Rosetta 3.4
Classes | Typedefs | Functions
protocols::antibody2 Namespace Reference

Classes

class  Ab_Assemble_Templates
class  Ab_CloseOneCDR_Mover
 Closes only one CDR onto a framework. More...
class  Ab_GraftOneCDR_Mover
 Grafts only one CDR onto a framework. More...
class  Ab_H3_cter_insert_mover
 H3 CDR, Fragment Insertion and CCD. More...
class  Ab_H3_perturb_ccd_build
class  Ab_Info
 antibody2 definition More...
class  Ab_LH_RepulsiveRamp_Mover
class  Ab_LH_SnugFit_Mover
class  Ab_ModelCDRH3
class  Ab_Relax_a_CDR_FullAtom
class  Ab_RelaxCDRs_Mover
 Closes only one CDR onto a framework. More...
class  Ab_TemplateInfo
 antibody2 definition More...
class  CDRH3Modeler2
 Ab initio modeling of CDR H3 loop. More...

Typedefs

typedef
utility::pointer::owning_ptr
< Ab_Assemble_Templates
Ab_Assemble_TemplatesOP
typedef
utility::pointer::owning_ptr
< Ab_Assemble_Templates const > 
Ab_Assemble_TemplatesCOP
typedef
utility::pointer::owning_ptr
< Ab_CloseOneCDR_Mover
Ab_CloseOneCDR_MoverOP
typedef
utility::pointer::owning_ptr
< Ab_CloseOneCDR_Mover const > 
Ab_CloseOneCDR_MoverCOP
typedef
utility::pointer::owning_ptr
< Ab_GraftOneCDR_Mover
Ab_GraftOneCDR_MoverOP
typedef
utility::pointer::owning_ptr
< const Ab_GraftOneCDR_Mover
Ab_GraftOneCDR_MoverCOP
typedef
utility::pointer::owning_ptr
< Ab_H3_cter_insert_mover
Ab_H3_cter_insert_moverOP
typedef
utility::pointer::owning_ptr
< Ab_H3_cter_insert_mover
const > 
Ab_H3_cter_insert_moverCOP
typedef
utility::pointer::owning_ptr
< Ab_H3_perturb_ccd_build
Ab_H3_perturb_ccd_buildOP
typedef
utility::pointer::owning_ptr
< Ab_H3_perturb_ccd_build
const > 
Ab_H3_perturb_ccd_buildCOP
typedef
utility::pointer::owning_ptr
< Ab_Info
Ab_InfoOP
typedef
utility::pointer::owning_ptr
< Ab_Info const > 
Ab_InfoCOP
typedef
utility::pointer::owning_ptr
< Ab_LH_RepulsiveRamp_Mover
Ab_LH_RepulsiveRamp_MoverOP
typedef
utility::pointer::owning_ptr
< Ab_LH_RepulsiveRamp_Mover
const > 
Ab_LH_RepulsiveRamp_MoverCOP
typedef
utility::pointer::owning_ptr
< Ab_LH_SnugFit_Mover
Ab_LH_SnugFit_MoverOP
typedef
utility::pointer::owning_ptr
< Ab_LH_SnugFit_Mover const > 
Ab_LH_SnugFit_MoverCOP
typedef
utility::pointer::owning_ptr
< Ab_ModelCDRH3
Ab_ModelCDRH3OP
typedef
utility::pointer::owning_ptr
< Ab_ModelCDRH3 const > 
Ab_ModelCDRH3COP
typedef
utility::pointer::owning_ptr
< Ab_Relax_a_CDR_FullAtom
Ab_Relax_a_CDR_FullAtomOP
typedef
utility::pointer::owning_ptr
< Ab_Relax_a_CDR_FullAtom
const > 
Ab_Relax_a_CDR_FullAtomCOP
typedef
utility::pointer::owning_ptr
< Ab_RelaxCDRs_Mover
Ab_RelaxCDRs_MoverOP
typedef
utility::pointer::owning_ptr
< Ab_RelaxCDRs_Mover const > 
Ab_RelaxCDRs_MoverCOP
typedef
utility::pointer::owning_ptr
< Ab_TemplateInfo
Ab_TemplateInfoOP
typedef
utility::pointer::owning_ptr
< Ab_TemplateInfo const > 
Ab_TemplateInfoCOP
typedef
utility::pointer::owning_ptr
< CDRH3Modeler2
CDRH3Modeler2OP
typedef
utility::pointer::owning_ptr
< CDRH3Modeler2 const > 
CDRH3Modeler2COP

Functions

std::ostream & operator<< (std::ostream &out, const Ab_Assemble_Templates &ab_m_2)
std::ostream & operator<< (std::ostream &out, const Ab_Info &ab_info)
std::ostream & operator<< (std::ostream &out, const Ab_ModelCDRH3 &ab_m_2)
static basic::Tracer TRL ("protocols.antibody2.Ab_RelaxCDRs_Mover")
std::ostream & operator<< (std::ostream &out, const Ab_TemplateInfo &ab_t_info)
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)
void setup_simple_fold_tree (Size jumppoint1, Size cutpoint, Size jumppoint2, Size nres, pose::Pose &pose_in)
bool CDR_H3_filter (const pose::Pose &pose_in, Size const loop_begin, Size const size, bool H3_filter, bool is_camelid)
 tests if a loop has H3 like base charachteristics
void setup_packer_task (pose::Pose &pose_in, core::pack::task::TaskFactoryOP tf)
bool cutpoints_separation (core::pose::Pose &pose, Ab_InfoOP &antibody_info)
 return false if any cdr cutpoint is broken
Real cutpoint_separation (pose::Pose &pose_in, Size cutpoint)
std::string get_seq_from_a_loop (core::pose::Pose &pose_in, loops::LoopOP loop)

Typedef Documentation


Function Documentation

bool protocols::antibody2::CDR_H3_filter ( const pose::Pose pose_in,
Size const  loop_begin,
Size const  size,
bool  H3_filter,
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
Global Write:
Remarks:
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(), core::TR(), and protocols::kinmatch::xyz().

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

return false if any cdr cutpoint is broken

References cutpoint_separation().

std::string protocols::antibody2::get_seq_from_a_loop ( core::pose::Pose pose_in,
loops::LoopOP  loop 
)
std::ostream& protocols::antibody2::operator<< ( std::ostream &  out,
const Ab_Info &  ab_info 
)
std::ostream& protocols::antibody2::operator<< ( std::ostream &  out,
const Ab_Assemble_Templates &  ab_m_2 
)
std::ostream& protocols::antibody2::operator<< ( std::ostream &  out,
const Ab_TemplateInfo &  ab_t_info 
)
std::ostream& protocols::antibody2::operator<< ( std::ostream &  out,
const Ab_ModelCDRH3 &  ab_m_2 
)
void protocols::antibody2::setup_packer_task ( pose::Pose pose_in,
core::pack::task::TaskFactoryOP  tf 
)
void protocols::antibody2::setup_simple_fold_tree ( Size  jumppoint1,
Size  cutpoint,
Size  jumppoint2,
Size  nres,
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 
)
static basic::Tracer protocols::antibody2::TRL ( "protocols.antibody2.Ab_RelaxCDRs_Mover"  ) [static]
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines