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protocols::antibody::AntibodyCDRGrafter Class Reference

Class to graft CDR loops from an antibody to a new antibody or from a CDR pose into a different antibody. Independant of antibody and CDR modeling. Results in 100 percent loop closure if using both graft algorithms. More...

#include <AntibodyCDRGrafter.hh>

Inheritance diagram for protocols::antibody::AntibodyCDRGrafter:
Inheritance graph
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Public Member Functions

 AntibodyCDRGrafter ()
 
 AntibodyCDRGrafter (AntibodyInfoOP ab_info)
 Default constructor. More...
 
 AntibodyCDRGrafter (AntibodyInfoOP ab_info, core::pose::Pose const &donor_structure, utility::vector1< bool > const &cdrs_to_graft, core::Size nter_overhang=3, core::Size cter_overhang=3)
 Constructor with most needed arguments. More...
 
 AntibodyCDRGrafter (AntibodyCDRGrafter const &src)
 
 ~AntibodyCDRGrafter () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void set_cdrs (utility::vector1< bool > const &cdrs)
 Set the CDRs to graft. Boolean vector of CDRNameEnums (1-8) (includes CDR4/DE loop) More...
 
void set_cdr_only (CDRNameEnum cdr)
 Set a single CDR we are going to graft in. More...
 
void set_donor_structure (core::pose::Pose const &pose)
 Set a donor structure. Culd be a single CDR, multiple CDRs or a whole other antibody. More...
 
void set_overhang (core::Size nter_overhang, core::Size cter_overhang)
 Set the N and Cterminal overhang used for superposition before the graft. More...
 
void set_stop_after_closure (bool stop_after_closure)
 Set a boolean for whether to stop after closure or not. Default TRUE. More...
 
void set_use_secondary_graft_mover_if_needed (bool use_secondary_graft_mover)
 Set a boolean for whether to use the secondary graft mover is the graft is not closed using the first. Default FALSE. More...
 
void set_optimize_cdrs (bool optimize_cdrs)
 Set to optimize any grafted and neighbor CDRs using dihdedral constrained relax on them. Default FALSE. Recommended if using secondary graft mover. More...
 
void set_include_cdr4_in_optimization (bool include_cdr4)
 Set to include the DE loop, or CDR4 if it is a neighbor to a grafted CDR and optimization is set to on. Recommended if optimizing. Default TRUE. More...
 
void set_dihedral_constraint_weight (core::Real dih_cst_wt)
 Set the dihedral constraint weight used if optimization is done and the scorefxn dihedral_constraint weight is zero. Default = 2.0. More...
 
void set_idealize_insert (bool idealize_insert)
 Idealize the insert. Default TRUE. More...
 
void set_scorefxn_pack (core::scoring::ScoreFunctionCOP scorefxn)
 Set the (all-atom) scorefunction used by the graft movers for packing Otherwise use cmd-line default. More...
 
void set_scorefxn_low (core::scoring::ScoreFunctionCOP scorefxn)
 Set the (low-res) scorefunction used by the graft movers to close loop. Default is to use Frank Dimaio's smoothed low-res terms. More...
 
protocols::grafting::CCDEndsGraftMoverget_primary_graft_mover ()
 Get a reference of the main graft mover to tweak settings. More...
 
protocols::grafting::AnchoredGraftMoverget_secondary_graft_mover ()
 Get a reference of the secondary graft mover to tweak settings. More...
 
std::pair< bool, core::Sizeapply_to_cdr (core::pose::Pose &pose, core::pose::Pose &cdr_region_with_overhang, CDRNameEnum const cdr, protocols::grafting::AnchoredGraftMoverOP grafter)
 Apply graft mover to pose, inserting the cdr_region. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
bool mover_provides_citation_info () const override
 Does this mover provide information about how to cite it? More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 Provide the citation. More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 This mover is published, but it can still provide unpublished info for the modules that it invokes. More...
 
- 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 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...
 
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
 
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_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...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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...
 

Private Member Functions

void setup_classes ()
 
void set_defaults ()
 

Private Attributes

AntibodyInfoOP ab_info_
 
core::pose::PoseOP donor_structure_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::scoring::ScoreFunctionOP scorefxn_low_
 
utility::vector1< boolcdrs_to_graft_
 
protocols::grafting::CCDEndsGraftMoverOP graft_mover_
 
protocols::grafting::AnchoredGraftMoverOP anchored_graft_mover_
 
bool use_secondary_graft_mover_
 
bool stop_after_closure_
 
core::Size nter_overhang_
 
core::Size cter_overhang_
 
AntibodyNumberingSchemeEnum numbering_scheme_
 Needed for default and RS constructor. More...
 
CDRDefinitionEnum cdr_definition_
 
bool optimize_cdrs_
 
bool include_cdr4_
 
utility::vector1
< utility::vector1< bool > > 
neighbor_cdrs_
 
core::Real dihedral_cst_weight_
 

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
 
- 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

Class to graft CDR loops from an antibody to a new antibody or from a CDR pose into a different antibody. Independant of antibody and CDR modeling. Results in 100 percent loop closure if using both graft algorithms.

Recommended to use cluster-based or general dihedral constraints on the CDR with a min or relax to optimize graft. Use optimiize_cdrs option to optimize the CDRs that were grafted and any neighbor CDRs using these dihedral constraints during relax.

By default, uses two residues on N and C terminal of insert CDR and scaffold to close loop. Use getters of primary and secondary graft mover to change this if needed. By default, stops after the graft is closed!

Constructor & Destructor Documentation

protocols::antibody::AntibodyCDRGrafter::AntibodyCDRGrafter ( )

References set_defaults(), and setup_classes().

protocols::antibody::AntibodyCDRGrafter::AntibodyCDRGrafter ( AntibodyInfoOP  ab_info)

Default constructor.

References set_defaults(), and setup_classes().

protocols::antibody::AntibodyCDRGrafter::AntibodyCDRGrafter ( AntibodyInfoOP  ab_info,
core::pose::Pose const &  donor_structure,
utility::vector1< bool > const &  cdrs_to_graft,
core::Size  nter_overhang = 3,
core::Size  cter_overhang = 3 
)

Constructor with most needed arguments.

Donor structure is what we will be grafting from. Either a CDR or a whole structure or chain. cdrs_to_graft: Boolean vector of CDRNameEnums (1-8) (includes CDR4/DE loop) overhangs: Set the N and Cterminal overhang used for superposition before the graft.

References cter_overhang_, nter_overhang_, set_cdrs(), set_defaults(), set_donor_structure(), and setup_classes().

protocols::antibody::AntibodyCDRGrafter::AntibodyCDRGrafter ( AntibodyCDRGrafter const &  src)
protocols::antibody::AntibodyCDRGrafter::~AntibodyCDRGrafter ( )
overridedefault

Member Function Documentation

void protocols::antibody::AntibodyCDRGrafter::apply ( core::pose::Pose )
overridevirtual
std::pair< bool, core::Size > protocols::antibody::AntibodyCDRGrafter::apply_to_cdr ( core::pose::Pose pose,
core::pose::Pose cdr_region_with_overhang,
CDRNameEnum const  cdr,
protocols::grafting::AnchoredGraftMoverOP  grafter 
)

Apply graft mover to pose, inserting the cdr_region.

Return success or failure of the graft and the position of the failure. Public in case one wants to use it by itself...

References ab_info_, protocols::antibody::design::check_cb(), cter_overhang_, core::sequence::end, nter_overhang_, protocols::loops::remove_cutpoint_variants(), core::pose::Pose::size(), protocols::loops::start, and protocols::antibody::TR().

Referenced by apply().

protocols::moves::MoverOP protocols::antibody::AntibodyCDRGrafter::clone ( ) const
overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

moves::MoverOP protocols::antibody::AntibodyCDRGrafter::fresh_instance ( ) const
overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

std::string protocols::antibody::AntibodyCDRGrafter::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

protocols::grafting::CCDEndsGraftMover & protocols::antibody::AntibodyCDRGrafter::get_primary_graft_mover ( )

Get a reference of the main graft mover to tweak settings.

References graft_mover_.

protocols::grafting::AnchoredGraftMover & protocols::antibody::AntibodyCDRGrafter::get_secondary_graft_mover ( )

Get a reference of the secondary graft mover to tweak settings.

References anchored_graft_mover_.

std::string protocols::antibody::AntibodyCDRGrafter::mover_name ( )
static
bool protocols::antibody::AntibodyCDRGrafter::mover_provides_citation_info ( ) const
overridevirtual

Does this mover provide information about how to cite it?

Returns true.

Author
Jared Adolf-Bryfogle

Reimplemented from protocols::moves::Mover.

void protocols::antibody::AntibodyCDRGrafter::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::antibody::AntibodyCDRGrafter::provide_authorship_info_for_unpublished ( ) const
overridevirtual

This mover is published, but it can still provide unpublished info for the modules that it invokes.

Reimplemented from protocols::moves::Mover.

References anchored_graft_mover_, and graft_mover_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::antibody::AntibodyCDRGrafter::provide_citation_info ( ) const
overridevirtual

Provide the citation.

Returns
A vector of citation collections. This allows the mover to provide citations for itself and for any modules that it invokes.

Reimplemented from protocols::moves::Mover.

References anchored_graft_mover_, and graft_mover_.

void protocols::antibody::AntibodyCDRGrafter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::antibody::AntibodyCDRGrafter::set_cdr_only ( CDRNameEnum  cdr)

Set a single CDR we are going to graft in.

References cdrs_to_graft_.

void protocols::antibody::AntibodyCDRGrafter::set_cdrs ( utility::vector1< bool > const &  cdrs)

Set the CDRs to graft. Boolean vector of CDRNameEnums (1-8) (includes CDR4/DE loop)

References protocols::antibody::CDRNameEnum_proto_total, and cdrs_to_graft_.

Referenced by AntibodyCDRGrafter().

void protocols::antibody::AntibodyCDRGrafter::set_defaults ( )
private
void protocols::antibody::AntibodyCDRGrafter::set_dihedral_constraint_weight ( core::Real  dih_cst_wt)

Set the dihedral constraint weight used if optimization is done and the scorefxn dihedral_constraint weight is zero. Default = 2.0.

References dihedral_cst_weight_.

void protocols::antibody::AntibodyCDRGrafter::set_donor_structure ( core::pose::Pose const &  pose)

Set a donor structure. Culd be a single CDR, multiple CDRs or a whole other antibody.

References donor_structure_.

Referenced by AntibodyCDRGrafter().

void protocols::antibody::AntibodyCDRGrafter::set_idealize_insert ( bool  idealize_insert)

Idealize the insert. Default TRUE.

References anchored_graft_mover_, and graft_mover_.

void protocols::antibody::AntibodyCDRGrafter::set_include_cdr4_in_optimization ( bool  include_cdr4)

Set to include the DE loop, or CDR4 if it is a neighbor to a grafted CDR and optimization is set to on. Recommended if optimizing. Default TRUE.

References include_cdr4_.

void protocols::antibody::AntibodyCDRGrafter::set_optimize_cdrs ( bool  optimize_cdrs)

Set to optimize any grafted and neighbor CDRs using dihdedral constrained relax on them. Default FALSE. Recommended if using secondary graft mover.

References optimize_cdrs_.

void protocols::antibody::AntibodyCDRGrafter::set_overhang ( core::Size  nter_overhang,
core::Size  cter_overhang 
)

Set the N and Cterminal overhang used for superposition before the graft.

References cter_overhang_, and nter_overhang_.

void protocols::antibody::AntibodyCDRGrafter::set_scorefxn_low ( core::scoring::ScoreFunctionCOP  scorefxn)

Set the (low-res) scorefunction used by the graft movers to close loop. Default is to use Frank Dimaio's smoothed low-res terms.

References scorefxn_low_.

void protocols::antibody::AntibodyCDRGrafter::set_scorefxn_pack ( core::scoring::ScoreFunctionCOP  scorefxn)

Set the (all-atom) scorefunction used by the graft movers for packing Otherwise use cmd-line default.

References scorefxn_.

void protocols::antibody::AntibodyCDRGrafter::set_stop_after_closure ( bool  stop_after_closure)

Set a boolean for whether to stop after closure or not. Default TRUE.

References anchored_graft_mover_, and graft_mover_.

void protocols::antibody::AntibodyCDRGrafter::set_use_secondary_graft_mover_if_needed ( bool  use_secondary_graft_mover)

Set a boolean for whether to use the secondary graft mover is the graft is not closed using the first. Default FALSE.

Using this results in 100% graft closure, however, in order to fix the structure, a dihedral constrained relax is done on the CDR while repacking neighbor residues. 85% Graft closure without (slight chainbreaks - not as bad as what used to be used for antibody modeling.)

References use_secondary_graft_mover_.

void protocols::antibody::AntibodyCDRGrafter::setup_classes ( )
private

References anchored_graft_mover_, and graft_mover_.

Referenced by AntibodyCDRGrafter().

Member Data Documentation

AntibodyInfoOP protocols::antibody::AntibodyCDRGrafter::ab_info_
private

Referenced by apply(), and apply_to_cdr().

protocols::grafting::AnchoredGraftMoverOP protocols::antibody::AntibodyCDRGrafter::anchored_graft_mover_
private
CDRDefinitionEnum protocols::antibody::AntibodyCDRGrafter::cdr_definition_
private

Referenced by apply(), parse_my_tag(), and set_defaults().

utility::vector1<bool> protocols::antibody::AntibodyCDRGrafter::cdrs_to_graft_
private
core::Size protocols::antibody::AntibodyCDRGrafter::cter_overhang_
private
core::Real protocols::antibody::AntibodyCDRGrafter::dihedral_cst_weight_
private
core::pose::PoseOP protocols::antibody::AntibodyCDRGrafter::donor_structure_
private
protocols::grafting::CCDEndsGraftMoverOP protocols::antibody::AntibodyCDRGrafter::graft_mover_
private
bool protocols::antibody::AntibodyCDRGrafter::include_cdr4_
private
utility::vector1< utility::vector1< bool > > protocols::antibody::AntibodyCDRGrafter::neighbor_cdrs_
private

Referenced by apply(), and set_defaults().

core::Size protocols::antibody::AntibodyCDRGrafter::nter_overhang_
private
AntibodyNumberingSchemeEnum protocols::antibody::AntibodyCDRGrafter::numbering_scheme_
private

Needed for default and RS constructor.

Referenced by apply(), parse_my_tag(), and set_defaults().

bool protocols::antibody::AntibodyCDRGrafter::optimize_cdrs_
private
core::scoring::ScoreFunctionOP protocols::antibody::AntibodyCDRGrafter::scorefxn_
private
core::scoring::ScoreFunctionOP protocols::antibody::AntibodyCDRGrafter::scorefxn_low_
private

Referenced by apply(), and set_scorefxn_low().

bool protocols::antibody::AntibodyCDRGrafter::stop_after_closure_
private

Referenced by parse_my_tag(), and set_defaults().

bool protocols::antibody::AntibodyCDRGrafter::use_secondary_graft_mover_
private

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