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protocols::antibody_legacy::CDRH3Modeler Class Reference

Ab initio modeling of CDR H3 loop. More...

#include <CDRH3Modeler.hh>

Inheritance diagram for protocols::antibody_legacy::CDRH3Modeler:
Inheritance graph
[legend]

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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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

protocols::antibody_legacy::CDRH3Modeler::CDRH3Modeler ( utility::vector1< core::fragment::FragSetOP cdr_h3_frags)

default constructor

References cdr_h3_frags_, and set_default().

protocols::antibody_legacy::CDRH3Modeler::~CDRH3Modeler ( )
overridedefault

default destructor

Member Function Documentation

void protocols::antibody_legacy::CDRH3Modeler::antibody_modeling_insert_ter ( )
void protocols::antibody_legacy::CDRH3Modeler::apply ( core::pose::Pose )
overridevirtual
void protocols::antibody_legacy::CDRH3Modeler::build_centroid_loop ( )
void protocols::antibody_legacy::CDRH3Modeler::build_fullatom_loop ( )
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]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
Global Write:
Remarks
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, H3_filter_, is_camelid_, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::TR(), and protocols::kinmatch::xyz().

Referenced by loop_fa_relax(), and scored_frag_close().

Real protocols::antibody_legacy::CDRH3Modeler::cutpoint_separation ( core::pose::Pose pose_in,
core::Size  cutpoint 
)
bool protocols::antibody_legacy::CDRH3Modeler::cutpoints_separation ( )
void protocols::antibody_legacy::CDRH3Modeler::enable_benchmark_mode ( bool  setting)
inline

enable benchmark mode

References benchmark_.

std::string protocols::antibody_legacy::CDRH3Modeler::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

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,loopbegin position, loop end position
Global Read: none
Global Write: none
Remarks
References:
Author
Aroop 05/07/2010

References core::pose::add_variant_type_to_pose_residue(), antibody_refine_, benchmark_, core::kinematics::FoldTree::clear(), 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().

void protocols::antibody_legacy::CDRH3Modeler::loop_fa_relax ( core::pose::Pose pose_in,
core::Size const  loop_begin,
core::Size const  loop_end 
)
void protocols::antibody_legacy::CDRH3Modeler::model_h3 ( bool  setting)
inline

enable CDR H3 loop building

References do_h3_modeling_.

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_mapin 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:
Author
Aroop 02/04/2010

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_, is_camelid_, core::pose::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().

void protocols::antibody_legacy::CDRH3Modeler::set_camelid ( bool  setting)
inline

enable camelid modeling mode

References docking_local_refine_, H3_filter_, is_camelid_, and snug_fit_.

void protocols::antibody_legacy::CDRH3Modeler::set_centroid_loop_building ( bool  setting)
inline

set centroid mode loop building

References apply_centroid_mode_.

void protocols::antibody_legacy::CDRH3Modeler::set_default ( )
void protocols::antibody_legacy::CDRH3Modeler::set_fullatom_loop_building ( bool  setting)
inline

set fullatom mode loop building

References apply_fullatom_mode_.

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_.

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_.

void protocols::antibody_legacy::CDRH3Modeler::setup_packer_task ( core::pose::Pose pose_in)
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

bool protocols::antibody_legacy::CDRH3Modeler::antibody_build_
private

build H3 only

Referenced by loop_fa_relax(), and set_default().

Antibody protocols::antibody_legacy::CDRH3Modeler::antibody_in_
private
bool protocols::antibody_legacy::CDRH3Modeler::antibody_refine_
private

refine H3 only

Referenced by apply(), loop_centroid_relax(), loop_fa_relax(), and set_default().

bool protocols::antibody_legacy::CDRH3Modeler::apply_centroid_mode_
private

Centroid mode loop building.

Referenced by apply(), build_centroid_loop(), set_centroid_loop_building(), and set_default().

bool protocols::antibody_legacy::CDRH3Modeler::apply_fullatom_mode_
private

Fullatom mode loop building.

Referenced by apply(), build_fullatom_loop(), set_default(), and set_fullatom_loop_building().

core::Size protocols::antibody_legacy::CDRH3Modeler::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().

bool protocols::antibody_legacy::CDRH3Modeler::benchmark_
private
core::Size protocols::antibody_legacy::CDRH3Modeler::c_ter_stem_
private
utility::vector1< core::fragment::FragSetOP > protocols::antibody_legacy::CDRH3Modeler::cdr_h3_frags_
private

Referenced by CDRH3Modeler(), and scored_frag_close().

core::Real protocols::antibody_legacy::CDRH3Modeler::cen_cst_
private

Referenced by set_default().

bool protocols::antibody_legacy::CDRH3Modeler::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().

core::Size protocols::antibody_legacy::CDRH3Modeler::cutoff_3_
private

size of loop above which 3mer frags are used

Referenced by set_default().

core::Size protocols::antibody_legacy::CDRH3Modeler::cutoff_9_
private

size of loop above which 9mer frags are used

Referenced by build_centroid_loop(), scored_frag_close(), and set_default().

core::Size protocols::antibody_legacy::CDRH3Modeler::decoy_loop_cutpoint_
private

cutpoint whose separation is computed in scorefile

Referenced by loop_fa_relax(), and set_default().

bool protocols::antibody_legacy::CDRH3Modeler::dle_flag_
private

insert fragment in docking

Referenced by set_default().

bool protocols::antibody_legacy::CDRH3Modeler::do_h3_modeling_
private

Referenced by apply(), model_h3(), and set_default().

bool protocols::antibody_legacy::CDRH3Modeler::docking_local_refine_
private

Referenced by set_camelid(), and set_default().

core::scoring::ScoreFunctionOP protocols::antibody_legacy::CDRH3Modeler::fa_scorefxn_
private
bool protocols::antibody_legacy::CDRH3Modeler::flank_relax_
private

relax flanking regions of h3

Referenced by loop_fa_relax(), and set_default().

bool protocols::antibody_legacy::CDRH3Modeler::freeze_h3_
private

freeze h3 during all cdr relax and local refine

Referenced by loop_fa_relax(), and set_default().

utility::vector1< core::fragment::FragData > protocols::antibody_legacy::CDRH3Modeler::H3_base_library
bool protocols::antibody_legacy::CDRH3Modeler::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().

core::Size protocols::antibody_legacy::CDRH3Modeler::h3_flank_
private

number of flanking residues:default 5

Referenced by loop_fa_relax(), and set_default().

bool protocols::antibody_legacy::CDRH3Modeler::h3_random_cut_
private

use random cutpoints for h3 modeling

Referenced by loop_fa_relax(), and set_default().

core::Real protocols::antibody_legacy::CDRH3Modeler::high_cst_
private

Referenced by set_default().

core::scoring::ScoreFunctionOP protocols::antibody_legacy::CDRH3Modeler::highres_scorefxn_
private
core::pack::task::TaskFactoryOP protocols::antibody_legacy::CDRH3Modeler::init_task_factory_
private

Referenced by setup_packer_task().

bool protocols::antibody_legacy::CDRH3Modeler::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().

bool protocols::antibody_legacy::CDRH3Modeler::loops_flag_
private

loop_building in docking

Referenced by set_default().

core::scoring::ScoreFunctionOP protocols::antibody_legacy::CDRH3Modeler::lowres_scorefxn_
private
bool protocols::antibody_legacy::CDRH3Modeler::min_base_relax_
private

lower amplitude during base relaxation

Referenced by loop_fa_relax(), and set_default().

bool protocols::antibody_legacy::CDRH3Modeler::refine_input_loop_
private

just refine input loop

Referenced by loop_centroid_relax(), loop_fa_relax(), and set_default().

bool protocols::antibody_legacy::CDRH3Modeler::snug_fit_
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().

core::pose::Pose protocols::antibody_legacy::CDRH3Modeler::start_pose_
private

Referenced by apply(), and loop_fa_relax().

core::pose::Pose protocols::antibody_legacy::CDRH3Modeler::template_pose_
private

Referenced by build_centroid_loop().

core::pack::task::TaskFactoryOP protocols::antibody_legacy::CDRH3Modeler::tf_
private

The documentation for this class was generated from the following files: