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protocols::antibody::design::AntibodyDesignMover Class Reference

This class designs antibodies by grafting, using cluster information and constraints to help. It represents the first step in The Rosetta Antibody Designer, but can be used outside of the application. A 2011 Antibody Database is included in the rosetta datase. Up-to-date versions can be downloaded from. More...

#include <AntibodyDesignMover.hh>

Inheritance diagram for protocols::antibody::design::AntibodyDesignMover:
Inheritance graph
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Public Member Functions

 AntibodyDesignMover ()
 
 AntibodyDesignMover (AntibodyInfoCOP ab_info)
 
 AntibodyDesignMover (AntibodyDesignMover const &src)
 
 ~AntibodyDesignMover () override
 
void set_defaults ()
 Reads default CDRGraftInstruction file and creates structs. More...
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
 Parse my tag for RosettaScripts. Main RS interface to full antibody design protocol. More...
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void set_light_chain (std::string const &light_chain)
 Set the light chain - lambda or kappa. More...
 
void set_random_start (bool const random_start)
 Set the protocol to start with random grafted CDRs for the CDRs set to graft design. Useful for starting a high-energy structure or doing benchmarks. More...
 
void set_design_protocol (AntibodyDesignProtocolEnum design_protocol)
 Set the design protocol. Default is classic_monte_carlo. Available options are: generalized_monte_carlo, deterministc_graft. More...
 
void set_seq_design_cdrs (utility::vector1< CDRNameEnum > seq_design_cdrs)
 Set the CDRs which will undergo Sequence-Design. More...
 
void set_graft_design_cdrs (utility::vector1< CDRNameEnum > graft_design_cdrs)
 Set the CDRs which will undergo Graft-Design. More...
 
void set_primary_cdrs (utility::vector1< CDRNameEnum > primary_cdrs)
 Manually set the CDRs which can be chosen in the outer cycle. More...
 
void set_outer_cycles (core::Size outer_cycles)
 Set the number of overall rounds. Each round will choose a CDR and design it and others based on options Default = 25. More...
 
void set_inner_cycles (core::Size inner_cycles)
 Set the number of inner cycles, which optimizes the structure and sequence of the antibody after any graft. Essentially min cycles. More...
 
void set_paratope_cdrs (utility::vector1< bool > const &cdrs)
 Set any paratope CDRs. If not set, will use all CDRs as the paratope where needed. Used mainly for constraints. More...
 
void set_epitope_residues (utility::vector1< PDBNumbering > epitope_residues)
 Set any epitope residues in PDB numbering. If not set, they will be detected automatically via the interface. More...
 
void set_use_epitope_constraints (bool use_epitope_csts)
 Setting to use epitope constraints. Without this false, will not use any set epitope residues. More...
 
void set_instruction_file (std::string instruction_file)
 Set the instruction file path to load options from instead of setting these via associated options functions Or loading via cmd-line option. Gotta love supporting 3 different Rosetta interfaces. More...
 
void set_cdr_set_options (AntibodyCDRSetOptions cdr_set_options)
 Set the options which will be used for querying the database. More...
 
void set_graft_design_options (AntibodyCDRGraftDesignOptions graft_design_options)
 Set CDR-specific GraftDesign options. More...
 
void set_seq_design_options (AntibodyCDRSeqDesignOptions seq_design_options)
 Set CDR-specific SeqDesign options. More...
 
void set_scorefunction (core::scoring::ScoreFunctionOP scorefxn)
 
void set_scorefunction_min (core::scoring::ScoreFunctionOP min_scorefxn)
 
void set_dock_post_graft (bool dock_post_graft)
 Set the algorithm to run a low-resolution docking step after each graft. Default false. More...
 
void set_dock_rounds (core::Size dock_rounds)
 
void set_keep_top_designs (core::Size top_designs)
 Sets the protocol to keep a specific number of top designs. Default is 10. More...
 
utility::vector1
< core::pose::PoseOP
get_top_designs ()
 Get the top designs found. You can then use them in other protocols, dump them, etc. They are in order. More...
 
void set_interface_dis (core::Real interface_dis)
 
void set_neighbor_dis (core::Real neighbor_dis)
 
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
core::pose::PoseOP get_additional_output () override
 Mechanism by which a mover may return multiple output poses from a single input pose. 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 can provide unpublished author info for 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...
 
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 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 read_command_line_options ()
 
void setup_options_classes ()
 Setup ALL options classes. More...
 
void setup_native_clusters (core::pose::Pose &pose)
 
void setup_native_sequence (core::pose::Pose &pose)
 
void setup_epitope_residues (core::pose::Pose const &pose)
 
void setup_paratope_epitope_constraints (core::pose::Pose &pose)
 
void setup_cart_minimizer ()
 
void setup_modeler ()
 
void finalize_setup (core::pose::Pose &pose)
 
void setup_scorefxn ()
 
void setup_random_start_pose (core::pose::Pose &pose, utility::vector1< CDRNameEnum > &cdrs_to_design)
 Extend the native CDRs to be designed for benchmarking. More...
 
void setup_default_graft_settings ()
 
void setup_cdr_pose_sampling_strategies ()
 Setup alternative cdr pose indexes and sampling strategies. More...
 
void initialize_cdr_set (core::pose::Pose const &pose)
 Uses instructions to Query the AntibodyDatabase and load poses. More...
 
void check_for_top_designs (core::pose::Pose &pose)
 
utility::vector1
< utility::vector1< core::Size > > 
get_cdr_set_index_list ()
 Gets a list of vectors whose indexes correspond to CDRNameEnum, and whose values correspond to the cdr_set index. If the value is 0, it means no cdr in set. More...
 
bool apply_to_cdr (core::pose::Pose &pose, CDRNameEnum cdr, core::Size index, bool min_post_graft=true)
 
bool graft_in_cdr (core::pose::Pose &pose, CDRNameEnum const cdr, CDRDBPose &cdr_pose)
 Grafts a single CDR into framework. Index is the vector index of CDRSet/CDRClusterMap. More...
 
std::pair< bool, core::Sizerun_graft (core::pose::Pose &pose, core::pose::Pose const &grafting_pose, CDRNameEnum const cdr, clusters::CDRClusterEnum const cluster, protocols::grafting::AnchoredGraftMoverOP grafter)
 
void run_optimization_cycle (core::pose::Pose &pose, protocols::moves::MonteCarlo &mc, CDRNameEnum cdr)
 Run the inner structure/sequence optimization cycle. More...
 
void run_final_IAM (bool run_IAM)
 Mutates framework residues needed to stay within a particular cluster. Only one (L1-11-1) is known to have framework dependencies. For now. Will be replaced by AntibodyDesignOptimizer. More...
 
void run_deterministic_graft_algorithm (core::pose::Pose &pose, utility::vector1< CDRNameEnum > &cdrs_to_design)
 . If rounds >= number of possible combinations - Try them all. More...
 
void run_basic_mc_algorithm (core::pose::Pose &pose, utility::vector1< CDRNameEnum > &cdrs_to_design, AntibodyDesignProtocolEnum mc_algorithm)
 Basic mc algorithm that randomly samples from the cdr set. More...
 
void print_str_vec (std::string const name, utility::vector1< std::string > const &vec, std::ostream &output=std::cout) const
 
void finalize_pose (AntibodyInfoCOP ab_info, core::pose::Pose &pose)
 Add cluster comments, fixes CDR numbering for certain cases, runs IAM. More...
 
AntibodyInfoOP init_ab_info (core::pose::Pose const &pose)
 

Private Attributes

AntibodyInfoOP ab_info_ = nullptr
 
AntibodyDesignEnumManagerOP design_enum_manager_ = nullptr
 
AntibodyDatabaseManagerOP db_manager_ = nullptr
 
AntibodyCDRSetOptions cdr_set_options_
 
AntibodyCDRGraftDesignOptions cdr_graft_design_options_
 
AntibodyCDRSeqDesignOptions cdr_seq_design_options_
 
AntibodySeqDesignTFCreatorOP seq_design_creator_ = nullptr
 
std::map< CDRNameEnum,
utility::vector1< CDRDBPose > > 
cdr_set_
 
std::map< CDRNameEnum,
std::map
< clusters::CDRClusterEnum,
utility::vector1< core::Size > > > 
cluster_based_CDRDBPose_indexes_
 Even cluster sampling (even_cluster_mc protocol) More...
 
std::map< CDRNameEnum,
std::map< core::Size, std::map
< clusters::CDRClusterEnum,
utility::vector1< core::Size > > > > 
length_based_CDRDBPose_indexes_
 Even Length and Cluster sampling (even_length_cluster_mc protocol) More...
 
protocols::grafting::CCDEndsGraftMoverOP graft_mover_
 
protocols::grafting::AnchoredGraftMoverOP anchored_graft_mover_
 
MutateFrameworkForClusterOP framework_mutator_ = nullptr
 
core::scoring::ScoreFunctionOP scorefxn_ = nullptr
 
core::scoring::ScoreFunctionOP scorefxn_min_ = nullptr
 
core::scoring::ScoreFunctionOP scorefxn_cart_graft_ = nullptr
 
GeneralAntibodyModelerOP modeler_ = nullptr
 
protocols::minimization_packing::MinMoverOP cart_min_graft_ = nullptr
 
protocols::moves::MonteCarloOP mc_ = nullptr
 
protocols::moves::MonteCarloOP inner_mc_ = nullptr
 
constraints::ParatopeEpitopeSiteConstraintMoverOP paratope_epitope_cst_mover_ = nullptr
 
constraints::ParatopeSiteConstraintMoverOP paratope_cst_mover_ = nullptr
 
constraints::CDRDihedralConstraintMoverOP cdr_dihedral_cst_mover_ = nullptr
 
core::Size overhang_
 
core::Size outer_cycles_
 
core::Size inner_cycles_
 
core::Size dock_cycles_
 
core::Size num_top_designs_
 
core::Real interface_dis_
 
core::Real neighbor_dis_
 
utility::vector1
< core::pose::PoseOP
top_designs_
 
utility::vector1< core::Realtop_scores_
 
core::Size total_permutations_
 
bool dock_post_graft_
 
bool rb_min_post_graft_
 
utility::vector1< boolparatope_cdrs_
 
utility::vector1< PDBNumberingepitope_residues_
 
bool adapt_graft_
 
bool enable_adapt_graft_cartesian_
 
bool benchmark_
 
bool use_light_chain_type_
 
bool use_epitope_constraints_
 
bool print_tracer_info_
 
bool idealize_graft_cdrs_
 
bool add_log_to_pose_
 
utility::vector1< std::string > graft_log_
 
utility::vector1< std::string > accept_log_
 
core::Real outer_kt_
 
core::Real inner_kt_
 
AntibodyDesignProtocolEnum design_protocol_
 
utility::vector1< CDRNameEnumseq_design_override_
 
utility::vector1< CDRNameEnumgraft_design_override_
 
utility::vector1< CDRNameEnumcdrs_to_design_
 
utility::vector1< CDRNameEnumprimary_cdrs_
 
std::string instruction_file_ = "NA"
 
core::Size stats_cutoff_
 
bool mutate_framework_for_cluster_
 
std::string mintype_ = "NA"
 
bool mc_optimize_dG_ = false
 
core::Real mc_interface_weight_ = 1.0
 
core::Real mc_total_weight_ = 0.0
 
bool run_final_AIM_ = true
 
bool remove_antigen_ = false
 
std::string light_chain_ = ""
 
core::Size additional_outputs_returned_ = 0
 

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

This class designs antibodies by grafting, using cluster information and constraints to help. It represents the first step in The Rosetta Antibody Designer, but can be used outside of the application. A 2011 Antibody Database is included in the rosetta datase. Up-to-date versions can be downloaded from.

To use this class: 1) Use default instruction path, or set one. Loads CDRs from AntibodyDatabase *See rosetta_database/sampling/antibodies for file format. 2) Use class interface settings to control sampling. Loads CDRs from AntibodyDatabase. 3) Use set_cdr_sets to set your own CDRs to graft.

Constructor & Destructor Documentation

protocols::antibody::design::AntibodyDesignMover::AntibodyDesignMover ( )
protocols::antibody::design::AntibodyDesignMover::AntibodyDesignMover ( AntibodyInfoCOP  ab_info)
protocols::antibody::design::AntibodyDesignMover::AntibodyDesignMover ( AntibodyDesignMover const &  src)
protocols::antibody::design::AntibodyDesignMover::~AntibodyDesignMover ( )
overridedefault

Member Function Documentation

void protocols::antibody::design::AntibodyDesignMover::apply ( core::pose::Pose )
overridevirtual
bool protocols::antibody::design::AntibodyDesignMover::apply_to_cdr ( core::pose::Pose pose,
CDRNameEnum  cdr,
core::Size  index,
bool  min_post_graft = true 
)
private
void protocols::antibody::design::AntibodyDesignMover::check_for_top_designs ( core::pose::Pose pose)
private
protocols::moves::MoverOP protocols::antibody::design::AntibodyDesignMover::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.

void protocols::antibody::design::AntibodyDesignMover::finalize_pose ( AntibodyInfoCOP  ab_info,
core::pose::Pose pose 
)
private
void protocols::antibody::design::AntibodyDesignMover::finalize_setup ( core::pose::Pose pose)
private
protocols::moves::MoverOP protocols::antibody::design::AntibodyDesignMover::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.

core::pose::PoseOP protocols::antibody::design::AntibodyDesignMover::get_additional_output ( )
overridevirtual

Mechanism by which a mover may return multiple output poses from a single input pose.

fpd

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

Mechanism by which a mover may return multiple output poses from a single input pose. After apply is called, calling this function will return subsequent output poses. NULL is returned if the mover has no more output poses remaining. The base class implementation returns NULL always; multi-output movers must override this. RosettaScripts uses this interface to produce a 'branched' protocol.

Reimplemented from protocols::moves::Mover.

References ab_info_, additional_outputs_returned_, finalize_pose(), init_ab_info(), and top_designs_.

vector1< vector1< core::Size > > protocols::antibody::design::AntibodyDesignMover::get_cdr_set_index_list ( )
private

Gets a list of vectors whose indexes correspond to CDRNameEnum, and whose values correspond to the cdr_set index. If the value is 0, it means no cdr in set.

References cdr_set_, protocols::antibody::CDRNameEnum_start, protocols::antibody::CDRNameEnum_total, and protocols::antibody::design::get_all_graft_permutations().

std::string protocols::antibody::design::AntibodyDesignMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

utility::vector1< core::pose::PoseOP> protocols::antibody::design::AntibodyDesignMover::get_top_designs ( )
inline

Get the top designs found. You can then use them in other protocols, dump them, etc. They are in order.

  • This should be refactored to get_additional_output.

References top_designs_.

bool protocols::antibody::design::AntibodyDesignMover::graft_in_cdr ( core::pose::Pose pose,
CDRNameEnum const  cdr,
CDRDBPose cdr_pose 
)
private

Grafts a single CDR into framework. Index is the vector index of CDRSet/CDRClusterMap.

Return success or failure

AntibodyInfoOP protocols::antibody::design::AntibodyDesignMover::init_ab_info ( core::pose::Pose const &  pose)
private
void protocols::antibody::design::AntibodyDesignMover::initialize_cdr_set ( core::pose::Pose const &  pose)
private

Uses instructions to Query the AntibodyDatabase and load poses.

References ab_info_, cdr_set_, cdr_set_options_, and db_manager_.

Referenced by finalize_setup().

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

Does this mover provide information about how to cite it?

Returns true.

Reimplemented from protocols::moves::Mover.

void protocols::antibody::design::AntibodyDesignMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::antibody::design::AntibodyDesignMover::print_str_vec ( std::string const  name,
utility::vector1< std::string > const &  vec,
std::ostream &  output = std::cout 
) const
private

References core::id::to_string().

Referenced by show().

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::antibody::design::AntibodyDesignMover::provide_authorship_info_for_unpublished ( ) const
overridevirtual

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

Reimplemented from protocols::moves::Mover.

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::antibody::design::AntibodyDesignMover::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.

void protocols::antibody::design::AntibodyDesignMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::antibody::design::AntibodyDesignMover::read_command_line_options ( )
private
void protocols::antibody::design::AntibodyDesignMover::run_basic_mc_algorithm ( core::pose::Pose pose,
utility::vector1< CDRNameEnum > &  cdrs_to_design,
AntibodyDesignProtocolEnum  mc_algorithm 
)
private
void protocols::antibody::design::AntibodyDesignMover::run_deterministic_graft_algorithm ( core::pose::Pose pose,
utility::vector1< CDRNameEnum > &  cdrs_to_design 
)
private

. If rounds >= number of possible combinations - Try them all.

Grafts CDRs on the input structure, in a random order.

References apply_to_cdr(), cdr_set_, check_for_top_designs(), mc_, and protocols::antibody::TR().

Referenced by apply().

void protocols::antibody::design::AntibodyDesignMover::run_final_IAM ( bool  run_IAM)
private

Mutates framework residues needed to stay within a particular cluster. Only one (L1-11-1) is known to have framework dependencies. For now. Will be replaced by AntibodyDesignOptimizer.

Run a final IAM at the end of the protocol? Default True.

std::pair< bool, core::Size > protocols::antibody::design::AntibodyDesignMover::run_graft ( core::pose::Pose pose,
core::pose::Pose const &  grafting_pose,
CDRNameEnum const  cdr,
clusters::CDRClusterEnum const  cluster,
protocols::grafting::AnchoredGraftMoverOP  grafter 
)
private
void protocols::antibody::design::AntibodyDesignMover::run_optimization_cycle ( core::pose::Pose pose,
protocols::moves::MonteCarlo mc,
CDRNameEnum  cdr 
)
private
void protocols::antibody::design::AntibodyDesignMover::set_cdr_set_options ( AntibodyCDRSetOptions  cdr_set_options)

Set the options which will be used for querying the database.

References cdr_set_options_.

void protocols::antibody::design::AntibodyDesignMover::set_defaults ( )

Reads default CDRGraftInstruction file and creates structs.

References cdr_graft_design_options_, cdr_seq_design_options_, cdr_set_options_, epitope_residues_, overhang_, paratope_cdrs_, and print_tracer_info_.

Referenced by AntibodyDesignMover().

void protocols::antibody::design::AntibodyDesignMover::set_design_protocol ( AntibodyDesignProtocolEnum  design_protocol)

Set the design protocol. Default is classic_monte_carlo. Available options are: generalized_monte_carlo, deterministc_graft.

. Deterministic Protocol only available if GraftDesigning a single CDR.

References design_protocol_.

void protocols::antibody::design::AntibodyDesignMover::set_dock_post_graft ( bool  dock_post_graft)

Set the algorithm to run a low-resolution docking step after each graft. Default false.

Uses command-line options for docking. Lower inner or outer cycles if you are grafting many CDRs. Still quicker then relax.

References dock_post_graft_.

Referenced by read_command_line_options().

void protocols::antibody::design::AntibodyDesignMover::set_dock_rounds ( core::Size  dock_rounds)

References dock_cycles_.

Referenced by read_command_line_options().

void protocols::antibody::design::AntibodyDesignMover::set_epitope_residues ( utility::vector1< PDBNumbering epitope_residues)

Set any epitope residues in PDB numbering. If not set, they will be detected automatically via the interface.

References epitope_residues_.

void protocols::antibody::design::AntibodyDesignMover::set_graft_design_cdrs ( utility::vector1< CDRNameEnum graft_design_cdrs)

Set the CDRs which will undergo Graft-Design.

References graft_design_override_.

void protocols::antibody::design::AntibodyDesignMover::set_graft_design_options ( AntibodyCDRGraftDesignOptions  graft_design_options)

Set CDR-specific GraftDesign options.

References cdr_graft_design_options_.

void protocols::antibody::design::AntibodyDesignMover::set_inner_cycles ( core::Size  inner_cycles)

Set the number of inner cycles, which optimizes the structure and sequence of the antibody after any graft. Essentially min cycles.

References inner_cycles_.

void protocols::antibody::design::AntibodyDesignMover::set_instruction_file ( std::string  instruction_file)

Set the instruction file path to load options from instead of setting these via associated options functions Or loading via cmd-line option. Gotta love supporting 3 different Rosetta interfaces.

References instruction_file_.

void protocols::antibody::design::AntibodyDesignMover::set_interface_dis ( core::Real  interface_dis)

References interface_dis_.

void protocols::antibody::design::AntibodyDesignMover::set_keep_top_designs ( core::Size  top_designs)

Sets the protocol to keep a specific number of top designs. Default is 10.

References num_top_designs_.

Referenced by read_command_line_options().

void protocols::antibody::design::AntibodyDesignMover::set_light_chain ( std::string const &  light_chain)

Set the light chain - lambda or kappa.

References light_chain_.

void protocols::antibody::design::AntibodyDesignMover::set_neighbor_dis ( core::Real  neighbor_dis)

References neighbor_dis_.

void protocols::antibody::design::AntibodyDesignMover::set_outer_cycles ( core::Size  outer_cycles)

Set the number of overall rounds. Each round will choose a CDR and design it and others based on options Default = 25.

References outer_cycles_.

void protocols::antibody::design::AntibodyDesignMover::set_paratope_cdrs ( utility::vector1< bool > const &  cdrs)

Set any paratope CDRs. If not set, will use all CDRs as the paratope where needed. Used mainly for constraints.

References paratope_cdrs_.

void protocols::antibody::design::AntibodyDesignMover::set_primary_cdrs ( utility::vector1< CDRNameEnum primary_cdrs)

Manually set the CDRs which can be chosen in the outer cycle.

These should be on for either Sequence-Design or Graft-Design. Normally, the outer cycles are whatever CDRs we are designing, including CDRs which are sequence-design only. Use this if you are primarily interested in specific CDRs (such as graft-designing H3 and allowing H1 and L3 to sequence design during the inner cycle.

References primary_cdrs_.

void protocols::antibody::design::AntibodyDesignMover::set_random_start ( bool const  random_start)

Set the protocol to start with random grafted CDRs for the CDRs set to graft design. Useful for starting a high-energy structure or doing benchmarks.

References benchmark_.

void protocols::antibody::design::AntibodyDesignMover::set_scorefunction ( core::scoring::ScoreFunctionOP  scorefxn)

References scorefxn_.

void protocols::antibody::design::AntibodyDesignMover::set_scorefunction_min ( core::scoring::ScoreFunctionOP  min_scorefxn)

References scorefxn_min_.

void protocols::antibody::design::AntibodyDesignMover::set_seq_design_cdrs ( utility::vector1< CDRNameEnum seq_design_cdrs)

Set the CDRs which will undergo Sequence-Design.

References seq_design_override_.

void protocols::antibody::design::AntibodyDesignMover::set_seq_design_options ( AntibodyCDRSeqDesignOptions  seq_design_options)

Set CDR-specific SeqDesign options.

References cdr_seq_design_options_.

void protocols::antibody::design::AntibodyDesignMover::set_use_epitope_constraints ( bool  use_epitope_csts)

Setting to use epitope constraints. Without this false, will not use any set epitope residues.

References use_epitope_constraints_.

void protocols::antibody::design::AntibodyDesignMover::setup_cart_minimizer ( )
private

References cart_min_graft_, and scorefxn_cart_graft_.

Referenced by apply().

void protocols::antibody::design::AntibodyDesignMover::setup_cdr_pose_sampling_strategies ( )
private

Setup alternative cdr pose indexes and sampling strategies.

References ab_info_, cdr_set_, cluster_based_CDRDBPose_indexes_, and length_based_CDRDBPose_indexes_.

Referenced by finalize_setup().

void protocols::antibody::design::AntibodyDesignMover::setup_default_graft_settings ( )
private
void protocols::antibody::design::AntibodyDesignMover::setup_epitope_residues ( core::pose::Pose const &  pose)
private
void protocols::antibody::design::AntibodyDesignMover::setup_modeler ( )
private
void protocols::antibody::design::AntibodyDesignMover::setup_native_clusters ( core::pose::Pose pose)
private

References ab_info_.

Referenced by apply().

void protocols::antibody::design::AntibodyDesignMover::setup_native_sequence ( core::pose::Pose pose)
private
void protocols::antibody::design::AntibodyDesignMover::setup_options_classes ( )
private
void protocols::antibody::design::AntibodyDesignMover::setup_paratope_epitope_constraints ( core::pose::Pose pose)
private
void protocols::antibody::design::AntibodyDesignMover::setup_random_start_pose ( core::pose::Pose pose,
utility::vector1< CDRNameEnum > &  cdrs_to_design 
)
private
void protocols::antibody::design::AntibodyDesignMover::setup_scorefxn ( )
private
void protocols::antibody::design::AntibodyDesignMover::show ( std::ostream &  output = std::cout) const
overridevirtual

Member Data Documentation

AntibodyInfoOP protocols::antibody::design::AntibodyDesignMover::ab_info_ = nullptr
private
utility::vector1<std::string> protocols::antibody::design::AntibodyDesignMover::accept_log_
private

Referenced by apply(), and run_basic_mc_algorithm().

bool protocols::antibody::design::AntibodyDesignMover::adapt_graft_
private
bool protocols::antibody::design::AntibodyDesignMover::add_log_to_pose_
private
core::Size protocols::antibody::design::AntibodyDesignMover::additional_outputs_returned_ = 0
private

Referenced by get_additional_output().

protocols::grafting::AnchoredGraftMoverOP protocols::antibody::design::AntibodyDesignMover::anchored_graft_mover_
private
bool protocols::antibody::design::AntibodyDesignMover::benchmark_
private
protocols::minimization_packing::MinMoverOP protocols::antibody::design::AntibodyDesignMover::cart_min_graft_ = nullptr
private
constraints::CDRDihedralConstraintMoverOP protocols::antibody::design::AntibodyDesignMover::cdr_dihedral_cst_mover_ = nullptr
private
AntibodyCDRGraftDesignOptions protocols::antibody::design::AntibodyDesignMover::cdr_graft_design_options_
private
AntibodyCDRSeqDesignOptions protocols::antibody::design::AntibodyDesignMover::cdr_seq_design_options_
private
std::map< CDRNameEnum, utility::vector1< CDRDBPose > > protocols::antibody::design::AntibodyDesignMover::cdr_set_
private
AntibodyCDRSetOptions protocols::antibody::design::AntibodyDesignMover::cdr_set_options_
private
utility::vector1<CDRNameEnum> protocols::antibody::design::AntibodyDesignMover::cdrs_to_design_
private

Referenced by apply(), and finalize_setup().

std::map< CDRNameEnum, std::map< clusters::CDRClusterEnum, utility::vector1< core::Size > > > protocols::antibody::design::AntibodyDesignMover::cluster_based_CDRDBPose_indexes_
private

Even cluster sampling (even_cluster_mc protocol)

Referenced by run_basic_mc_algorithm(), and setup_cdr_pose_sampling_strategies().

AntibodyDatabaseManagerOP protocols::antibody::design::AntibodyDesignMover::db_manager_ = nullptr
private
AntibodyDesignEnumManagerOP protocols::antibody::design::AntibodyDesignMover::design_enum_manager_ = nullptr
private
AntibodyDesignProtocolEnum protocols::antibody::design::AntibodyDesignMover::design_protocol_
private
core::Size protocols::antibody::design::AntibodyDesignMover::dock_cycles_
private
bool protocols::antibody::design::AntibodyDesignMover::dock_post_graft_
private
bool protocols::antibody::design::AntibodyDesignMover::enable_adapt_graft_cartesian_
private
utility::vector1<PDBNumbering > protocols::antibody::design::AntibodyDesignMover::epitope_residues_
private
MutateFrameworkForClusterOP protocols::antibody::design::AntibodyDesignMover::framework_mutator_ = nullptr
private
utility::vector1<CDRNameEnum> protocols::antibody::design::AntibodyDesignMover::graft_design_override_
private
utility::vector1<std::string> protocols::antibody::design::AntibodyDesignMover::graft_log_
private

Referenced by apply(), apply_to_cdr(), and finalize_setup().

protocols::grafting::CCDEndsGraftMoverOP protocols::antibody::design::AntibodyDesignMover::graft_mover_
private
bool protocols::antibody::design::AntibodyDesignMover::idealize_graft_cdrs_
private
core::Size protocols::antibody::design::AntibodyDesignMover::inner_cycles_
private
core::Real protocols::antibody::design::AntibodyDesignMover::inner_kt_
private
protocols::moves::MonteCarloOP protocols::antibody::design::AntibodyDesignMover::inner_mc_ = nullptr
private
std::string protocols::antibody::design::AntibodyDesignMover::instruction_file_ = "NA"
private
core::Real protocols::antibody::design::AntibodyDesignMover::interface_dis_
private
std::map< CDRNameEnum, std::map< core::Size, std::map< clusters::CDRClusterEnum, utility::vector1< core::Size > > > > protocols::antibody::design::AntibodyDesignMover::length_based_CDRDBPose_indexes_
private

Even Length and Cluster sampling (even_length_cluster_mc protocol)

Referenced by run_basic_mc_algorithm(), and setup_cdr_pose_sampling_strategies().

std::string protocols::antibody::design::AntibodyDesignMover::light_chain_ = ""
private
protocols::moves::MonteCarloOP protocols::antibody::design::AntibodyDesignMover::mc_ = nullptr
private
core::Real protocols::antibody::design::AntibodyDesignMover::mc_interface_weight_ = 1.0
private

Referenced by parse_my_tag().

bool protocols::antibody::design::AntibodyDesignMover::mc_optimize_dG_ = false
private
core::Real protocols::antibody::design::AntibodyDesignMover::mc_total_weight_ = 0.0
private

Referenced by parse_my_tag().

std::string protocols::antibody::design::AntibodyDesignMover::mintype_ = "NA"
private
GeneralAntibodyModelerOP protocols::antibody::design::AntibodyDesignMover::modeler_ = nullptr
private
bool protocols::antibody::design::AntibodyDesignMover::mutate_framework_for_cluster_
private
core::Real protocols::antibody::design::AntibodyDesignMover::neighbor_dis_
private
core::Size protocols::antibody::design::AntibodyDesignMover::num_top_designs_
private
core::Size protocols::antibody::design::AntibodyDesignMover::outer_cycles_
private
core::Real protocols::antibody::design::AntibodyDesignMover::outer_kt_
private
core::Size protocols::antibody::design::AntibodyDesignMover::overhang_
private

Referenced by run_graft(), and set_defaults().

utility::vector1<bool> protocols::antibody::design::AntibodyDesignMover::paratope_cdrs_
private
constraints::ParatopeSiteConstraintMoverOP protocols::antibody::design::AntibodyDesignMover::paratope_cst_mover_ = nullptr
private
constraints::ParatopeEpitopeSiteConstraintMoverOP protocols::antibody::design::AntibodyDesignMover::paratope_epitope_cst_mover_ = nullptr
private
utility::vector1<CDRNameEnum> protocols::antibody::design::AntibodyDesignMover::primary_cdrs_
private
bool protocols::antibody::design::AntibodyDesignMover::print_tracer_info_
private
bool protocols::antibody::design::AntibodyDesignMover::rb_min_post_graft_
private
bool protocols::antibody::design::AntibodyDesignMover::remove_antigen_ = false
private
bool protocols::antibody::design::AntibodyDesignMover::run_final_AIM_ = true
private
core::scoring::ScoreFunctionOP protocols::antibody::design::AntibodyDesignMover::scorefxn_ = nullptr
private
core::scoring::ScoreFunctionOP protocols::antibody::design::AntibodyDesignMover::scorefxn_cart_graft_ = nullptr
private
core::scoring::ScoreFunctionOP protocols::antibody::design::AntibodyDesignMover::scorefxn_min_ = nullptr
private
AntibodySeqDesignTFCreatorOP protocols::antibody::design::AntibodyDesignMover::seq_design_creator_ = nullptr
private
utility::vector1<CDRNameEnum> protocols::antibody::design::AntibodyDesignMover::seq_design_override_
private
core::Size protocols::antibody::design::AntibodyDesignMover::stats_cutoff_
private
utility::vector1< core::pose::PoseOP > protocols::antibody::design::AntibodyDesignMover::top_designs_
private
utility::vector1< core::Real> protocols::antibody::design::AntibodyDesignMover::top_scores_
private
core::Size protocols::antibody::design::AntibodyDesignMover::total_permutations_
private

Referenced by finalize_setup().

bool protocols::antibody::design::AntibodyDesignMover::use_epitope_constraints_
private
bool protocols::antibody::design::AntibodyDesignMover::use_light_chain_type_
private

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