Rosetta Protocols  2014.35
Namespaces | Classes | Typedefs | Enumerations | Functions | Variables
protocols::antibody Namespace Reference

Namespaces

 clusters
 
 design
 

Classes

class  Ab_TemplateInfo
 Specifically for AntibodyModeling protocol templates. Not for general use. 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  AntibodyNumberingParser
 Class responsible for reading database Numbering Scheme definitions and their transforms from the database. 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
 
class  ModelCDRH3
 Ab initio modeling of CDR H3 loop. More...
 
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 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
 
class  RefineOneCDRLoop
 
class  RefineOneCDRLoopCentroid
 
class  SnugDock
 MoveSet step of Snugdock as described in: More...
 
class  SnugDockProtocol
 

Typedefs

typedef
utility::pointer::owning_ptr
< Ab_TemplateInfo
Ab_TemplateInfoOP
 
typedef
utility::pointer::owning_ptr
< Ab_TemplateInfo const > 
Ab_TemplateInfoCOP
 
typedef
utility::pointer::owning_ptr
< AntibodyEnumManager
AntibodyEnumManagerOP
 
typedef
utility::pointer::owning_ptr
< AntibodyEnumManager const > 
AntibodyEnumManagerCOP
 
typedef
utility::pointer::owning_ptr
< AntibodyFeatures
AntibodyFeaturesOP
 
typedef
utility::pointer::owning_ptr
< AntibodyFeatures const > 
AntibodyFeaturesCOP
 
typedef
utility::pointer::owning_ptr
< AntibodyInfo
AntibodyInfoOP
 
typedef
utility::pointer::owning_ptr
< AntibodyInfo const > 
AntibodyInfoCOP
 
typedef
utility::pointer::access_ptr
< AntibodyInfo
AntibodyInfoAP
 
typedef
utility::pointer::access_ptr
< AntibodyInfo const > 
AntibodyInfoCAP
 
typedef
utility::pointer::owning_ptr
< AntibodyModelerProtocol
AntibodyModelerProtocolOP
 
typedef
utility::pointer::owning_ptr
< AntibodyModelerProtocol
const > 
AntibodyModelerProtocolCOP
 
typedef
utility::pointer::owning_ptr
< AntibodyNumberingParser
AntibodyNumberingParserOP
 
typedef
utility::pointer::owning_ptr
< AntibodyNumberingParser
const > 
AntibodyNumberingParserCOP
 
typedef
utility::pointer::owning_ptr
< PDBLandmark
PDBLandmarkOP
 
typedef
utility::pointer::owning_ptr
< PDBLandmark const > 
PDBLandmarkCOP
 
typedef vector1< vector1< Size > > Vector2DSize
 
typedef
utility::pointer::owning_ptr
< CDRsMinPackMin
CDRsMinPackMinOP
 
typedef
utility::pointer::owning_ptr
< CDRsMinPackMin const > 
CDRsMinPackMinCOP
 
typedef
utility::pointer::owning_ptr
< CloseOneCDRLoop
CloseOneCDRLoopOP
 
typedef
utility::pointer::owning_ptr
< CloseOneCDRLoop const > 
CloseOneCDRLoopCOP
 
typedef
utility::pointer::owning_ptr
< GraftCDRLoopsProtocol
GraftCDRLoopsProtocolOP
 
typedef
utility::pointer::owning_ptr
< GraftCDRLoopsProtocol const > 
GraftCDRLoopsProtocolCOP
 
typedef
utility::pointer::owning_ptr
< GraftedStemOptimizer
GraftedStemOptimizerOP
 
typedef
utility::pointer::owning_ptr
< const GraftedStemOptimizer
GraftedStemOptimizerCOP
 
typedef
utility::pointer::owning_ptr
< GraftOneCDRLoop
GraftOneCDRLoopOP
 
typedef
utility::pointer::owning_ptr
< const GraftOneCDRLoop
GraftOneCDRLoopCOP
 
typedef
utility::pointer::owning_ptr
< H3CterInsert
H3CterInsertOP
 
typedef
utility::pointer::owning_ptr
< H3CterInsert const > 
H3CterInsertCOP
 
typedef
utility::pointer::owning_ptr
< H3PerturbCCD
H3PerturbCCDOP
 
typedef
utility::pointer::owning_ptr
< H3PerturbCCD const > 
H3PerturbCCDCOP
 
typedef
utility::pointer::owning_ptr
< H3RefineCCD
H3RefineCCDOP
 
typedef
utility::pointer::owning_ptr
< H3RefineCCD const > 
H3RefineCCDCOP
 
typedef
utility::pointer::owning_ptr
< LHRepulsiveRamp
LHRepulsiveRampOP
 
typedef
utility::pointer::owning_ptr
< LHRepulsiveRamp const > 
LHRepulsiveRampCOP
 
typedef
utility::pointer::owning_ptr
< ModelCDRH3
ModelCDRH3OP
 
typedef
utility::pointer::owning_ptr
< ModelCDRH3 const > 
ModelCDRH3COP
 
typedef
utility::pointer::owning_ptr
< RefineBetaBarrel
RefineBetaBarrelOP
 
typedef
utility::pointer::owning_ptr
< RefineBetaBarrel const > 
RefineBetaBarrelCOP
 
typedef
utility::pointer::owning_ptr
< RefineOneCDRLoop
RefineOneCDRLoopOP
 
typedef
utility::pointer::owning_ptr
< RefineOneCDRLoop const > 
RefineOneCDRLoopCOP
 
typedef
utility::pointer::owning_ptr
< RefineOneCDRLoopCentroid
RefineOneCDRLoopCentroidOP
 
typedef
utility::pointer::owning_ptr
< RefineOneCDRLoopCentroid
const > 
RefineOneCDRLoopCentroidCOP
 
typedef
utility::pointer::owning_ptr
< SnugDock
SnugDockOP
 
typedef
utility::pointer::owning_ptr
< SnugDock const > 
SnugDockCOP
 
typedef
utility::pointer::owning_ptr
< SnugDockProtocol
SnugDockProtocolOP
 
typedef
utility::pointer::owning_ptr
< SnugDockProtocol const > 
SnugDockProtocolCOP
 
typedef
utility::pointer::owning_ptr
< LHRepulsiveRampLegacy
LHRepulsiveRampLegacyOP
 
typedef
utility::pointer::owning_ptr
< LHRepulsiveRampLegacy const > 
LHRepulsiveRampLegacyCOP
 
typedef
utility::pointer::owning_ptr
< LHSnugFitLegacy
LHSnugFitLegacyOP
 
typedef
utility::pointer::owning_ptr
< LHSnugFitLegacy const > 
LHSnugFitLegacyCOP
 

Enumerations

enum  CDRNameEnum {
  h1 = 1, h2, h3, l1,
  l2, l3, 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
}
 
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  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)
 
std::ostream & operator<< (std::ostream &out, const AntibodyModelerProtocol &ab_m)
 
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)
 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)
 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...
 
std::ostream & operator<< (std::ostream &out, SnugDock const &)
 
std::ostream & operator<< (std::ostream &out, SnugDockProtocol const &snugdockprotocol)
 
void simple_one_loop_fold_tree (pose::Pose &pose_in, loops::Loop const &loop)
 
void simple_fold_tree (pose::Pose &pose_in, Size jumppoint1, Size cutpoint, Size jumppoint2)
 
std::string setup_LH_A_foldtree (AntibodyInfoCOP ab_info, core::pose::Pose &pose)
 Setup LH_A foldtree. Return dock_chains string. More...
 
std::string setup_A_LH_foldtree (AntibodyInfoCOP ab_info, core::pose::Pose &pose)
 Setup A_LH foldtree. 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)
 
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, 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...
 
std::map< CDRNameEnum, booladd_harmonic_cluster_constraints (AntibodyInfoOP ab_info, pose::Pose &pose)
 Adds dihedral harmonic constraints to Pose CDRs using cluster info in AntibodyInfo. More...
 
std::map< CDRNameEnum, booladd_harmonic_cluster_constraints (AntibodyInfoOP ab_info, pose::Pose &pose, utility::vector1< core::scoring::constraints::ConstraintCOP > constraints)
 Same as above, but adds constraints to the vector so they can be identified and removed from the pose if needed. More...
 
bool add_harmonic_cluster_constraint (AntibodyInfoCOP ab_info, pose::Pose &pose, CDRClusterEnum const cluster)
 Adds a harmonic constraint to a Pose CDR based on cluster type. More...
 
bool add_harmonic_cluster_constraint (AntibodyInfoCOP ab_info, pose::Pose &pose, CDRClusterEnum const cluster, utility::vector1< core::scoring::constraints::ConstraintCOP > constraints)
 Same as above, but adds constraints to the vector so they can be identified and removed from the pose if needed. More...
 
std::string get_harmonic_cluster_constraint_filename (AntibodyInfoCOP ab_info, CDRClusterEnum const cluster)
 Gets the cluster constraint name. Returns NA if not found. More...
 

Variables

static basic::Tracer TR ("protocols.antibody.AntibodyNumberingParser")
 

Typedef Documentation

Enumeration Type Documentation

Enumerator
Chothia_Scheme 
Kabat_Scheme 
Enhanced_Chothia_Scheme 
IMGT_Scheme 
AHO_Scheme 
AntibodyNumberingSchemeEnum_start 
AntibodyNumberingSchemeEnum_total 
NONE 
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 
start_cdr_loop 
H_chain_last_loop 
L_chain_last_loop 
camelid_last_loop 
num_cdr_loops 
CDRNameEnum_start 
CDRNameEnum_total 
Enumerator
Kinked 
Extended 
Neutral 
Unknown 
H3BaseTypeEnum_start 
H3BaseTypeEnum_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

bool protocols::antibody::add_harmonic_cluster_constraint ( AntibodyInfoCOP  ab_info,
pose::Pose pose,
CDRClusterEnum const  cluster 
)
bool protocols::antibody::add_harmonic_cluster_constraint ( AntibodyInfoCOP  ab_info,
pose::Pose pose,
CDRClusterEnum const  cluster,
utility::vector1< core::scoring::constraints::ConstraintCOP constraints 
)

Same as above, but adds constraints to the vector so they can be identified and removed from the pose if needed.

Returns true or false depending on success

References core::pose::Pose::add_constraints(), cst, core::scoring::constraints::ConstraintSet::get_all_constraints(), get_harmonic_cluster_constraint_filename(), NA, and TR.

Referenced by add_harmonic_cluster_constraints().

std::map< CDRNameEnum, bool > protocols::antibody::add_harmonic_cluster_constraints ( AntibodyInfoOP  ab_info,
pose::Pose pose 
)

Adds dihedral harmonic constraints to Pose CDRs using cluster info in AntibodyInfo.

Currently requires North_AHO numbering. Returns map of success/failure

References add_harmonic_cluster_constraint().

std::map< CDRNameEnum, bool > protocols::antibody::add_harmonic_cluster_constraints ( AntibodyInfoOP  ab_info,
pose::Pose pose,
utility::vector1< core::scoring::constraints::ConstraintCOP constraints 
)

Same as above, but adds constraints to the vector so they can be identified and removed from the pose if needed.

Returns map of success/failure

References add_harmonic_cluster_constraint().

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 
)
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 numeric::xyzVector< class >::distance(), 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::energies(), 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

CDR_H3_filter

Detailed: 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
Authors
Aroop 02/04/2010
Last Modified: 02/04/2010

References protocols::frag_picker::CA, numeric::dihedral_degrees(), 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().

core::Real protocols::antibody::cutpoint_separation ( core::pose::Pose pose_in,
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 C, 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::ModelCDRH3::apply(), and protocols::antibody::H3RefineCCD::apply().

scoring::ScoreFunctionCOP protocols::antibody::get_Dock_ScoreFxn ( void  )
std::string protocols::antibody::get_harmonic_cluster_constraint_filename ( AntibodyInfoCOP  ab_info,
CDRClusterEnum const  cluster 
)

Gets the cluster constraint name. Returns NA if not found.

References utility::file::file_exists(), basic::database::full_name(), path, and TR.

Referenced by add_harmonic_cluster_constraint().

scoring::ScoreFunctionCOP protocols::antibody::get_LoopCentral_ScoreFxn ( void  )
scoring::ScoreFunctionCOP protocols::antibody::get_LoopHighRes_ScoreFxn ( void  )
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 
)
core::Real protocols::antibody::kink_bb_Hbond ( const core::pose::Pose pose,
const protocols::antibody::AntibodyInfo ab_info 
)
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 &  out,
SnugDockProtocol const &  snugdockprotocol 
)
std::ostream& protocols::antibody::operator<< ( std::ostream &  out,
SnugDock const &   
)
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 
)
std::pair< ParatopeMetric< core::Real >, ParatopeMetric< core::Real > > protocols::antibody::paratope_sasa ( const core::pose::Pose pose,
const protocols::antibody::AntibodyInfo ab_info 
)
core::SSize protocols::antibody::pose_charge ( core::pose::Pose const &  pose)
std::string protocols::antibody::setup_A_LH_foldtree ( AntibodyInfoCOP  ab_info,
core::pose::Pose pose 
)

Setup A_LH foldtree. 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. 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,
Size  jumppoint1,
Size  cutpoint,
Size  jumppoint2 
)
void protocols::antibody::simple_one_loop_fold_tree ( pose::Pose pose_in,
loops::Loop const &  loop 
)
utility::vector1< core::Real > protocols::antibody::vl_vh_orientation_coords ( const core::pose::Pose pose_in,
const AntibodyInfo &  ab_info 
)

Variable Documentation

basic::Tracer protocols::antibody::TR("protocols.antibody.AntibodyNumberingParser")
static

Referenced by protocols::antibody::RefineBetaBarrel::apply(), protocols::antibody::SnugDockProtocol::apply(), protocols::antibody::GraftCDRLoopsProtocol::apply(), protocols::antibody::AntibodyModelerProtocol::apply(), protocols::antibody::H3CterInsert::apply(), protocols::antibody::design::ResidueProbDesignOperation::apply(), protocols::antibody::ModelCDRH3::apply(), protocols::antibody::RefineOneCDRLoopCentroid::apply(), protocols::antibody::H3PerturbCCD::apply(), protocols::antibody::LHRepulsiveRamp::apply(), protocols::antibody::SnugDock::apply(), protocols::antibody::LHRepulsiveRampLegacy::apply(), protocols::antibody::RefineOneCDRLoop::apply(), protocols::antibody::H3RefineCCD::apply(), protocols::antibody::design::AntibodyDesignMover::apply(), protocols::antibody::design::AntibodyGraftDesignMover::apply(), protocols::antibody::design::AntibodySeqDesignMover::apply(), protocols::antibody::AntibodyFeatures::calculate_cdr_contacts_nres(), protocols::antibody::AntibodyFeatures::calculate_residue_atomic_contacts(), 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::GraftCDRLoopsProtocol::display_constraint_residues(), protocols::antibody::AntibodyModelerProtocol::display_constraint_residues(), protocols::antibody::design::AntibodyDesignModeler::dock_A_LH_high_res(), protocols::antibody::design::AntibodyDesignModeler::dock_A_LH_low_res(), protocols::antibody::design::AntibodyDesignModeler::dock_H_L_high_res(), protocols::antibody::design::AntibodyDesignModeler::dock_H_L_low_res(), protocols::antibody::design::AntibodyDesignModeler::dock_high_res(), protocols::antibody::design::AntibodyDesignModeler::dock_L_H_high_res(), protocols::antibody::design::AntibodyDesignModeler::dock_L_H_low_res(), protocols::antibody::design::AntibodyDesignModeler::dock_LH_A_high_res(), protocols::antibody::design::AntibodyDesignModeler::dock_LH_A_low_res(), protocols::antibody::design::AntibodyDesignModeler::dock_low_res(), protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2(), protocols::antibody::design::AntibodyGraftDesignMover::extend_native_cdrs(), protocols::antibody::RefineOneCDRLoopCentroid::finalize_setup(), protocols::antibody::CDRsMinPackMin::finalize_setup(), protocols::antibody::RefineBetaBarrel::finalize_setup(), protocols::antibody::GraftCDRLoopsProtocol::finalize_setup(), protocols::antibody::LHRepulsiveRampLegacy::finalize_setup(), protocols::antibody::AntibodyModelerProtocol::finalize_setup(), protocols::antibody::design::AntibodyGraftDesignMover::fix_pdb_info(), protocols::antibody::AntibodyInfo::get_landmark_resnum(), protocols::antibody::AntibodyInfo::get_MoveMap_for_AllCDRsSideChains_and_H3backbone(), protocols::antibody::design::AntibodyGraftDesignMover::graft_cdr(), protocols::antibody::AntibodyInfo::identify_CDR_from_a_sequence(), protocols::antibody::GraftCDRLoopsProtocol::init_from_options(), protocols::antibody::AntibodyModelerProtocol::init_from_options(), protocols::antibody::design::AntibodyDatabaseManager::load_cdr_design_data(), protocols::antibody::design::AntibodyDatabaseManager::load_cdrs_for_grafting(), protocols::antibody::design::ConservativeDesignOperation::load_data_from_db(), protocols::antibody::design::AntibodyDesignModeler::minimize_cdrs(), protocols::antibody::design::AntibodyDesignModeler::minimize_cdrs_and_neighbor_sc(), protocols::antibody::design::AntibodyDesignModeler::minimize_interface(), protocols::antibody::design::AntibodyDesignMover::model_post_graft(), protocols::antibody::design::AntibodyDesignMover::output_ensemble(), protocols::antibody::AntibodyFeatures::parse_my_tag(), protocols::antibody::H3PerturbCCD::read_and_store_fragments(), protocols::antibody::AntibodyNumberingParser::read_cdr_definition_file(), protocols::antibody::design::DesignInstructionsParser::read_cdr_graft_instructions(), protocols::antibody::H3CterInsert::read_H3_cter_fragment(), protocols::antibody::AntibodyNumberingParser::read_numbering_scheme_file(), protocols::antibody::design::AntibodyDesignModeler::relax_cdrs(), protocols::antibody::design::AntibodyDesignModeler::relax_cdrs_and_neighbor_sc(), protocols::antibody::design::AntibodyDesignModeler::relax_interface(), protocols::antibody::design::AntibodySeqDesignMover::remove_conservative_design_residues_from_prob_set(), protocols::antibody::design::AntibodyDesignModeler::repack_antibody_interface(), protocols::antibody::design::AntibodyDesignModeler::repack_antigen_ab_interface(), protocols::antibody::design::AntibodyDesignModeler::repack_antigen_interface(), protocols::antibody::design::AntibodyDesignModeler::repack_CDRs(), protocols::antibody::design::AntibodyDesignModeler::repack_CDRs_and_neighbors(), protocols::antibody::AntibodyFeatures::report_features(), protocols::antibody::design::AntibodyGraftDesignMover::run_basic_mc_algorithm(), protocols::antibody::design::AntibodyGraftDesignMover::run_deterministic_graft_algorithm(), protocols::antibody::AntibodyModelerProtocol::set_default(), protocols::antibody::GraftCDRLoopsProtocol::set_default(), protocols::antibody::RefineOneCDRLoopCentroid::set_default(), protocols::antibody::AntibodyInfo::set_default(), protocols::antibody::AntibodyInfo::setup_CDR_clusters(), protocols::antibody::AntibodyInfo::setup_CDRsInfo(), protocols::antibody::design::AntibodySeqDesignMover::setup_constraints(), protocols::antibody::SnugDockProtocol::setup_objects(), protocols::antibody::SnugDock::setup_objects(), and protocols::antibody::design::AntibodySeqDesignMover::setup_task_factory().