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protocols::antibody2 Namespace Reference

Classes

class  Ab_TemplateInfo
 antibody2 definition More...
 
struct  FrameWork
 
class  AntibodyInfo
 
class  AntibodyModelerProtocol
 
class  CDRsMinPackMin
 
class  CloseOneCDRLoop
 Closes only one CDR onto a framework. More...
 
class  GraftCDRLoopsProtocol
 
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...
 
class  RefineBetaBarrel
 
class  RefineOneCDRLoop
 
class  RefineOneCDRLoopCentroid
 
class  SnugDock
 
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
< AntibodyInfo
AntibodyInfoOP
 
typedef
utility::pointer::owning_ptr
< AntibodyInfo const > 
AntibodyInfoCOP
 
typedef
utility::pointer::owning_ptr
< AntibodyModelerProtocol
AntibodyModelerProtocolOP
 
typedef
utility::pointer::owning_ptr
< AntibodyModelerProtocol
const > 
AntibodyModelerProtocolCOP
 
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
< 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
< 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
 
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
 

Enumerations

enum  AntibodyCDRNameEnum {
  start_cdr_loop = 1, h1 = start_cdr_loop, h2, h3,
  H_chain_last_loop = h3, camelid_last_loop = h3, l1, l2,
  l3, L_chain_last_loop = l3, num_cdr_loops = l3
}
 
enum  AntibodyNumberingEnum {
  Aroop = 1, Chothia, Kabat, Enhanced_Chothia,
  AHO, IMGT
}
 
enum  BeginEndEnum { Begin = 1, End, Pack_Angle_Begin, Pack_Angle_End }
 
enum  H3BaseTypeEnum { Kinked = 1, Extended, Neutral }
 

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)
 
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)
 
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 (pose::Pose &pose_in)
 
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)
 
Real vl_vh_packing_angle (const pose::Pose &pose_in, AntibodyInfoOP ab_info)
 
void align_to_native (core::pose::Pose &pose, core::pose::Pose &native_pose, AntibodyInfoOP ab_info, AntibodyInfoOP native_ab_info)
 align current Fv to native.Fv More...
 
std::ostream & operator<< (std::ostream &out, const CDRsMinPackMin &ab_m_2)
 
std::ostream & operator<< (std::ostream &out, const GraftCDRLoopsProtocol &ab_m_2)
 
std::ostream & operator<< (std::ostream &out, SnugDock const &)
 
std::ostream & operator<< (std::ostream &out, SnugDockProtocol const &snugdockprotocol)
 

Typedef Documentation

Enumeration Type Documentation

Enumerator
start_cdr_loop 
h1 
h2 
h3 
H_chain_last_loop 
camelid_last_loop 
l1 
l2 
l3 
L_chain_last_loop 
num_cdr_loops 
Enumerator
Aroop 
Chothia 
Kabat 
Enhanced_Chothia 
AHO 
IMGT 
Enumerator
Begin 
End 
Pack_Angle_Begin 
Pack_Angle_End 
Enumerator
Kinked 
Extended 
Neutral 

Function Documentation

void protocols::antibody2::align_to_native ( core::pose::Pose pose,
core::pose::Pose native_pose,
AntibodyInfoOP  ab_info,
AntibodyInfoOP  native_ab_info 
)
bool protocols::antibody2::CDR_H3_cter_filter ( const pose::Pose pose_in,
AntibodyInfoOP  ab_info 
)
bool protocols::antibody2::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]pose,:full 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, 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, core::TR(), and core::conformation::Residue::xyz().

core::Real protocols::antibody2::cutpoint_separation ( pose::Pose pose_in,
Size  cutpoint 
)
bool protocols::antibody2::cutpoints_separation ( core::pose::Pose pose,
AntibodyInfoOP &  antibody_info 
)

return false if any cdr cutpoint is broken

References cutpoint_separation().

Referenced by protocols::antibody2::ModelCDRH3::apply(), and protocols::antibody2::H3RefineCCD::apply().

scoring::ScoreFunctionCOP protocols::antibody2::get_Dock_ScoreFxn ( void  )
scoring::ScoreFunctionCOP protocols::antibody2::get_LoopCentral_ScoreFxn ( void  )
scoring::ScoreFunctionCOP protocols::antibody2::get_LoopHighRes_ScoreFxn ( void  )
scoring::ScoreFunctionCOP protocols::antibody2::get_Pack_ScoreFxn ( void  )
core::Real protocols::antibody2::global_loop_rmsd ( const pose::Pose pose_in,
const pose::Pose native_pose,
loops::LoopsOP  current_loop 
)
std::ostream& protocols::antibody2::operator<< ( std::ostream &  out,
const Ab_TemplateInfo &  ab_t_info 
)
std::ostream& protocols::antibody2::operator<< ( std::ostream &  out,
SnugDockProtocol const &  snugdockprotocol 
)
std::ostream& protocols::antibody2::operator<< ( std::ostream &  out,
const CDRsMinPackMin &  ab_m_2 
)
std::ostream& protocols::antibody2::operator<< ( std::ostream &  out,
SnugDock const &   
)
std::ostream& protocols::antibody2::operator<< ( std::ostream &  out,
const GraftCDRLoopsProtocol &  ab_m_2 
)
std::ostream& protocols::antibody2::operator<< ( std::ostream &  out,
const AntibodyModelerProtocol &  ab_m 
)
std::ostream& protocols::antibody2::operator<< ( std::ostream &  out,
const AntibodyInfo &  ab_info 
)
core::pack::task::TaskFactoryOP protocols::antibody2::setup_packer_task ( pose::Pose pose_in)
void protocols::antibody2::simple_fold_tree ( pose::Pose pose_in,
Size  jumppoint1,
Size  cutpoint,
Size  jumppoint2 
)
void protocols::antibody2::simple_one_loop_fold_tree ( pose::Pose pose_in,
loops::Loop const &  loop 
)
core::Real protocols::antibody2::vl_vh_packing_angle ( const pose::Pose pose_in,
AntibodyInfoOP  ab_info 
)