Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::antibody::design::AntibodyGraftDesignMover 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. The Antibody Database that this class uses will be available online (Too large for the rosetta_database) Till then, email me for access to the github repository. More...

#include <AntibodyGraftDesignMover.hh>

Public Member Functions

 AntibodyGraftDesignMover (AntibodyInfoOP ab_info)
 
 AntibodyGraftDesignMover (AntibodyInfoOP ab_info, std::string instruction_path)
 
virtual ~AntibodyGraftDesignMover ()
 
void set_defaults ()
 Reads default CDRGraftInstruction file and creates structs. More...
 
virtual void apply (pose::Pose &pose)
 
void set_cdr_set (CDRSet &cdr_set, CDRClusterMap &cdr_cluster_map, core::Size overhang)
 Will not initialize CDRs from the AntibodyDatabase. Use if you have your own CDR's you are interested in grafting. More...
 
void set_scorefunction (ScoreFunctionOP scorefxn)
 
void set_graft_rounds (core::Size graft_rounds)
 
void set_mintype (CDRNameEnum const cdr_name, MinTypeEnum mintype)
 Options are: relax, minimize, repack. Default is minimize. More...
 
void set_mintype_range (CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, MinTypeEnum mintype)
 
void set_min_rb (CDRNameEnum const cdr_name, bool const setting)
 Use rigid body optimization during minimization of the CDR (Minimize jump bt antigen and antibody)? More...
 
void set_min_rb_range (CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, bool const setting)
 
void set_min_neighbor_sc (CDRNameEnum const cdr_name, bool const setting)
 Use Neighbor sidechains during minimization of this CDR post-graft? More...
 
void set_min_neighbor_sc_range (CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, bool const setting)
 
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_pack_post_graft (bool pack_post_graft)
 Set the algorithm to run a packing step with neighbor detection post graft. Before any minimization or docking. More...
 
void set_rb_min_post_graft (bool rb_min_post_graft)
 Set the algorithm to run a final rigid-body minimization of antigen/antibody interface post graft. Useful if not docking - quicker, but less reliable then full dock. More...
 
void set_keep_top_designs (core::Size top_designs)
 Sets the protocol to keep a specific number of top designs. Default is 10. More...
 
vector1< pose::PoseOPget_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_cluster (CDRNameEnum const cdr, CDRClusterEnum const cluster, bool const setting)
 Leave out or include only clusters added here. More...
 
void set_cluster_range (CDRNameEnum const cdr, CDRClusterEnum const cluster_start, CDRClusterEnum const cluster_end, bool const setting)
 Leave out or include only clusters added here. More...
 
void set_cdr (CDRNameEnum const cdr, bool const setting)
 Use this CDR during design. More...
 
void set_cdr_range (CDRNameEnum const cdr_start, CDRNameEnum cdr_end, bool const setting)
 Use this range of CDRs during design. Default is all of them. More...
 
void set_cdr_stay_in_native_cluster (CDRNameEnum const cdr, bool const setting)
 Set to only sample within the native cluster of this CDR. More...
 
void set_cdr_range_stay_in_native_cluster (CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, bool const setting)
 Set a range of CDRs for which to only sample their native clusters. More...
 
void set_cdr_stay_in_type (CDRNameEnum const cdr, core::Size const type, bool const setting)
 Set to only sample with clusters of the given type for this CDR. Default is to only use type 1. More...
 
void set_cdr_range_stay_in_type (CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, core::Size const type, bool const setting)
 set a range of CDRs for which to stay within a particular type. Default is to only use type 1. More...
 
void set_cdr_min_length (CDRNameEnum const cdr, core::Size length)
 set the minimum cdr length to sample. Nothing shorter then this will be used during graft. More...
 
void set_cdr_min_length_range (CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, core::Size length)
 
void set_cdr_max_length (CDRNameEnum const cdr, core::Size length)
 set the maximum cdr length to sample. Nothing longer then this will be used. Useful for H3. More...
 
void set_cdr_max_length_range (CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, core::Size length)
 
void set_cdr_cluster_centers_only (CDRNameEnum const cdr, bool setting)
 Only sample cluster centers for this CDR. More...
 
void set_cdr_cluster_centers_only_range (CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, bool setting)
 
virtual string get_name () const
 Leave out these PDBs from sampling. Mainly for testing, but who knows. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
void set_type (std::string const &setting)
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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 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...
 
void type (const std::string &type_in)
 
virtual MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
std::string get_type () const
 
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...
 
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 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 

Private Member Functions

void read_command_line_options ()
 
void read_instructions (std::string instruction_path)
 Call DesignInstructionParser to determine settings for the design run. More...
 
void setup_native_clusters (pose::Pose &pose)
 
void initialize_cdr_set ()
 Uses instructions to Query the AntibodyDatabase and load poses. More...
 
void check_for_top_designs (pose::Pose &pose)
 
bool graft_cdr (pose::Pose &pose, CDRNameEnum cdr, core::Size index)
 Grafts a single CDR. Index is the vector index of CDRSet/CDRClusterMap. More...
 
void run_deterministic_graft_algorithm (pose::Pose &pose, vector1< CDRNameEnum > &cdrs_to_design)
 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_basic_mc_algorithm (pose::Pose &pose, vector1< CDRNameEnum > &cdrs_to_design)
 Basic mc algorithm that randomly samples from the cdr set. More...
 
void fix_pdb_info (pose::Pose &pose, CDRNameEnum cdr, CDRClusterEnum cluster, core::Size original_start, core::Size original_pdb_end)
 Fix PDB info as somehow the code for pdbinfo changed and my other method no longer works. No idea why. More...
 
void extend_native_cdrs (pose::Pose &pose, vector1< CDRNameEnum > &cdrs_to_design)
 Extend the native CDRs to be designed for benchmarking. More...
 
void set_default_graft_settings ()
 
vector1< vector1< 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...
 

Private Attributes

map< CDRNameEnum, CDRClusterOPnative_clusters_
 
map< CDRNameEnum,
CDRGraftInstructions
cdr_instructions_
 
map< CDRNameEnum, SamplingWeightssampling_instructions_
 
map< CDRNameEnum,
utility::vector1
< core::scoring::constraints::ConstraintCOP > > 
constraint_map_
 
std::string instruction_path_
 
CDRSet cdr_set_
 
CDRClusterMap cdr_cluster_map_
 
PDBMap pdbmap_
 
AntibodyInfoOP ab_info_
 
CCDEndsGraftMoverOP graft_mover_
 
ScoreFunctionOP scorefxn_
 
AntibodyDesignModelerOP modeler_
 
protocols::moves::MonteCarloOP mc_
 
core::Size overhang_
 
core::Size graft_rounds_
 
core::Size dock_rounds_
 
core::Size num_top_designs_
 
vector1< pose::PoseOPtop_designs_
 
vector1< core::Realtop_scores_
 
core::Size total_permutations_
 
bool dock_post_graft_
 
bool pack_post_graft_
 
bool rb_min_post_graft_
 
bool initial_perturb_
 
bool use_deterministic_algorithm_
 
core::Real max_linear_chainbreak_
 
bool extend_native_cdrs_
 
bool benchmark_
 

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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 
- 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

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. The Antibody Database that this class uses will be available online (Too large for the rosetta_database) Till then, email me for access to the github repository.

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::AntibodyGraftDesignMover::AntibodyGraftDesignMover ( AntibodyInfoOP  ab_info)
protocols::antibody::design::AntibodyGraftDesignMover::AntibodyGraftDesignMover ( AntibodyInfoOP  ab_info,
std::string  instruction_path 
)
protocols::antibody::design::AntibodyGraftDesignMover::~AntibodyGraftDesignMover ( )
virtual

Member Function Documentation

void protocols::antibody::design::AntibodyGraftDesignMover::apply ( pose::Pose pose)
virtual
void protocols::antibody::design::AntibodyGraftDesignMover::check_for_top_designs ( pose::Pose pose)
private
void protocols::antibody::design::AntibodyGraftDesignMover::extend_native_cdrs ( pose::Pose pose,
vector1< CDRNameEnum > &  cdrs_to_design 
)
private

Extend the native CDRs to be designed for benchmarking.

References ab_info_, protocols::antibody::AntibodyInfo::get_CDR_name(), modeler_, and protocols::antibody::TR.

Referenced by apply().

void protocols::antibody::design::AntibodyGraftDesignMover::fix_pdb_info ( pose::Pose pose,
CDRNameEnum  cdr,
CDRClusterEnum  cluster,
core::Size  original_start,
core::Size  original_pdb_end 
)
private

Fix PDB info as somehow the code for pdbinfo changed and my other method no longer works. No idea why.

References ab_info_, chain, protocols::antibody::AntibodyInfo::get_CDR_chain(), protocols::antibody::AntibodyInfo::get_cluster_length(), core::pose::Pose::pdb_info(), and protocols::antibody::TR.

vector1< vector1< Size > > protocols::antibody::design::AntibodyGraftDesignMover::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::AntibodyGraftDesignMover::get_name ( ) const
virtual

Leave out these PDBs from sampling. Mainly for testing, but who knows.

Implements protocols::moves::Mover.

vector1< pose::PoseOP> protocols::antibody::design::AntibodyGraftDesignMover::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.
bool protocols::antibody::design::AntibodyGraftDesignMover::graft_cdr ( pose::Pose pose,
CDRNameEnum  cdr,
core::Size  index 
)
private

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

Return success or failure

References ab_info_, core::scoring::constraints::add_coordinate_constraints(), protocols::antibody::add_harmonic_cluster_constraint(), protocols::grafting::CCDEndsGraftMover::apply(), cdr_cluster_map_, cdr_instructions_, cdr_set_, protocols::antibody::design::centroid_relax, constraint_map_, dock_post_graft_, dock_rounds_, end, core::pose::Pose::fold_tree(), protocols::antibody::AntibodyInfo::get_antigen_chains(), protocols::antibody::AntibodyInfo::get_CDR_end(), protocols::antibody::AntibodyInfo::get_CDR_name(), protocols::antibody::AntibodyInfo::get_CDR_start(), protocols::antibody::AntibodyInfo::get_cluster_name(), protocols::grafting::AnchoredGraftMover::get_cterm_scaffold_flexibility(), protocols::grafting::AnchoredGraftMover::get_nterm_scaffold_flexibility(), graft_mover_, protocols::antibody::h3, initial_perturb_, protocols::forge::methods::linear_chainbreak(), max_linear_chainbreak_, protocols::antibody::design::minimize, modeler_, protocols::antibody::design::no_min, overhang_, pack_post_graft_, core::pose::Pose::pdb_info(), pdbmap_, rb_min_post_graft_, protocols::antibody::design::relax, core::pose::Pose::remove_constraints(), core::scoring::constraints::remove_constraints_of_type(), protocols::grafting::AnchoredGraftMover::set_cycles(), set_default_graft_settings(), protocols::grafting::AnchoredGraftMover::set_insert_flexibility(), protocols::grafting::GraftMoverBase::set_insert_region(), protocols::grafting::GraftMoverBase::set_piece(), protocols::grafting::AnchoredGraftMover::set_scaffold_flexibility(), protocols::docking::setup_foldtree(), protocols::loops::start, and protocols::antibody::TR.

Referenced by run_basic_mc_algorithm(), and run_deterministic_graft_algorithm().

void protocols::antibody::design::AntibodyGraftDesignMover::initialize_cdr_set ( )
private

Uses instructions to Query the AntibodyDatabase and load poses.

References ab_info_, cdr_cluster_map_, cdr_instructions_, cdr_set_, and pdbmap_.

Referenced by apply().

void protocols::antibody::design::AntibodyGraftDesignMover::read_command_line_options ( )
private
void protocols::antibody::design::AntibodyGraftDesignMover::read_instructions ( std::string  instruction_path)
private

Call DesignInstructionParser to determine settings for the design run.

References ab_info_, cdr_instructions_, parser, and protocols::antibody::design::DesignInstructionsParser::read_cdr_graft_instructions().

Referenced by set_defaults().

void protocols::antibody::design::AntibodyGraftDesignMover::run_basic_mc_algorithm ( pose::Pose pose,
vector1< CDRNameEnum > &  cdrs_to_design 
)
private
void protocols::antibody::design::AntibodyGraftDesignMover::run_deterministic_graft_algorithm ( pose::Pose pose,
vector1< CDRNameEnum > &  cdrs_to_design 
)
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.

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

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

References cdr_set_, check_for_top_designs(), protocols::moves::MonteCarlo::eval_lowest_score_pose(), graft_cdr(), mc_, protocols::moves::MonteCarlo::recover_low(), protocols::moves::MonteCarlo::show_counters(), and protocols::antibody::TR.

Referenced by apply().

void protocols::antibody::design::AntibodyGraftDesignMover::set_cdr ( CDRNameEnum const  cdr,
bool const  setting 
)

Use this CDR during design.

References cdr_instructions_.

void protocols::antibody::design::AntibodyGraftDesignMover::set_cdr_cluster_centers_only ( CDRNameEnum const  cdr,
bool  setting 
)

Only sample cluster centers for this CDR.

References cdr_instructions_.

Referenced by set_cdr_cluster_centers_only_range().

void protocols::antibody::design::AntibodyGraftDesignMover::set_cdr_cluster_centers_only_range ( CDRNameEnum const  cdr_start,
CDRNameEnum const  cdr_end,
bool  setting 
)
void protocols::antibody::design::AntibodyGraftDesignMover::set_cdr_max_length ( CDRNameEnum const  cdr,
core::Size  length 
)

set the maximum cdr length to sample. Nothing longer then this will be used. Useful for H3.

References cdr_instructions_.

Referenced by set_cdr_max_length_range().

void protocols::antibody::design::AntibodyGraftDesignMover::set_cdr_max_length_range ( CDRNameEnum const  cdr_start,
CDRNameEnum const  cdr_end,
core::Size  length 
)
void protocols::antibody::design::AntibodyGraftDesignMover::set_cdr_min_length ( CDRNameEnum const  cdr,
core::Size  length 
)

set the minimum cdr length to sample. Nothing shorter then this will be used during graft.

References cdr_instructions_.

Referenced by set_cdr_min_length_range().

void protocols::antibody::design::AntibodyGraftDesignMover::set_cdr_min_length_range ( CDRNameEnum const  cdr_start,
CDRNameEnum const  cdr_end,
core::Size  length 
)
void protocols::antibody::design::AntibodyGraftDesignMover::set_cdr_range ( CDRNameEnum const  cdr_start,
CDRNameEnum  cdr_end,
bool const  setting 
)

Use this range of CDRs during design. Default is all of them.

References protocols::antibody::cdr_end, and cdr_instructions_.

Referenced by set_defaults().

void protocols::antibody::design::AntibodyGraftDesignMover::set_cdr_range_stay_in_native_cluster ( CDRNameEnum const  cdr_start,
CDRNameEnum const  cdr_end,
bool const  setting 
)

Set a range of CDRs for which to only sample their native clusters.

References protocols::antibody::cdr_end, and cdr_instructions_.

Referenced by set_defaults().

void protocols::antibody::design::AntibodyGraftDesignMover::set_cdr_range_stay_in_type ( CDRNameEnum const  cdr_start,
CDRNameEnum const  cdr_end,
core::Size const  type,
bool const  setting 
)

set a range of CDRs for which to stay within a particular type. Default is to only use type 1.

References protocols::antibody::cdr_end, cdr_instructions_, and protocols::moves::Mover::type().

Referenced by set_defaults().

void protocols::antibody::design::AntibodyGraftDesignMover::set_cdr_set ( CDRSet cdr_set,
CDRClusterMap cdr_cluster_map,
core::Size  overhang 
)

Will not initialize CDRs from the AntibodyDatabase. Use if you have your own CDR's you are interested in grafting.

Overhang residues will be used for superposition. To identify your CDRs, use the functions in AntibodyInfo or the pilot app identify_cdr_clusters in pilot/jadolfbr/cluster_utils

References cdr_cluster_map_, cdr_set_, and overhang_.

void protocols::antibody::design::AntibodyGraftDesignMover::set_cdr_stay_in_native_cluster ( CDRNameEnum const  cdr,
bool const  setting 
)

Set to only sample within the native cluster of this CDR.

References cdr_instructions_.

void protocols::antibody::design::AntibodyGraftDesignMover::set_cdr_stay_in_type ( CDRNameEnum const  cdr,
core::Size const  type,
bool const  setting 
)

Set to only sample with clusters of the given type for this CDR. Default is to only use type 1.

References cdr_instructions_, and protocols::moves::Mover::type().

void protocols::antibody::design::AntibodyGraftDesignMover::set_cluster ( CDRNameEnum const  cdr,
CDRClusterEnum const  cluster,
bool const  setting 
)

Leave out or include only clusters added here.

References cdr_instructions_.

void protocols::antibody::design::AntibodyGraftDesignMover::set_cluster_range ( CDRNameEnum const  cdr,
CDRClusterEnum const  cluster_start,
CDRClusterEnum const  cluster_end,
bool const  setting 
)

Leave out or include only clusters added here.

References cdr_instructions_, and cluster.

void protocols::antibody::design::AntibodyGraftDesignMover::set_default_graft_settings ( )
private
void protocols::antibody::design::AntibodyGraftDesignMover::set_defaults ( )
void protocols::antibody::design::AntibodyGraftDesignMover::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::AntibodyGraftDesignMover::set_dock_rounds ( core::Size  dock_rounds)

References dock_rounds_.

Referenced by read_command_line_options().

void protocols::antibody::design::AntibodyGraftDesignMover::set_graft_rounds ( core::Size  graft_rounds)

References graft_rounds_.

Referenced by read_command_line_options().

void protocols::antibody::design::AntibodyGraftDesignMover::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::AntibodyGraftDesignMover::set_min_neighbor_sc ( CDRNameEnum const  cdr_name,
bool const  setting 
)

Use Neighbor sidechains during minimization of this CDR post-graft?

References cdr_instructions_.

Referenced by set_min_neighbor_sc_range().

void protocols::antibody::design::AntibodyGraftDesignMover::set_min_neighbor_sc_range ( CDRNameEnum const  cdr_start,
CDRNameEnum const  cdr_end,
bool const  setting 
)
void protocols::antibody::design::AntibodyGraftDesignMover::set_min_rb ( CDRNameEnum const  cdr_name,
bool const  setting 
)

Use rigid body optimization during minimization of the CDR (Minimize jump bt antigen and antibody)?

dock_chains is LH_antigen. Does nothing if repacking the cdr. Default False.

References cdr_instructions_.

Referenced by set_min_rb_range().

void protocols::antibody::design::AntibodyGraftDesignMover::set_min_rb_range ( CDRNameEnum const  cdr_start,
CDRNameEnum const  cdr_end,
bool const  setting 
)

References protocols::antibody::cdr_end, and set_min_rb().

Referenced by set_defaults().

void protocols::antibody::design::AntibodyGraftDesignMover::set_mintype ( CDRNameEnum const  cdr_name,
MinTypeEnum  mintype 
)

Options are: relax, minimize, repack. Default is minimize.

References cdr_instructions_.

Referenced by set_mintype_range().

void protocols::antibody::design::AntibodyGraftDesignMover::set_mintype_range ( CDRNameEnum const  cdr_start,
CDRNameEnum const  cdr_end,
MinTypeEnum  mintype 
)
void protocols::antibody::design::AntibodyGraftDesignMover::set_pack_post_graft ( bool  pack_post_graft)

Set the algorithm to run a packing step with neighbor detection post graft. Before any minimization or docking.

References pack_post_graft_.

Referenced by read_command_line_options().

void protocols::antibody::design::AntibodyGraftDesignMover::set_rb_min_post_graft ( bool  rb_min_post_graft)

Set the algorithm to run a final rigid-body minimization of antigen/antibody interface post graft. Useful if not docking - quicker, but less reliable then full dock.

References rb_min_post_graft_.

Referenced by read_command_line_options().

void protocols::antibody::design::AntibodyGraftDesignMover::set_scorefunction ( ScoreFunctionOP  scorefxn)
void protocols::antibody::design::AntibodyGraftDesignMover::setup_native_clusters ( pose::Pose pose)
private

Member Data Documentation

AntibodyInfoOP protocols::antibody::design::AntibodyGraftDesignMover::ab_info_
private
bool protocols::antibody::design::AntibodyGraftDesignMover::benchmark_
private
CDRClusterMap protocols::antibody::design::AntibodyGraftDesignMover::cdr_cluster_map_
private
map< CDRNameEnum, CDRGraftInstructions > protocols::antibody::design::AntibodyGraftDesignMover::cdr_instructions_
private
CDRSet protocols::antibody::design::AntibodyGraftDesignMover::cdr_set_
private
map< CDRNameEnum, utility::vector1< core::scoring::constraints::ConstraintCOP > > protocols::antibody::design::AntibodyGraftDesignMover::constraint_map_
private

Referenced by graft_cdr().

bool protocols::antibody::design::AntibodyGraftDesignMover::dock_post_graft_
private

Referenced by graft_cdr(), and set_dock_post_graft().

core::Size protocols::antibody::design::AntibodyGraftDesignMover::dock_rounds_
private

Referenced by graft_cdr(), and set_dock_rounds().

bool protocols::antibody::design::AntibodyGraftDesignMover::extend_native_cdrs_
private

Referenced by apply(), and read_command_line_options().

CCDEndsGraftMoverOP protocols::antibody::design::AntibodyGraftDesignMover::graft_mover_
private
core::Size protocols::antibody::design::AntibodyGraftDesignMover::graft_rounds_
private
bool protocols::antibody::design::AntibodyGraftDesignMover::initial_perturb_
private
std::string protocols::antibody::design::AntibodyGraftDesignMover::instruction_path_
private
core::Real protocols::antibody::design::AntibodyGraftDesignMover::max_linear_chainbreak_
private
protocols::moves::MonteCarloOP protocols::antibody::design::AntibodyGraftDesignMover::mc_
private
AntibodyDesignModelerOP protocols::antibody::design::AntibodyGraftDesignMover::modeler_
private
map< CDRNameEnum, CDRClusterOP> protocols::antibody::design::AntibodyGraftDesignMover::native_clusters_
private

Referenced by setup_native_clusters().

core::Size protocols::antibody::design::AntibodyGraftDesignMover::num_top_designs_
private
core::Size protocols::antibody::design::AntibodyGraftDesignMover::overhang_
private
bool protocols::antibody::design::AntibodyGraftDesignMover::pack_post_graft_
private

Referenced by graft_cdr(), and set_pack_post_graft().

PDBMap protocols::antibody::design::AntibodyGraftDesignMover::pdbmap_
private

Referenced by graft_cdr(), and initialize_cdr_set().

bool protocols::antibody::design::AntibodyGraftDesignMover::rb_min_post_graft_
private

Referenced by graft_cdr(), and set_rb_min_post_graft().

map< CDRNameEnum, SamplingWeights > protocols::antibody::design::AntibodyGraftDesignMover::sampling_instructions_
private
ScoreFunctionOP protocols::antibody::design::AntibodyGraftDesignMover::scorefxn_
private
vector1< pose::PoseOP > protocols::antibody::design::AntibodyGraftDesignMover::top_designs_
private
vector1< core::Real> protocols::antibody::design::AntibodyGraftDesignMover::top_scores_
private
core::Size protocols::antibody::design::AntibodyGraftDesignMover::total_permutations_
private

Referenced by apply().

bool protocols::antibody::design::AntibodyGraftDesignMover::use_deterministic_algorithm_
private

Referenced by apply(), and read_command_line_options().


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