Ab initio modeling of CDR H3 loop. More...
#include <CDRH3Modeler.hh>
Public Member Functions | |
| CDRH3Modeler (utility::vector1< core::fragment::FragSetOP > cdr_h3_frags) | |
| default constructor More... | |
| ~CDRH3Modeler () override | |
| default destructor More... | |
| void | model_h3 (bool setting) |
| enable CDR H3 loop building More... | |
| void | enable_benchmark_mode (bool setting) |
| enable benchmark mode More... | |
| void | set_camelid (bool setting) |
| enable camelid modeling mode More... | |
| void | set_centroid_loop_building (bool setting) |
| set centroid mode loop building More... | |
| void | set_fullatom_loop_building (bool setting) |
| set fullatom mode loop building More... | |
| void | set_default () |
| void | apply (core::pose::Pose &pose_in) override |
| Main Method. More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| void | build_centroid_loop () |
| Build centroid mode CDR H3 loop. More... | |
| void | build_fullatom_loop () |
| Build fullatom mode CDR H3 loop. More... | |
| void | set_lowres_score_func (core::scoring::ScoreFunctionOP lowres_scorefxn) |
| set scorefunction for low resolution of CDR H3 modeling More... | |
| void | set_highres_score_func (core::scoring::ScoreFunctionOP highres_scorefxn) |
| set scorefunction for high resolution of CDR H3 modeling More... | |
| void | antibody_modeling_insert_ter () |
| insert C-terminal fragments More... | |
| void | store_H3_cter_fragment (utility::vector1< core::fragment::FragData > &base_library_in) |
| store CDR H3 C-terminal fragments More... | |
| bool | cutpoints_separation () |
| return false if any cdr cutpoint is broken More... | |
| core::Real | cutpoint_separation (core::pose::Pose &pose_in, core::Size cutpoint) |
| void | scored_frag_close (core::pose::Pose &pose_in, loops::Loop const trimmed_cdr_h3) |
| builds a loop from fragments file. More... | |
| bool | CDR_H3_filter (const core::pose::Pose &pose_in, core::Size const loop_begin, core::Size const size, char const light_chain='L') |
| tests if a loop has H3 like base charachteristics More... | |
| void | loop_fa_relax (core::pose::Pose &pose_in, core::Size const loop_begin, core::Size const loop_end) |
| actually relaxes the region specified More... | |
| void | loop_centroid_relax (core::pose::Pose &pose_in, core::Size const loop_begin, core::Size const loop_end) |
| actually relaxes the region specified More... | |
| void | setup_packer_task (core::pose::Pose &pose_in) |
 Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual MoverOP | create () |
| MoverCOP | get_self_ptr () const |
| MoverOP | get_self_ptr () |
| MoverCAP | get_self_weak_ptr () const |
| MoverAP | get_self_weak_ptr () |
| Mover (std::string const &type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| virtual void | test_move (Pose &pose) |
| : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More... | |
| virtual MoverOP | clone () const |
| Return a clone of the Mover object. More... | |
| virtual bool | reinitialize_for_each_job () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More... | |
| virtual bool | reinitialize_for_new_input () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More... | |
| virtual MoverOP | fresh_instance () const |
| Generates a new Mover object freshly created with the default ctor. More... | |
| MoverStatus | get_last_move_status () const |
| end parser interface, start Job Distributor interface///////////// More... | |
| void | reset_status () |
| resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More... | |
| virtual core::pose::PoseOP | get_additional_output () |
| Mechanism by which a mover may return multiple output poses from a single input pose. More... | |
| void | set_type (std::string const &setting) |
| Set the 'type' string. More... | |
| std::string | get_type () const |
| void | type (const std::string &type_in) |
| Set the 'type' string. More... | |
| std::string const & | type () const |
| Get the set 'type' string. More... | |
| virtual void | set_input_pose (PoseCOP pose) |
| setter for poses contained for rms More... | |
| virtual void | set_native_pose (PoseCOP pose) |
| setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More... | |
| PoseCOP | get_input_pose () const |
| PoseCOP | get_native_pose () const |
| virtual void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
| virtual void | set_current_tag (std::string const &new_tag) |
| std::string | get_current_tag () const |
| A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More... | |
| virtual void | show (std::ostream &output=std::cout) const |
| Outputs details about the Mover, including current settings. More... | |
| virtual core::Real | last_proposal_density_ratio () |
| virtual void | clear_info () |
| Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More... | |
| virtual Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Public Attributes | |
| utility::vector1< core::fragment::FragData > | H3_base_library |
Private Attributes | |
| core::pose::Pose | template_pose_ |
| core::pose::Pose | start_pose_ |
| core::Size | base_ |
| Number of ADDITIONAL residues modeled from H3_CTERM These residues range from H:n-2,n-1,n,n+1 of H3. More... | |
| core::Size | c_ter_stem_ |
| core::Real | cen_cst_ |
| core::Real | high_cst_ |
| bool | do_h3_modeling_ |
| core::scoring::ScoreFunctionOP | fa_scorefxn_ |
| utility::vector1< core::fragment::FragSetOP > | cdr_h3_frags_ |
| core::scoring::ScoreFunctionOP | lowres_scorefxn_ |
| core::scoring::ScoreFunctionOP | highres_scorefxn_ |
| bool | benchmark_ |
| benchmark flag More... | |
| bool | apply_centroid_mode_ |
| Centroid mode loop building. More... | |
| bool | apply_fullatom_mode_ |
| Fullatom mode loop building. More... | |
| bool | current_loop_is_H3_ |
| flag indicating that current loop being modeled is CDR H3 More... | |
| bool | H3_filter_ |
| actually enables H3 filter for H3 operations More... | |
| bool | antibody_build_ |
| build H3 only More... | |
| bool | antibody_refine_ |
| refine H3 only More... | |
| bool | min_base_relax_ |
| lower amplitude during base relaxation More... | |
| bool | h3_random_cut_ |
| use random cutpoints for h3 modeling More... | |
| core::Size | decoy_loop_cutpoint_ |
| cutpoint whose separation is computed in scorefile More... | |
| bool | snug_fit_ |
| enable docking local refine of LH chains & simultaneous H3 min More... | |
| bool | loops_flag_ |
| loop_building in docking More... | |
| bool | docking_local_refine_ |
| bool | dle_flag_ |
| insert fragment in docking More... | |
| bool | refine_input_loop_ |
| just refine input loop More... | |
| core::Size | h3_flank_ |
| number of flanking residues:default 5 More... | |
| bool | flank_relax_ |
| relax flanking regions of h3 More... | |
| bool | freeze_h3_ |
| freeze h3 during all cdr relax and local refine More... | |
| bool | is_camelid_ |
| is camelid antibody without light chain More... | |
| core::Size | cutoff_9_ |
| size of loop above which 9mer frags are used More... | |
| core::Size | cutoff_3_ |
| size of loop above which 3mer frags are used More... | |
| Antibody | antibody_in_ |
| core::pack::task::TaskFactoryOP | tf_ |
| core::pack::task::TaskFactoryOP | init_task_factory_ |
Additional Inherited Members | |
| Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagCOP | TagCOP |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef std::list< std::string > | Strings |
| Static Public Member Functions inherited from protocols::moves::Mover | |
| static std::string | name () |
| static void | register_options () |
| Overload this static method if you access options within the mover. More... | |
| Protected Member Functions inherited from protocols::moves::Mover | |
| void | set_last_move_status (MoverStatus status) |
| nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More... | |
Detailed Description
Ab initio modeling of CDR H3 loop.
Constructor & Destructor Documentation
◆ CDRH3Modeler()
| protocols::antibody_legacy::CDRH3Modeler::CDRH3Modeler | ( | utility::vector1< core::fragment::FragSetOP > | cdr_h3_frags | ) |
default constructor
References cdr_h3_frags_, and set_default().
◆ ~CDRH3Modeler()
|
overridedefault |
default destructor
Member Function Documentation
◆ antibody_modeling_insert_ter()
| void protocols::antibody_legacy::CDRH3Modeler::antibody_modeling_insert_ter | ( | ) |
insert C-terminal fragments
References antibody_in_, core::fragment::FragData::apply(), protocols::antibody_legacy::Antibody::cdrh_, core::pose::Pose::fold_tree(), protocols::antibody_legacy::Antibody::Fv, H3_base_library, is_camelid_, core::scoring::rg, protocols::antibody_legacy::simple_one_loop_fold_tree(), and protocols::TR().
Referenced by build_centroid_loop().
◆ apply()
|
overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References antibody_in_, antibody_refine_, protocols::simple_moves::ReturnSidechainMover::apply(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), apply_centroid_mode_, apply_fullatom_mode_, benchmark_, build_centroid_loop(), build_fullatom_loop(), c_ter_stem_, protocols::antibody_legacy::Antibody::cdrh_, core::chemical::CENTROID, current_loop_is_H3_, cutpoints_separation(), do_h3_modeling_, protocols::antibody_legacy::Antibody::extended_, core::chemical::FA_STANDARD, protocols::antibody_legacy::Antibody::Fv, H3_filter_, highres_scorefxn_, is_camelid_, protocols::antibody_legacy::Antibody::kinked_, loop_centroid_relax(), loop_fa_relax(), protocols::antibody_legacy::Antibody::set_Fv(), setup_packer_task(), protocols::antibody_legacy::simple_one_loop_fold_tree(), core::pose::Pose::size(), snug_fit_, start_pose_, tf_, protocols::medal::to_centroid(), and protocols::TR().
◆ build_centroid_loop()
| void protocols::antibody_legacy::CDRH3Modeler::build_centroid_loop | ( | ) |
Build centroid mode CDR H3 loop.
References antibody_in_, antibody_modeling_insert_ter(), apply_centroid_mode_, c_ter_stem_, protocols::antibody_legacy::Antibody::cdrh_, protocols::antibody_legacy::Antibody::current_start, cutoff_9_, cutpoints_separation(), protocols::antibody_legacy::Antibody::Fv, core::pose::Pose::omega(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::pose::Pose::psi(), scored_frag_close(), core::pose::Pose::set_omega(), core::pose::Pose::set_psi(), protocols::antibody_legacy::simple_one_loop_fold_tree(), protocols::loops::Loop::size(), template_pose_, and protocols::TR().
Referenced by apply().
◆ build_fullatom_loop()
| void protocols::antibody_legacy::CDRH3Modeler::build_fullatom_loop | ( | ) |
Build fullatom mode CDR H3 loop.
References antibody_in_, apply_fullatom_mode_, base_, protocols::antibody_legacy::Antibody::cdrh_, cutpoints_separation(), protocols::antibody_legacy::Antibody::Fv, loop_fa_relax(), and protocols::TR().
Referenced by apply().
◆ CDR_H3_filter()
| bool protocols::antibody_legacy::CDRH3Modeler::CDR_H3_filter | ( | const core::pose::Pose & | pose_in, |
| core::Size const | loop_begin, | ||
| core::Size const | size, | ||
| char const | light_chain = 'L' |
||
| ) |
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] 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
References protocols::frag_picker::CA, H3_filter_, is_camelid_, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::TR(), and core::conformation::Residue::xyz().
Referenced by loop_fa_relax(), and scored_frag_close().
◆ cutpoint_separation()
| Real protocols::antibody_legacy::CDRH3Modeler::cutpoint_separation | ( | core::pose::Pose & | pose_in, |
| core::Size | cutpoint | ||
| ) |
References core::chemical::element::C, core::chemical::element::N, core::pose::Pose::residue(), and core::conformation::Residue::xyz().
Referenced by cutpoints_separation().
◆ cutpoints_separation()
| bool protocols::antibody_legacy::CDRH3Modeler::cutpoints_separation | ( | ) |
return false if any cdr cutpoint is broken
References protocols::antibody_legacy::Antibody::all_cdr_loops, antibody_in_, cutpoint_separation(), and protocols::antibody_legacy::Antibody::Fv.
Referenced by apply(), build_centroid_loop(), and build_fullatom_loop().
◆ enable_benchmark_mode()
|
inline |
enable benchmark mode
References benchmark_.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ loop_centroid_relax()
| void protocols::antibody_legacy::CDRH3Modeler::loop_centroid_relax | ( | core::pose::Pose & | pose_in, |
| core::Size const | loop_begin, | ||
| core::Size const | loop_end | ||
| ) |
actually relaxes the region specified
This is all done in low resolution. Intention was to give camelid CDR H1 a larger perturbation.
- Parameters
-
[in] pose,loop begin position, loop end position
- Global Read: none
- Global Write: none
- Remarks
- References:
References core::pose::add_variant_type_to_pose_residue(), antibody_refine_, benchmark_, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_upper_terminus(), lowres_scorefxn_, protocols::mean_field::max(), refine_input_loop_, core::pose::Pose::residue(), protocols::antibody_legacy::simple_one_loop_fold_tree(), core::pose::Pose::size(), snug_fit_, and protocols::TR().
Referenced by apply().
◆ loop_fa_relax()
| void protocols::antibody_legacy::CDRH3Modeler::loop_fa_relax | ( | core::pose::Pose & | pose_in, |
| core::Size const | loop_begin, | ||
| core::Size const | loop_end | ||
| ) |
actually relaxes the region specified
This is all done in high resolution.Hence there are no rigid body moves relative to the docking partners. Only small moves are carried out here to see if there are better fits. Repacking is carried out extensively after each move.
- Parameters
-
[in] pose,loop begin position, loop end position
- Global Read: none
- Global Write: none
- Remarks
- References:
References core::pose::add_variant_type_to_pose_residue(), antibody_build_, antibody_in_, antibody_refine_, benchmark_, CDR_H3_filter(), protocols::antibody_legacy::Antibody::cdrh_, current_loop_is_H3_, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, decoy_loop_cutpoint_, flank_relax_, core::pose::Pose::fold_tree(), freeze_h3_, H3_filter_, h3_flank_, h3_random_cut_, core::conformation::Residue::has_variant_type(), highres_scorefxn_, core::pose::Pose::is_fullatom(), core::conformation::Residue::is_upper_terminus(), protocols::mean_field::max(), min_base_relax_, refine_input_loop_, core::pose::Pose::residue(), protocols::loops::select_loop_residues(), setup_packer_task(), protocols::antibody_legacy::simple_fold_tree(), core::pose::Pose::size(), snug_fit_, start_pose_, tf_, and protocols::TR().
Referenced by apply(), and build_fullatom_loop().
◆ model_h3()
|
inline |
enable CDR H3 loop building
References do_h3_modeling_.
◆ scored_frag_close()
| void protocols::antibody_legacy::CDRH3Modeler::scored_frag_close | ( | core::pose::Pose & | pose_in, |
| loops::Loop const | trimmed_cdr_h3 | ||
| ) |
builds a loop from fragments file.
Loop is built by a monte carlo simulation using fragments from a fragment files. CCD moves are used to close loops with gaps at cutpoint.H3_check is enforced if H3_filter flag is set in command line. Loop building results in many files containing differnt conformations of the same loop in phi-psi-omega angles. Parallel processing is utilized.
- Parameters
-
[in] weight_map in this case its a centroid weight pose_in: loop to be built on this template provided loop_begin/loop_end: loop termini definition frag_size: 3-mer or 9-mer frag_offset:agreement in frag file numbering & pose numberng cycles1: max cycles to be spent building loops cycles2: # of fragment swaps for each loop(depends on size) do_ccd_moves: should ccd moves be used to close gaps
- Global Read: benchmark_
- Global Write:
- Remarks
- References:
References core::pose::add_variant_type_to_pose_residue(), antibody_in_, CDR_H3_filter(), cdr_h3_frags_, protocols::antibody_legacy::Antibody::cdrh_, current_loop_is_H3_, protocols::loops::Loop::cut(), cutoff_9_, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, protocols::antibody_legacy::Antibody::extended_, core::pose::Pose::fold_tree(), H3_filter_, core::conformation::Residue::has_variant_type(), is_camelid_, core::conformation::Residue::is_upper_terminus(), lowres_scorefxn_, core::pose::Pose::residue(), core::scoring::rg, protocols::antibody_legacy::simple_one_loop_fold_tree(), protocols::loops::Loop::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and protocols::TR().
Referenced by build_centroid_loop().
◆ set_camelid()
|
inline |
enable camelid modeling mode
References docking_local_refine_, H3_filter_, is_camelid_, and snug_fit_.
◆ set_centroid_loop_building()
|
inline |
set centroid mode loop building
References apply_centroid_mode_.
◆ set_default()
| void protocols::antibody_legacy::CDRH3Modeler::set_default | ( | ) |
References antibody_build_, antibody_refine_, apply_centroid_mode_, apply_fullatom_mode_, core::scoring::atom_pair_constraint, base_, benchmark_, c_ter_stem_, cen_cst_, core::scoring::chainbreak, current_loop_is_H3_, cutoff_3_, cutoff_9_, decoy_loop_cutpoint_, dle_flag_, do_h3_modeling_, docking_local_refine_, flank_relax_, freeze_h3_, core::scoring::get_score_function(), H3_filter_, h3_flank_, h3_random_cut_, high_cst_, highres_scorefxn_, is_camelid_, loops_flag_, lowres_scorefxn_, min_base_relax_, core::scoring::overlap_chainbreak, refine_input_loop_, snug_fit_, and protocols::TR().
Referenced by CDRH3Modeler().
◆ set_fullatom_loop_building()
|
inline |
set fullatom mode loop building
References apply_fullatom_mode_.
◆ set_highres_score_func()
| void protocols::antibody_legacy::CDRH3Modeler::set_highres_score_func | ( | core::scoring::ScoreFunctionOP | highres_scorefxn | ) |
set scorefunction for high resolution of CDR H3 modeling
References highres_scorefxn_.
◆ set_lowres_score_func()
| void protocols::antibody_legacy::CDRH3Modeler::set_lowres_score_func | ( | core::scoring::ScoreFunctionOP | lowres_scorefxn | ) |
set scorefunction for low resolution of CDR H3 modeling
References lowres_scorefxn_.
◆ setup_packer_task()
| void protocols::antibody_legacy::CDRH3Modeler::setup_packer_task | ( | core::pose::Pose & | pose_in | ) |
References init_task_factory_, core::pack::dunbrack::load_unboundrot(), tf_, and protocols::TR().
Referenced by apply(), and loop_fa_relax().
◆ store_H3_cter_fragment()
| void protocols::antibody_legacy::CDRH3Modeler::store_H3_cter_fragment | ( | utility::vector1< core::fragment::FragData > & | base_library_in | ) |
store CDR H3 C-terminal fragments
References H3_base_library.
Member Data Documentation
◆ antibody_build_
|
private |
build H3 only
Referenced by loop_fa_relax(), and set_default().
◆ antibody_in_
|
private |
◆ antibody_refine_
|
private |
refine H3 only
Referenced by apply(), loop_centroid_relax(), loop_fa_relax(), and set_default().
◆ apply_centroid_mode_
|
private |
Centroid mode loop building.
Referenced by apply(), build_centroid_loop(), set_centroid_loop_building(), and set_default().
◆ apply_fullatom_mode_
|
private |
Fullatom mode loop building.
Referenced by apply(), build_fullatom_loop(), set_default(), and set_fullatom_loop_building().
◆ base_
|
private |
Number of ADDITIONAL residues modeled from H3_CTERM These residues range from H:n-2,n-1,n,n+1 of H3.
Referenced by build_fullatom_loop(), and set_default().
◆ benchmark_
|
private |
benchmark flag
Referenced by apply(), enable_benchmark_mode(), loop_centroid_relax(), loop_fa_relax(), and set_default().
◆ c_ter_stem_
|
private |
Referenced by apply(), build_centroid_loop(), and set_default().
◆ cdr_h3_frags_
|
private |
Referenced by CDRH3Modeler(), and scored_frag_close().
◆ cen_cst_
|
private |
Referenced by set_default().
◆ current_loop_is_H3_
|
private |
flag indicating that current loop being modeled is CDR H3
Referenced by apply(), loop_fa_relax(), scored_frag_close(), and set_default().
◆ cutoff_3_
|
private |
size of loop above which 3mer frags are used
Referenced by set_default().
◆ cutoff_9_
|
private |
size of loop above which 9mer frags are used
Referenced by build_centroid_loop(), scored_frag_close(), and set_default().
◆ decoy_loop_cutpoint_
|
private |
cutpoint whose separation is computed in scorefile
Referenced by loop_fa_relax(), and set_default().
◆ dle_flag_
|
private |
insert fragment in docking
Referenced by set_default().
◆ do_h3_modeling_
|
private |
Referenced by apply(), model_h3(), and set_default().
◆ docking_local_refine_
|
private |
Referenced by set_camelid(), and set_default().
◆ fa_scorefxn_
|
private |
◆ flank_relax_
|
private |
relax flanking regions of h3
Referenced by loop_fa_relax(), and set_default().
◆ freeze_h3_
|
private |
freeze h3 during all cdr relax and local refine
Referenced by loop_fa_relax(), and set_default().
◆ H3_base_library
| utility::vector1< core::fragment::FragData > protocols::antibody_legacy::CDRH3Modeler::H3_base_library |
◆ H3_filter_
|
private |
actually enables H3 filter for H3 operations
Referenced by apply(), CDR_H3_filter(), loop_fa_relax(), scored_frag_close(), set_camelid(), and set_default().
◆ h3_flank_
|
private |
number of flanking residues:default 5
Referenced by loop_fa_relax(), and set_default().
◆ h3_random_cut_
|
private |
use random cutpoints for h3 modeling
Referenced by loop_fa_relax(), and set_default().
◆ high_cst_
|
private |
Referenced by set_default().
◆ highres_scorefxn_
|
private |
Referenced by apply(), loop_fa_relax(), set_default(), and set_highres_score_func().
◆ init_task_factory_
|
private |
Referenced by setup_packer_task().
◆ is_camelid_
|
private |
is camelid antibody without light chain
Referenced by antibody_modeling_insert_ter(), apply(), CDR_H3_filter(), scored_frag_close(), set_camelid(), and set_default().
◆ loops_flag_
|
private |
loop_building in docking
Referenced by set_default().
◆ lowres_scorefxn_
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private |
Referenced by loop_centroid_relax(), scored_frag_close(), set_default(), and set_lowres_score_func().
◆ min_base_relax_
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private |
lower amplitude during base relaxation
Referenced by loop_fa_relax(), and set_default().
◆ refine_input_loop_
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private |
just refine input loop
Referenced by loop_centroid_relax(), loop_fa_relax(), and set_default().
◆ snug_fit_
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private |
enable docking local refine of LH chains & simultaneous H3 min
Referenced by apply(), loop_centroid_relax(), loop_fa_relax(), set_camelid(), and set_default().
◆ start_pose_
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private |
Referenced by apply(), and loop_fa_relax().
◆ template_pose_
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private |
Referenced by build_centroid_loop().
◆ tf_
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private |
Referenced by apply(), loop_fa_relax(), and setup_packer_task().
The documentation for this class was generated from the following files:
- src/protocols/antibody_legacy/CDRH3Modeler.hh
- src/protocols/antibody_legacy/CDRH3Modeler.cc
