class  CDRSetOptions
 Class that holds instructions for a single CDR for loading from the antibody database. Default is instructions to load all CDRs from the database. More...
 
class  CDRSetOptionsParser
 Parses CDRSetOptions for a single CDR at a time from a simple instruction file. More...
 
class  CDRsMinPackMin
 
class  CloseOneCDRLoop
 Closes only one CDR onto a framework. More...
 
struct  FrameWork
 
class  GraftCDRLoopsProtocol
 
class  GraftedStemOptimizer
 Grafts only one CDR onto a framework. More...
 
class  GraftOneCDRLoop
 Grafts only one CDR onto a framework. More...
 
class  H3CterInsert
 H3 CDR, Fragment Insertion and CCD. More...
 
class  H3PerturbCCD
 
class  H3RefineCCD
 
class  LHRepulsiveRamp
 
class  LHRepulsiveRampLegacy
 
class  LHSnugFitLegacy
 
struct  ParatopeMetric
 Convenience struct for passing around paratope data, including individual data for cdrs. CDRs not present default to 0. Templates are used mainly to have core::Size/ Real or string values. More...
 
class  PDBLandmark
 Class that was once a struct; Used for matching pdb information between numbering schemes and cdr definitions. More...
 
class  RefineBetaBarrel
 

Typedefs

typedef
utility::pointer::shared_ptr
< Ab_TemplateInfo
Ab_TemplateInfoOP
 
typedef
utility::pointer::shared_ptr
< Ab_TemplateInfo const > 
Ab_TemplateInfoCOP
 
typedef
utility::pointer::shared_ptr
< AntibodyCDRGrafter
AntibodyCDRGrafterOP
 
typedef
utility::pointer::shared_ptr
< AntibodyCDRGrafter const > 
AntibodyCDRGrafterCOP
 
typedef
utility::pointer::shared_ptr
< AntibodyEnumManager
AntibodyEnumManagerOP
 
typedef
utility::pointer::shared_ptr
< AntibodyEnumManager const > 
AntibodyEnumManagerCOP
 
typedef
utility::pointer::shared_ptr
< AntibodyFeatures
AntibodyFeaturesOP
 
typedef
utility::pointer::shared_ptr
< AntibodyFeatures const > 
AntibodyFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< AntibodyInfo
AntibodyInfoOP
 
typedef
utility::pointer::shared_ptr
< AntibodyInfo const > 
AntibodyInfoCOP
 
typedef
utility::pointer::weak_ptr
< AntibodyInfo
AntibodyInfoAP
 
typedef
utility::pointer::weak_ptr
< AntibodyInfo const > 
AntibodyInfoCAP
 
typedef
utility::pointer::shared_ptr
< AntibodyModelerProtocol
AntibodyModelerProtocolOP
 
typedef
utility::pointer::shared_ptr
< AntibodyModelerProtocol
const > 
AntibodyModelerProtocolCOP
 
typedef
utility::pointer::shared_ptr
< AntibodyNumberingConverterMover
AntibodyNumberingConverterMoverOP
 
typedef
utility::pointer::shared_ptr
< AntibodyNumberingConverterMover
const > 
AntibodyNumberingConverterMoverCOP
 
typedef
utility::pointer::shared_ptr
< AntibodyNumberingParser
AntibodyNumberingParserOP
 
typedef
utility::pointer::shared_ptr
< AntibodyNumberingParser
const > 
AntibodyNumberingParserCOP
 
typedef
utility::pointer::shared_ptr
< PDBLandmark
PDBLandmarkOP
 
typedef
utility::pointer::shared_ptr
< PDBLandmark const > 
PDBLandmarkCOP
 
typedef utility::vector1
< utility::vector1< core::Size > > 
Vector2DSize
 
typedef
utility::pointer::shared_ptr
< CDRsMinPackMin
CDRsMinPackMinOP
 
typedef
utility::pointer::shared_ptr
< CDRsMinPackMin const > 
CDRsMinPackMinCOP
 
typedef
utility::pointer::shared_ptr
< CloseOneCDRLoop
CloseOneCDRLoopOP
 
typedef
utility::pointer::shared_ptr
< CloseOneCDRLoop const > 
CloseOneCDRLoopCOP
 
typedef std::map< CDRNameEnum,
vector1< CDRDBPose > > 
CDRDBPoseSet
 
typedef
utility::pointer::shared_ptr
< AntibodyDatabaseManager
AntibodyDatabaseManagerOP
 
typedef
utility::pointer::shared_ptr
< AntibodyDatabaseManager
const > 
AntibodyDatabaseManagerCOP
 
typedef std::map< CDRNameEnum,
utility::vector1
< CDRDBSequence > > 
CDRDBSequenceSet
 
typedef std::map
< core::chemical::AA,
core::Real
AAProbabilities
 
typedef
utility::pointer::shared_ptr
< CDRSetOptions
CDRSetOptionsOP
 
typedef
utility::pointer::shared_ptr
< CDRSetOptions const > 
CDRSetOptionsCOP
 
typedef utility::vector1
< CDRSetOptionsOP
AntibodyCDRSetOptions
 
typedef
utility::pointer::shared_ptr
< CDRSetOptionsParser
CDRSetOptionsParserOP
 
typedef
utility::pointer::shared_ptr
< CDRSetOptionsParser const > 
CDRSetOptionsParserCOP
 
typedef
utility::pointer::shared_ptr
< GraftCDRLoopsProtocol
GraftCDRLoopsProtocolOP
 
typedef
utility::pointer::shared_ptr
< GraftCDRLoopsProtocol const > 
GraftCDRLoopsProtocolCOP
 
typedef
utility::pointer::shared_ptr
< GraftedStemOptimizer
GraftedStemOptimizerOP
 
typedef
utility::pointer::shared_ptr
< const GraftedStemOptimizer
GraftedStemOptimizerCOP
 
typedef
utility::pointer::shared_ptr
< GraftOneCDRLoop
GraftOneCDRLoopOP
 
typedef
utility::pointer::shared_ptr
< const GraftOneCDRLoop
GraftOneCDRLoopCOP
 
typedef
utility::pointer::shared_ptr
< H3CterInsert
H3CterInsertOP
 
typedef
utility::pointer::shared_ptr
< H3CterInsert const > 
H3CterInsertCOP
 
typedef
utility::pointer::shared_ptr
< H3PerturbCCD
H3PerturbCCDOP
 
typedef
utility::pointer::shared_ptr
< H3PerturbCCD const > 
H3PerturbCCDCOP
 
typedef
utility::pointer::shared_ptr
< H3RefineCCD
H3RefineCCDOP
 
typedef
utility::pointer::shared_ptr
< H3RefineCCD const > 
H3RefineCCDCOP
 
typedef
utility::pointer::shared_ptr
< LHRepulsiveRamp
LHRepulsiveRampOP
 
typedef
utility::pointer::shared_ptr
< LHRepulsiveRamp const > 
LHRepulsiveRampCOP
 
typedef
utility::pointer::shared_ptr
< RefineBetaBarrel
RefineBetaBarrelOP
 
typedef
utility::pointer::shared_ptr
< RefineBetaBarrel const > 
RefineBetaBarrelCOP
 
typedef
utility::pointer::shared_ptr
< LHRepulsiveRampLegacy
LHRepulsiveRampLegacyOP
 
typedef
utility::pointer::shared_ptr
< LHRepulsiveRampLegacy const > 
LHRepulsiveRampLegacyCOP
 
typedef
utility::pointer::shared_ptr
< LHSnugFitLegacy
LHSnugFitLegacyOP
 
typedef
utility::pointer::shared_ptr
< LHSnugFitLegacy const > 
LHSnugFitLegacyCOP
 

Enumerations

enum  CDRNameEnum {
  h1 = 1, h2, h3, l1,
  l2, l3, proto_h4, proto_l4,
  start_cdr_loop = h1, H_chain_last_loop = h3, L_chain_last_loop = l3, camelid_last_loop = h3,
  num_cdr_loops = l3, CDRNameEnum_start = h1, CDRNameEnum_total = l3, CDRNameEnum_proto_start = proto_h4,
  CDRNameEnum_proto_total = proto_l4, l4 = proto_l4, h4 = proto_h4, L1 = l1,
  L2 = l2, L3 = l3, H1 = h1, H2 = h2,
  H3 = h3, L4 = l4, H4 = h4
}
 
enum  AntibodyNumberingSchemeEnum {
  Chothia_Scheme = 1, Kabat_Scheme, Enhanced_Chothia_Scheme, IMGT_Scheme,
  AHO_Scheme, AntibodyNumberingSchemeEnum_start = Chothia_Scheme, AntibodyNumberingSchemeEnum_total = AHO_Scheme, NONE
}
 
enum  CDRDefinitionEnum {
  Chothia = 1, Aroop, Kabat, Martin,
  North, CDRDefinitionEnum_start = Chothia, CDRDefinitionEnum_total = North
}
 
enum  LightChainTypeEnum {
  lambda =1, kappa, lambda6, unknown,
  LightChainTypeEnum_start = lambda, LightChainTypeEnum_total = unknown
}
 
enum  AntibodyRegionEnum {
  antigen_region = 1, cdr_region, framework_region, AntibodyRegionEnum_start = antigen_region,
  AntibodyRegionEnum_total = framework_region, unknown_ab_region
}
 
enum  CDRLandmarkEnum { cdr_start = 1, cdr_end, CDRLandmarkEnum_total = cdr_end }
 Main enumerator for AntibodyNumbering. More...
 
enum  H3BaseTypeEnum {
  Kinked = 1, Extended, Neutral, Unknown,
  H3BaseTypeEnum_start = Kinked, H3BaseTypeEnum_total = Unknown
}
 
enum  PackingAngleEnum {
  VL_sheet_1 = 1, VL_sheet_2, VH_sheet_1, VH_sheet_2,
  PackingAngleEnum_start = VL_sheet_1, PackingAngleEnum_total = VH_sheet_2
}
 These are used to determine the VL_VH packing angle. More...
 

Functions

std::ostream & operator<< (std::ostream &out, const Ab_TemplateInfo &ab_t_info)
 
scoring::ScoreFunctionCOP get_Pack_ScoreFxn (void)
 
scoring::ScoreFunctionCOP get_Dock_ScoreFxn (void)
 
scoring::ScoreFunctionCOP get_LoopCentral_ScoreFxn (void)
 
scoring::ScoreFunctionCOP get_LoopHighRes_ScoreFxn (void)
 
std::ostream & operator<< (std::ostream &out, const AntibodyInfo &ab_info)
 
AntibodyInfoOP deep_copy (AntibodyInfo const &source)
 
std::ostream & operator<< (std::ostream &out, const AntibodyModelerProtocol &ab_m)
 
std::ostream & operator<< (std::ostream &os, AntibodyNumberingConverterMover const &mover)
 
static basic::Tracer TR ("protocols.antibody.AntibodyNumberingParser")
 
std::ostream & operator<< (std::ostream &out, const CDRsMinPackMin &ab_m_2)
 
std::ostream & operator<< (std::ostream &out, const GraftCDRLoopsProtocol &ab_m_2)
 
vector1< Realvl_vh_orientation_coords (const core::pose::Pose &pose_in, const AntibodyInfo &ab_info)
 calculate the VH_VL packing angle from 2 sheet definitions on each antibody chain More...
 
std::pair< core::Real, core::Realkink_dihedral (const core::pose::Pose &pose, const protocols::antibody::AntibodyInfo &ab_info, bool debug)
 
core::Real kink_bb_Hbond (const core::pose::Pose &pose, const protocols::antibody::AntibodyInfo &ab_info)
 
core::Real kink_RD_Hbond (const core::pose::Pose &pose, const protocols::antibody::AntibodyInfo &ab_info)
 
core::Real kink_Trp_Hbond (const core::pose::Pose &pose, const protocols::antibody::AntibodyInfo &ab_info)
 
std::pair< ParatopeMetric
< core::Real >, ParatopeMetric
< core::Real > > 
paratope_sasa (const core::pose::Pose &pose, const AntibodyInfo &ab_info, bool include_de_loop=false)
 calculate the SASA of the antibody paratope. Returns all and hydrophobic components. More...
 
core::SSize pose_charge (core::pose::Pose const &pose)
 calculate the net charge of the antibody More...
 
ParatopeMetric< core::SSizeparatope_charge (core::pose::Pose const &pose, const protocols::antibody::AntibodyInfo &abinfo, bool include_de_loop=false)
 calculate the net charge of the paratope More...
 
core::Real cdr_energy (core::pose::Pose const &pose, AntibodyInfoCOP ab_info, core::scoring::ScoreFunctionCOP scorefxn, CDRNameEnum const &cdr)
 calculate dSASA of the paratope and antigen using result of InterfaceAnalyzerMover More...
 
core::Real cdr_CN_anchor_distance (core::pose::Pose const &pose, AntibodyInfoCOP ab_info, CDRNameEnum const &cdr)
 Calculate the distance between the carbon and nitrogen of each residue before and after the CDR respectively. More...
 
vector1< Realcdr_backbone_rmsds (core::pose::Pose &p1, core::pose::Pose const &p2, AntibodyInfoOP const a1, AntibodyInfoOP const a2, core::Size aln_thresh=10)
 Align two sequence matching antibodies and calculate CDR rmsds (add OCD), then store in scores. More...
 
utility::vector1< boolget_cdr_bool_from_tag (utility::tag::TagCOP tag, std::string const &name, bool include_cdr4=false)
 Geta boolean vector of CDRs from a RosettaScripts tag. Companion function for XSD generation: attributes_for_get_cdr_bool_from_tag. More...
 
void attributes_for_get_cdr_bool_from_tag (utility::tag::AttributeList &attlist, std::string const &tagname, std::string const &Description)
 
protocols::loops::LoopsOP get_cdr_loops (AntibodyInfoCOP ab_info, core::pose::Pose const &pose, utility::vector1< bool > const &cdrs, core::Size stem_size)
 Get a set of loops for a boolean vector of CDRNameEnums including any stem residues. More...
 
core::pack::task::TaskFactoryOP setup_packer_task (core::pose::Pose &pose_in)
 Very specific packertask,. More...
 
bool cutpoints_separation (core::pose::Pose &pose, AntibodyInfoOP &antibody_info)
 return false if any cdr cutpoint is broken More...
 
Real cutpoint_separation (pose::Pose &pose_in, core::Size cutpoint)
 
Real global_loop_rmsd (const pose::Pose &pose_in, const pose::Pose &native_pose, loops::LoopsOP current_loop)
 
void align_to_native (core::pose::Pose &pose, core::pose::Pose const &native_pose, AntibodyInfoOP const ab_info, AntibodyInfoOP const native_ab_info, std::string const &request_chain="LH")
 align current Fv to native.Fv More...
 
vector1< boolselect_epitope_residues (AntibodyInfoCOP ab_info, core::pose::Pose const &pose, core::Size const interface_distance=10.0)
 Get the epitope residues using the InterGroupNeighborsCalculator. More...
 
void check_fix_aho_cdr_numbering (AntibodyInfoCOP ab_info, CDRNameEnum cdr, core::pose::Pose &pose)
 Checks the length of the CDR, fixes AHO numbering for longer CDR loops that don't fit within the numbering scheme. More...
 
void check_fix_aho_cdr_numbering (AntibodyInfoCOP ab_info, core::pose::Pose &pose)
 
void simple_one_loop_fold_tree (pose::Pose &pose_in, loops::Loop const &loop)
 
void simple_fold_tree (pose::Pose &pose_in, core::Size jumppoint1, core::Size cutpoint, core::Size jumppoint2)
 
std::string setup_LH_A_foldtree (AntibodyInfoCOP ab_info, core::pose::Pose &pose)
 Setup LH_A foldtree via docking. Return dock_chains string. More...
 
std::string setup_A_LH_foldtree (AntibodyInfoCOP ab_info, core::pose::Pose &pose)
 Setup A_LH foldtree via docking. Return dock_chains string. More...
 
bool CDR_H3_filter_legacy_code_with_old_rule (const pose::Pose &pose_in, loops::Loop &input_loop, bool is_camelid)
 tests if a loop has H3 like base charachteristics More...
 
bool CDR_H3_cter_filter (const pose::Pose &pose_in, AntibodyInfoOP ab_info)
 
bool is_H3_rama_kinked (std::string const &rama)
 Very basic kink function based on rama groups. Kink is defined as having AB + DB at the C-terminal stem. This is in the North/Dunbrack CDR definition. Avoid this definition if you can and talk to brain. This is currently used for a quick filtering for design. More...
 
void kink_constrain_antibody_H3 (core::pose::Pose &pose, AntibodyInfoOP const antibody_info)
 
void kink_constrain_antibody_H3 (core::pose::Pose &pose, core::Size kink_begin)
 Apply auto-generated kink constraint. More...
 
void qq_constrain_antibody (core::pose::Pose &pose, core::Size VH_qq_resi, core::Size VL_qq_resi)
 
PDBLandmarkCOP get_matching_landmark (AntibodyNumbering const &numbering, PDBLandmark const &landmark, AntibodyNumberingSchemeEnum const from_scheme, AntibodyNumberingSchemeEnum const to_scheme)
 get the equivalent landmark in a numbering scheme. Set the resnum to zero if not found. More...
 
vector1< Realget_conserved_residue_list (char chain)
 return vector of Chothia-nubmered, conserved residues for grafting and alignment More...
 

Typedef Documentation

typedef utility::pointer::shared_ptr< Ab_TemplateInfo const > protocols::antibody::Ab_TemplateInfoCOP
typedef utility::pointer::shared_ptr< Ab_TemplateInfo > protocols::antibody::Ab_TemplateInfoOP
typedef utility::pointer::shared_ptr< AntibodyCDRGrafter const > protocols::antibody::AntibodyCDRGrafterCOP
typedef utility::pointer::shared_ptr< AntibodyCDRGrafter > protocols::antibody::AntibodyCDRGrafterOP
typedef utility::pointer::shared_ptr< AntibodyDatabaseManager const > protocols::antibody::AntibodyDatabaseManagerCOP
typedef utility::pointer::shared_ptr< AntibodyEnumManager const > protocols::antibody::AntibodyEnumManagerCOP
typedef utility::pointer::shared_ptr< AntibodyEnumManager > protocols::antibody::AntibodyEnumManagerOP
typedef utility::pointer::shared_ptr< AntibodyFeatures const > protocols::antibody::AntibodyFeaturesCOP
typedef utility::pointer::shared_ptr< AntibodyFeatures > protocols::antibody::AntibodyFeaturesOP
typedef utility::pointer::weak_ptr< AntibodyInfo > protocols::antibody::AntibodyInfoAP
typedef utility::pointer::weak_ptr< AntibodyInfo const > protocols::antibody::AntibodyInfoCAP
typedef utility::pointer::shared_ptr< AntibodyInfo const > protocols::antibody::AntibodyInfoCOP
typedef utility::pointer::shared_ptr< AntibodyInfo > protocols::antibody::AntibodyInfoOP
typedef utility::pointer::shared_ptr< AntibodyModelerProtocol const > protocols::antibody::AntibodyModelerProtocolCOP
typedef utility::pointer::shared_ptr< AntibodyNumberingParser const > protocols::antibody::AntibodyNumberingParserCOP
typedef std::map< CDRNameEnum, utility::vector1< CDRDBPose > > protocols::antibody::CDRDBPoseSet
typedef std::map<CDRNameEnum, utility::vector1<CDRDBSequence> > protocols::antibody::CDRDBSequenceSet
typedef utility::pointer::shared_ptr< CDRSetOptions const > protocols::antibody::CDRSetOptionsCOP
typedef utility::pointer::shared_ptr< CDRSetOptions > protocols::antibody::CDRSetOptionsOP
typedef utility::pointer::shared_ptr< CDRSetOptionsParser const > protocols::antibody::CDRSetOptionsParserCOP
typedef utility::pointer::shared_ptr< CDRSetOptionsParser > protocols::antibody::CDRSetOptionsParserOP
typedef utility::pointer::shared_ptr< CDRsMinPackMin const > protocols::antibody::CDRsMinPackMinCOP
typedef utility::pointer::shared_ptr< CDRsMinPackMin > protocols::antibody::CDRsMinPackMinOP
typedef utility::pointer::shared_ptr< CloseOneCDRLoop const > protocols::antibody::CloseOneCDRLoopCOP
typedef utility::pointer::shared_ptr< CloseOneCDRLoop > protocols::antibody::CloseOneCDRLoopOP
typedef utility::pointer::shared_ptr< GraftCDRLoopsProtocol const > protocols::antibody::GraftCDRLoopsProtocolCOP
typedef utility::pointer::shared_ptr<const GraftedStemOptimizer> protocols::antibody::GraftedStemOptimizerCOP
typedef utility::pointer::shared_ptr< GraftedStemOptimizer > protocols::antibody::GraftedStemOptimizerOP
typedef utility::pointer::shared_ptr<const GraftOneCDRLoop> protocols::antibody::GraftOneCDRLoopCOP
typedef utility::pointer::shared_ptr< GraftOneCDRLoop > protocols::antibody::GraftOneCDRLoopOP
typedef utility::pointer::shared_ptr< H3CterInsert const > protocols::antibody::H3CterInsertCOP
typedef utility::pointer::shared_ptr< H3CterInsert > protocols::antibody::H3CterInsertOP
typedef utility::pointer::shared_ptr< H3PerturbCCD const > protocols::antibody::H3PerturbCCDCOP
typedef utility::pointer::shared_ptr< H3PerturbCCD > protocols::antibody::H3PerturbCCDOP
typedef utility::pointer::shared_ptr< H3RefineCCD const > protocols::antibody::H3RefineCCDCOP
typedef utility::pointer::shared_ptr< H3RefineCCD > protocols::antibody::H3RefineCCDOP
typedef utility::pointer::shared_ptr< LHRepulsiveRamp const > protocols::antibody::LHRepulsiveRampCOP
typedef utility::pointer::shared_ptr< LHRepulsiveRampLegacy const > protocols::antibody::LHRepulsiveRampLegacyCOP
typedef utility::pointer::shared_ptr< LHRepulsiveRamp > protocols::antibody::LHRepulsiveRampOP
typedef utility::pointer::shared_ptr< LHSnugFitLegacy const > protocols::antibody::LHSnugFitLegacyCOP
typedef utility::pointer::shared_ptr< LHSnugFitLegacy > protocols::antibody::LHSnugFitLegacyOP
typedef utility::pointer::shared_ptr< PDBLandmark const > protocols::antibody::PDBLandmarkCOP
typedef utility::pointer::shared_ptr< PDBLandmark > protocols::antibody::PDBLandmarkOP
typedef utility::pointer::shared_ptr< RefineBetaBarrel const > protocols::antibody::RefineBetaBarrelCOP
typedef utility::pointer::shared_ptr< RefineBetaBarrel > protocols::antibody::RefineBetaBarrelOP
typedef utility::vector1< utility::vector1< core::Size > > protocols::antibody::Vector2DSize

Enumeration Type Documentation

Enumerator
Chothia_Scheme 
Kabat_Scheme 
Enhanced_Chothia_Scheme 
IMGT_Scheme 
AHO_Scheme 
AntibodyNumberingSchemeEnum_start 
AntibodyNumberingSchemeEnum_total 
NONE 
Enumerator
antigen_region 
cdr_region 
framework_region 
AntibodyRegionEnum_start 
AntibodyRegionEnum_total 
unknown_ab_region 
Enumerator
Chothia 
Aroop 
Kabat 
Martin 
North 
CDRDefinitionEnum_start 
CDRDefinitionEnum_total 

Main enumerator for AntibodyNumbering.

Enumerator
cdr_start 
cdr_end 
CDRLandmarkEnum_total 
Enumerator
h1 
h2 
h3 
l1 
l2 
l3 
proto_h4 

Proto, not quite CDR loops for design and analysis /// Also known as the DE loop ///

proto_l4 
start_cdr_loop 
H_chain_last_loop 
L_chain_last_loop 
camelid_last_loop 
num_cdr_loops 
CDRNameEnum_start 
CDRNameEnum_total 
CDRNameEnum_proto_start 
CDRNameEnum_proto_total 
l4 
h4 
L1 
L2 
L3 
H1 
H2 
H3 
L4 
H4 
Enumerator
Kinked 
Extended 
Neutral 
Unknown 
H3BaseTypeEnum_start 
H3BaseTypeEnum_total 
Enumerator
lambda 
kappa 
lambda6 
unknown 
LightChainTypeEnum_start 
LightChainTypeEnum_total 

These are used to determine the VL_VH packing angle.

Enumerator
VL_sheet_1 
VL_sheet_2 
VH_sheet_1 
VH_sheet_2 
PackingAngleEnum_start 
PackingAngleEnum_total 

Function Documentation

void protocols::antibody::align_to_native ( core::pose::Pose pose,
core::pose::Pose const &  native_pose,
AntibodyInfoOP const  ab_info,
AntibodyInfoOP const  native_ab_info,
std::string const &  reqeust_chain 
)
void protocols::antibody::attributes_for_get_cdr_bool_from_tag ( utility::tag::AttributeList &  attlist,
std::string const &  tagname,
std::string const &  Description 
)
utility::vector1< core::Real > protocols::antibody::cdr_backbone_rmsds ( core::pose::Pose p1,
core::pose::Pose const &  p2,
AntibodyInfoOP const  a1,
AntibodyInfoOP const  a2,
core::Size  aln_thresh = 10 
)
core::Real protocols::antibody::cdr_CN_anchor_distance ( core::pose::Pose const &  pose,
AntibodyInfoCOP  ab_info,
CDRNameEnum const &  cdr 
)

Calculate the distance between the carbon and nitrogen of each residue before and after the CDR respectively.

References core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::antibody::AntibodyFeatures::report_cdr_metrics_features().

core::Real protocols::antibody::cdr_energy ( core::pose::Pose const &  pose,
AntibodyInfoCOP  ab_info,
core::scoring::ScoreFunctionCOP  scorefxn,
CDRNameEnum const &  cdr 
)

calculate dSASA of the paratope and antigen using result of InterfaceAnalyzerMover

calculate dSASA of the paratope using data held in PerResidueInterfaceData returned from InterfaceAnalyzerMover calculate dSASA of a cdr and antigen using InterfaceAnalyzerMover. Returns all and hydrophobic components. calculate dSASA of a cdr using data held in PerResidueInterfaceData returned from InterfaceAnalyzerMover. Calculates energy of cdr by decomposing scorefxn into pair and then summing. This means it includes hbonding components, etc.

References cdr_end, cdr_start, core::pose::Pose::clone(), core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies(), core::pose::Pose::energies(), core::scoring::methods::EnergyMethodOptions::hbond_options(), and core::scoring::Energies::residue_total_energy().

Referenced by protocols::antibody::AntibodyFeatures::report_cdr_metrics_features().

bool protocols::antibody::CDR_H3_cter_filter ( const pose::Pose pose_in,
AntibodyInfoOP  ab_info 
)
bool protocols::antibody::CDR_H3_filter_legacy_code_with_old_rule ( const pose::Pose pose_in,
loops::Loop &  input_loop,
bool  is_camelid 
)

tests if a loop has H3 like base charachteristics

Uses the Shirai rules to find out if the dihedral angle formed by CA atoms of residues n-2,n-1,n and n+1 conform to a kinked/extended structure in accordance with the sequence. If there is a match, a true value is returned

Parameters
[in]posefull actual protein loop_begin: seq numbered loop begin corresponding to pose size: size of loop to compute loop_end
Global Read: reads -command line flag -base stored in dle_ns
to determine to do the complete H3 filter check or just do a prediction of the H3 base type based on the aforementioned dihedral angle
References: Structural classification of CDR-H3 in antibodies
Hiroki Shirai, Akinori Kidera, Haruki Nakamura FEBS Letters 399 (1996) 1-8
Author
Aroop 02/04/2010

References protocols::frag_picker::CA, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::loops::Loop::start(), protocols::loops::start, protocols::loops::Loop::stop(), protocols::loops::stop, TR(), and core::conformation::Residue::xyz().

void protocols::antibody::check_fix_aho_cdr_numbering ( AntibodyInfoCOP  ab_info,
CDRNameEnum  cdr,
core::pose::Pose pose 
)

Checks the length of the CDR, fixes AHO numbering for longer CDR loops that don't fit within the numbering scheme.

References core::pose::Pose::pdb_info(), and TR().

Referenced by protocols::antibody::AntibodyCDRGrafter::apply(), check_fix_aho_cdr_numbering(), and protocols::antibody::design::AntibodyDesignMover::finalize_pose().

void protocols::antibody::check_fix_aho_cdr_numbering ( AntibodyInfoCOP  ab_info,
core::pose::Pose pose 
)
core::Real protocols::antibody::cutpoint_separation ( core::pose::Pose pose_in,
core::Size  cutpoint 
)

Compute the separation at the cutpoint. The N-C distance of the peptide bond which should be formed at the cutpoint. A closed loop is assumed to have a gap < 1.9 Ang

References core::chemical::element::C, core::chemical::element::N, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by cutpoints_separation().

bool protocols::antibody::cutpoints_separation ( core::pose::Pose pose,
AntibodyInfoOP &  antibody_info 
)

return false if any cdr cutpoint is broken

References cutpoint_separation().

Referenced by protocols::antibody::H3RefineCCD::apply().

AntibodyInfoOP protocols::antibody::deep_copy ( AntibodyInfo const &  source)
inline
utility::vector1< bool > protocols::antibody::get_cdr_bool_from_tag ( utility::tag::TagCOP  tag,
std::string const &  name,
bool  include_cdr4 
)
protocols::loops::LoopsOP protocols::antibody::get_cdr_loops ( AntibodyInfoCOP  ab_info,
core::pose::Pose const &  pose,
utility::vector1< bool > const &  cdrs,
core::Size  stem_size 
)

Get a set of loops for a boolean vector of CDRNameEnums including any stem residues.

References CDRNameEnum_proto_total.

Referenced by protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::apply(), and protocols::antibody::design::AntibodySeqDesignTFCreator::get_design_cdr_loops().

utility::vector1< core::Real > protocols::antibody::get_conserved_residue_list ( char  chain)

return vector of Chothia-nubmered, conserved residues for grafting and alignment

Referenced by cdr_backbone_rmsds().

scoring::ScoreFunctionCOP protocols::antibody::get_Dock_ScoreFxn ( void  )
scoring::ScoreFunctionCOP protocols::antibody::get_LoopCentral_ScoreFxn ( void  )
scoring::ScoreFunctionCOP protocols::antibody::get_LoopHighRes_ScoreFxn ( void  )
PDBLandmarkCOP protocols::antibody::get_matching_landmark ( AntibodyNumbering const &  numbering,
PDBLandmark const &  query_landmark,
AntibodyNumberingSchemeEnum const  from_scheme,
AntibodyNumberingSchemeEnum const  to_scheme 
)

get the equivalent landmark in a numbering scheme. Set the resnum to zero if not found.

References protocols::antibody::AntibodyNumbering::numbering_scheme_transform.

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

scoring::ScoreFunctionCOP protocols::antibody::get_Pack_ScoreFxn ( void  )
core::Real protocols::antibody::global_loop_rmsd ( const pose::Pose pose_in,
const pose::Pose native_pose,
loops::LoopsOP  current_loop 
)
bool protocols::antibody::is_H3_rama_kinked ( std::string const &  rama)

Very basic kink function based on rama groups. Kink is defined as having AB + DB at the C-terminal stem. This is in the North/Dunbrack CDR definition. Avoid this definition if you can and talk to brain. This is currently used for a quick filtering for design.

Referenced by protocols::antibody::AntibodyDatabaseManager::load_cdr_poses(), and protocols::antibody::AntibodyDatabaseManager::load_cdr_sequences_for_cdr().

core::Real protocols::antibody::kink_bb_Hbond ( const core::pose::Pose pose,
const protocols::antibody::AntibodyInfo ab_info 
)
void protocols::antibody::kink_constrain_antibody_H3 ( core::pose::Pose pose,
AntibodyInfoOP const  antibody_info 
)
void protocols::antibody::kink_constrain_antibody_H3 ( core::pose::Pose pose,
core::Size  kink_begin 
)
std::pair< core::Real, core::Real > protocols::antibody::kink_dihedral ( const core::pose::Pose pose,
const protocols::antibody::AntibodyInfo ab_info,
bool  debug 
)
core::Real protocols::antibody::kink_RD_Hbond ( const core::pose::Pose pose,
const protocols::antibody::AntibodyInfo ab_info 
)
core::Real protocols::antibody::kink_Trp_Hbond ( const core::pose::Pose pose,
const protocols::antibody::AntibodyInfo ab_info 
)
std::ostream& protocols::antibody::operator<< ( std::ostream &  out,
const Ab_TemplateInfo &  ab_t_info 
)
std::ostream& protocols::antibody::operator<< ( std::ostream &  out,
const CDRsMinPackMin &  ab_m_2 
)
std::ostream & protocols::antibody::operator<< ( std::ostream &  os,
AntibodyNumberingConverterMover const &  mover 
)
std::ostream& protocols::antibody::operator<< ( std::ostream &  out,
const GraftCDRLoopsProtocol &  ab_m_2 
)
std::ostream& protocols::antibody::operator<< ( std::ostream &  out,
const AntibodyModelerProtocol &  ab_m 
)
std::ostream& protocols::antibody::operator<< ( std::ostream &  out,
const AntibodyInfo &  ab_info 
)
ParatopeMetric< core::SSize > protocols::antibody::paratope_charge ( core::pose::Pose const &  pose,
const protocols::antibody::AntibodyInfo ab_info,
bool  include_de_loop 
)
std::pair< ParatopeMetric< core::Real >, ParatopeMetric< core::Real > > protocols::antibody::paratope_sasa ( const core::pose::Pose pose,
const protocols::antibody::AntibodyInfo ab_info,
bool  include_de_loop 
)
core::SSize protocols::antibody::pose_charge ( core::pose::Pose const &  pose)
void protocols::antibody::qq_constrain_antibody ( core::pose::Pose pose,
core::Size  VH_qq_resi,
core::Size  VL_qq_resi 
)
utility::vector1< bool > protocols::antibody::select_epitope_residues ( AntibodyInfoCOP  ab_info,
core::pose::Pose const &  pose,
core::Size const  interface_distance 
)
std::string protocols::antibody::setup_A_LH_foldtree ( AntibodyInfoCOP  ab_info,
core::pose::Pose pose 
)

Setup A_LH foldtree via docking. Return dock_chains string.

References protocols::docking::setup_foldtree().

std::string protocols::antibody::setup_LH_A_foldtree ( AntibodyInfoCOP  ab_info,
core::pose::Pose pose 
)

Setup LH_A foldtree via docking. Return dock_chains string.

References protocols::docking::setup_foldtree().

core::pack::task::TaskFactoryOP protocols::antibody::setup_packer_task ( core::pose::Pose pose_in)
void protocols::antibody::simple_fold_tree ( pose::Pose pose_in,
core::Size  jumppoint1,
core::Size  cutpoint,
core::Size  jumppoint2 
)
void protocols::antibody::simple_one_loop_fold_tree ( pose::Pose pose_in,
loops::Loop const &  loop 
)
static basic::Tracer protocols::antibody::TR ( "protocols.antibody.AntibodyNumberingParser"  )
static

Referenced by protocols::antibody::constraints::CDRDihedralConstraintMover::add_harmonic_cluster_constraint(), protocols::antibody::H3CterInsert::apply(), protocols::antibody::GraftCDRLoopsProtocol::apply(), protocols::antibody::AntibodyModelerProtocol::apply(), protocols::antibody::RefineBetaBarrel::apply(), protocols::antibody::H3PerturbCCD::apply(), protocols::antibody::constraints::ParatopeSiteConstraintMover::apply(), protocols::antibody::LHRepulsiveRamp::apply(), protocols::antibody::snugdock::SnugDockProtocol::apply(), protocols::antibody::snugdock::SnugDock::apply(), protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::apply(), protocols::antibody::AntibodyNumberingConverterMover::apply(), protocols::antibody::LHRepulsiveRampLegacy::apply(), protocols::antibody::AntibodyCDRGrafter::apply(), protocols::antibody::constraints::CDRDihedralConstraintMover::apply(), protocols::antibody::task_operations::AddCDRProfileSetsOperation::apply(), protocols::antibody::H3RefineCCD::apply(), protocols::antibody::design::MutateFrameworkForCluster::apply(), protocols::antibody::design::AntibodyDesignMover::apply(), protocols::antibody::task_operations::AddCDRProfilesOperation::apply(), protocols::antibody::AntibodyCDRGrafter::apply_to_cdr(), protocols::antibody::design::AntibodyDesignMover::apply_to_cdr(), protocols::antibody::design::GeneralAntibodyModeler::backrub_cdrs(), protocols::antibody::AntibodyFeatures::calculate_cdr_contacts_nres(), protocols::antibody::AntibodyFeatures::calculate_residue_atomic_contacts(), CDR_H3_cter_filter(), CDR_H3_filter_legacy_code_with_old_rule(), check_fix_aho_cdr_numbering(), protocols::antibody::AntibodyDatabaseManager::create_database_session(), protocols::antibody::AntibodyNumberingParser::debug_print(), protocols::antibody::AntibodyInfo::detect_and_set_camelid_CDR_H3_stem_type(), protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type(), protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type_new_rule(), protocols::antibody::design::AntibodySeqDesignTFCreator::disable_disallowed_aa(), protocols::antibody::AntibodyModelerProtocol::display_constraint_residues(), protocols::antibody::GraftCDRLoopsProtocol::display_constraint_residues(), protocols::antibody::design::GeneralAntibodyModeler::dock_high_res(), protocols::antibody::design::GeneralAntibodyModeler::dock_low_res(), protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_output(), protocols::antibody::RefineBetaBarrel::finalize_setup(), protocols::antibody::CDRsMinPackMin::finalize_setup(), protocols::antibody::GraftCDRLoopsProtocol::finalize_setup(), protocols::antibody::LHRepulsiveRampLegacy::finalize_setup(), protocols::antibody::AntibodyModelerProtocol::finalize_setup(), protocols::antibody::design::AntibodyDesignMover::finalize_setup(), protocols::antibody::design::get_cdr_set_options(), protocols::antibody::design::AntibodySeqDesignTFCreator::get_design_cdr_loops(), protocols::antibody::design::get_dock_chains_from_ab_dock_chains(), protocols::antibody::design::AntibodySeqDesignTFCreator::get_framework_conservative_op(), protocols::antibody::design::get_graft_design_options(), protocols::antibody::constraints::CDRDihedralConstraintMover::get_harmonic_cluster_constraint_filename(), protocols::antibody::AntibodyInfo::get_landmark_resnum(), protocols::antibody::AntibodyInfo::get_MoveMap_for_AllCDRsSideChains_and_H3backbone(), protocols::antibody::design::get_pdb_numbering_from_single_string(), protocols::antibody::design::get_resnums_from_strings_with_ranges(), protocols::antibody::design::get_seq_design_options(), protocols::antibody::AntibodyInfo::identify_CDR_from_a_sequence(), protocols::antibody::GraftCDRLoopsProtocol::init_from_options(), protocols::antibody::AntibodyModelerProtocol::init_from_options(), kink_constrain_antibody_H3(), protocols::antibody::AntibodyDatabaseManager::load_cdr_design_data(), protocols::antibody::AntibodyDatabaseManager::load_cdr_design_data_for_cdrs(), protocols::antibody::AntibodyDatabaseManager::load_cdr_pose(), protocols::antibody::AntibodyDatabaseManager::load_cdr_poses(), protocols::antibody::AntibodyDatabaseManager::load_cdr_sequences(), protocols::antibody::AntibodyDatabaseManager::load_cdr_sequences_for_cdr(), protocols::antibody::AntibodyDatabaseManager::load_structure_loading_info(), protocols::antibody::design::GeneralAntibodyModeler::minimize_cdrs(), protocols::antibody::design::GeneralAntibodyModeler::minimize_interface(), protocols::antibody::constraints::ParatopeSiteConstraintMover::parse_my_tag(), protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::parse_my_tag(), protocols::antibody::AntibodyFeatures::parse_my_tag(), protocols::antibody::residue_selector::AntibodyRegionSelector::parse_my_tag(), protocols::antibody::residue_selector::CDRResidueSelector::parse_my_tag(), protocols::antibody::AntibodyCDRGrafter::parse_my_tag(), protocols::antibody::task_operations::DisableAntibodyRegionOperation::parse_tag(), protocols::antibody::task_operations::DisableCDRsOperation::parse_tag(), protocols::antibody::task_operations::AddCDRProfileSetsOperation::parse_tag(), protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::parse_tag(), protocols::antibody::task_operations::AddCDRProfilesOperation::parse_tag(), protocols::antibody::task_operations::AddCDRProfileSetsOperation::pre_load_data(), protocols::antibody::task_operations::AddCDRProfilesOperation::pre_load_data(), qq_constrain_antibody(), protocols::antibody::AntibodyInfo::qq_heavy_residue(), protocols::antibody::AntibodyInfo::qq_light_residue(), protocols::antibody::H3PerturbCCD::read_and_store_fragments(), protocols::antibody::AntibodyNumberingParser::read_cdr_definition_file(), protocols::antibody::design::AntibodyDesignMover::read_command_line_options(), protocols::antibody::H3CterInsert::read_H3_cter_fragment(), protocols::antibody::AntibodyNumberingParser::read_numbering_scheme_file(), protocols::antibody::design::GeneralAntibodyModeler::relax_cdrs(), protocols::antibody::design::GeneralAntibodyModeler::repack_antibody_interface(), protocols::antibody::design::GeneralAntibodyModeler::repack_antigen_ab_interface(), protocols::antibody::design::GeneralAntibodyModeler::repack_antigen_interface(), protocols::antibody::design::GeneralAntibodyModeler::repack_cdrs(), protocols::antibody::AntibodyFeatures::report_features(), protocols::antibody::design::AntibodyDesignMover::run_basic_mc_algorithm(), protocols::antibody::design::AntibodyDesignMover::run_deterministic_graft_algorithm(), protocols::antibody::design::AntibodyDesignMover::run_graft(), protocols::antibody::design::AntibodyDesignMover::run_optimization_cycle(), protocols::antibody::CDRSetOptionsParser::set_cdr_set_include_options(), protocols::antibody::AntibodyModelerProtocol::set_default(), protocols::antibody::GraftCDRLoopsProtocol::set_default(), protocols::antibody::AntibodyInfo::set_default(), protocols::antibody::AntibodyInfo::set_light_chain_type(), protocols::antibody::design::set_native_cdr_sequence(), protocols::antibody::snugdock::SnugDockProtocol::setup_ab_ag_foldtree(), protocols::antibody::AntibodyInfo::setup_CDR_cluster(), protocols::antibody::AntibodyInfo::setup_CDRsInfo(), protocols::antibody::snugdock::SnugDockProtocol::setup_objects(), protocols::antibody::snugdock::SnugDock::setup_objects(), protocols::antibody::AntibodyModelerProtocol::setup_objects(), setup_packer_task(), protocols::antibody::design::AntibodyDesignMover::setup_random_start_pose(), protocols::antibody::AntibodyInfo::setup_VL_VH_packing_angle(), simple_fold_tree(), and simple_one_loop_fold_tree().

utility::vector1< core::Real > protocols::antibody::vl_vh_orientation_coords ( const core::pose::Pose pose_in,
const AntibodyInfo &  ab_info 
)