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protocols::antibody::design Namespace Reference

Classes

class  AntibodyDesignEnumManager
 
class  AntibodyDesignMover
 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...
 
class  AntibodyDesignMoverCreator
 
class  AntibodySeqDesignTFCreator
 Create a TaskFactory or individual TaskOperations based on a set of options These options are mainly for per-CDR and per-framework control of sequence design. More...
 
class  CDRGraftDesignOptions
 Class that holds CDRGraftDesign Options. Now that GraftDesign is not a separate 'thing', this should be split into CDRGraftOptions and CDRMinOptions eventually. More...
 
class  CDRGraftDesignOptionsParser
 
class  CDRSeqDesignOptions
 
class  CDRSeqDesignOptionsParser
 
class  GeneralAntibodyModeler
 Basic Class that can run modeling for various protocols. Does not do any design. Setup design TF via AntibodySeqDesignTFCreator. More...
 
struct  MutantPosition
 
class  MutateFrameworkForCluster
 Mutates framework positions to what is needed for a particular cluster if that cluster has needed mutations. More...
 
class  MutateFrameworkForClusterCreator
 
class  NativeAntibodySeq
 Class that keeps track of the 'native' sequence during design. Native means that no design has occured. Used for conservative base design to keep it from hopping around residue types. More...
 
struct  PDBNumbering
 Super-basic numbering struct. More...
 
class  ResnumFromStringsWithRangesSelector
 A selector which uses the protocols::antibody::design::get_resnums_from_strings_with_ranges() approach. More...
 

Typedefs

typedef
utility::pointer::shared_ptr
< AntibodyDesignEnumManager
AntibodyDesignEnumManagerOP
 
typedef
utility::pointer::shared_ptr
< AntibodyDesignEnumManager
const > 
AntibodyDesignEnumManagerCOP
 
typedef
utility::pointer::shared_ptr
< AntibodyDesignMover
AntibodyDesignMoverOP
 
typedef
utility::pointer::shared_ptr
< AntibodyDesignMover const > 
AntibodyDesignMoverCOP
 
typedef
utility::pointer::shared_ptr
< AntibodySeqDesignTFCreator
AntibodySeqDesignTFCreatorOP
 
typedef
utility::pointer::shared_ptr
< AntibodySeqDesignTFCreator
const > 
AntibodySeqDesignTFCreatorCOP
 
typedef
utility::pointer::shared_ptr
< CDRGraftDesignOptions
CDRGraftDesignOptionsOP
 
typedef
utility::pointer::shared_ptr
< CDRGraftDesignOptions const > 
CDRGraftDesignOptionsCOP
 
typedef
utility::pointer::shared_ptr
< CDRGraftDesignOptionsParser
CDRGraftDesignOptionsParserOP
 
typedef
utility::pointer::shared_ptr
< CDRGraftDesignOptionsParser
const > 
CDRGraftDesignOptionsParserCOP
 
typedef utility::vector1
< CDRGraftDesignOptionsOP
AntibodyCDRGraftDesignOptions
 
typedef
utility::pointer::shared_ptr
< CDRSeqDesignOptions
CDRSeqDesignOptionsOP
 
typedef
utility::pointer::shared_ptr
< CDRSeqDesignOptions const > 
CDRSeqDesignOptionsCOP
 
typedef
utility::pointer::shared_ptr
< CDRSeqDesignOptionsParser
CDRSeqDesignOptionsParserOP
 
typedef
utility::pointer::shared_ptr
< CDRSeqDesignOptionsParser
const > 
CDRSeqDesignOptionsParserCOP
 
typedef utility::vector1
< CDRSeqDesignOptionsOP
AntibodyCDRSeqDesignOptions
 
typedef
utility::pointer::shared_ptr
< GeneralAntibodyModeler
GeneralAntibodyModelerOP
 
typedef
utility::pointer::shared_ptr
< GeneralAntibodyModeler const > 
GeneralAntibodyModelerCOP
 
typedef
utility::pointer::shared_ptr
< MutateFrameworkForCluster
MutateFrameworkForClusterOP
 
typedef
utility::pointer::shared_ptr
< MutateFrameworkForCluster
const > 
MutateFrameworkForClusterCOP
 
typedef
utility::pointer::shared_ptr
< NativeAntibodySeq
NativeAntibodySeqOP
 
typedef
utility::pointer::shared_ptr
< NativeAntibodySeq const > 
NativeAntibodySeqCOP
 

Enumerations

enum  MinTypeEnum {
  relax = 1, centroid_relax, minimize, minimize_cartesian,
  dualspace, repack, backrub_protocol, no_min,
  MinTypeEnum_total = no_min
}
 
enum  SeqDesignStrategyEnum {
  seq_design_profiles = 1, seq_design_conservative, seq_design_profile_sets, seq_design_profile_sets_combined,
  seq_design_basic, seq_design_none, SeqDesignStrategyEnum_total = seq_design_none
}
 
enum  AntibodyDesignProtocolEnum {
  generalized_monte_carlo = 1, even_cluster_monte_carlo, even_length_cluster_monte_carlo, deterministic_graft,
  DesignProtocolEnum_total = deterministic_graft
}
 

Functions

CDRSeqDesignOptionsOP deep_copy (CDRSeqDesignOptions const &)
 
ScoreFunctionOP get_ab_design_global_scorefxn ()
 
ScoreFunctionOP get_ab_design_global_scorefxn (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
 Get Global Scorefxn from RS; XSD companion function: attributes_for_get_ab_design_global_scorefxn. More...
 
void attributes_for_get_ab_design_global_scorefxn (utility::tag::AttributeList &attlist)
 adds the required attribute to the AttributeList for XMLSchema generation More...
 
ScoreFunctionOP get_ab_design_dock_high_scorefxn ()
 
ScoreFunctionOP get_ab_design_dock_low_scorefxn ()
 
ScoreFunctionOP get_ab_design_min_scorefxn ()
 XSD companion function: attributes_for_get_ab_design_min_scorefxn. More...
 
ScoreFunctionOP get_ab_design_min_scorefxn (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
 
void attributes_for_get_ab_design_min_scorefxn (utility::tag::AttributeList &attlist)
 adds the required attribute to the AttributeList for XMLSchema generation More...
 
void insert_cdr_into_antibody (AntibodyInfoCOP ab_info, CDRNameEnum const cdr, core::pose::Pose &pose, core::pose::Pose &cdr_piece, core::Size overhang=3)
 Use insert_pose_into_pose to replace the cdr_piece with the current antibody's CDR. No modeling or superposition. For that, use protocols/grafting. More...
 
vector1< vector1< core::Size > > get_all_graft_permutations (vector1< vector1< core::Size > > permutations, vector1< core::Size > totals, core::Size const n)
 Gets all possible graft permutations. More...
 
AntibodyDesignProtocolEnum design_protocol_to_enum (std::string const &design_type)
 
std::string design_protocol_to_string (AntibodyDesignProtocolEnum const design_type)
 
SeqDesignStrategyEnum seq_design_strategy_to_enum (std::string const &strategy)
 
std::string seq_design_strategy_to_string (SeqDesignStrategyEnum strategy)
 
std::string get_dock_chains_from_ab_dock_chains (AntibodyInfoCOP ab_info, std::string const &ab_dock_chains)
 Convert an ab_dock_chain (L_H/ LH_A, etc. to the full dock chain string) More...
 
PDBNumbering get_pdb_numbering_from_single_string (std::string const &pdb_residue)
 These all need better names and they need to be moved to a general place. Make the ResidueKey of PDBInfo a public class: More...
 
core::Size get_resnum_from_single_string (core::pose::Pose const &pose, std::string const &pdb_residue)
 Get a resnum from strings such as: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code. More...
 
core::Size get_resnum_from_single_string_w_landmark (AntibodyInfoCOP ab_info, core::pose::Pose const &pose, std::string const &pdb_residue, AntibodyNumberingSchemeEnum const &scheme)
 Get a resnum using the PDBLandmark from strings such as: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code. More...
 
vector1< PDBNumberingget_pdb_numbering_from_strings (vector1< std::string > const &pdb_residues)
 
vector1< boolget_resnums_from_strings_with_ranges (core::pose::Pose const &pose, vector1< std::string > const &pdb_residues)
 
vector1< boolget_resnum_from_pdb_numbering (core::pose::Pose const &pose, vector1< PDBNumbering > const &pdb_residues)
 Get a boolean vector from a string of PDBNumbering. No error checking. Use with caution. More...
 
vector1< boolget_resnum_from_strings (core::pose::Pose const &pose, utility::vector1< std::string > const &pdb_residues)
 get a boolean vector from a vector of strings: Example: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code. More...
 
void add_loops_from_bool_vector (loops::Loops &loops, utility::vector1< bool > residues, bool add_cutpoints=false)
 Add this across protocol... More...
 
std::pair< bool, core::Sizecheck_cb (core::pose::Pose const &pose, utility::vector1< bool > const &residues)
 Check for severe peptide bond issues. Return pair of chainbreak, and position of wonky peptide bond. More...
 
std::pair< bool, core::Sizecheck_cb (core::pose::Pose const &pose, protocols::loops::Loops const &loops)
 Check for severe peptide bond issues. Return pair of chainbreak, and position of wonky peptide bond. More...
 
core::pack::task::operation::RestrictResidueToRepackingOP disable_design_region (AntibodyInfoCOP ab_info, const core::pose::Pose &pose, AntibodyRegionEnum region, bool cdr4_as_framework=true)
 Disable design of any particular region of the antibody complex. More...
 
core::pack::task::operation::RestrictResidueToRepackingOP disable_design_antigen (AntibodyInfoCOP ab_info, const core::pose::Pose &pose)
 Disable design of the antigen residues. More...
 
core::pack::task::operation::RestrictResidueToRepackingOP disable_design_framework (AntibodyInfoCOP ab_info, const core::pose::Pose &pose, bool cdr4_as_framework=true)
 Disable design of the framework residues. More...
 
core::pack::task::operation::RestrictResidueToRepackingOP disable_design_cdrs (AntibodyInfoCOP ab_info, const core::pose::Pose &pose)
 Get a Restrict operation to turn OFF design for all CDRs. More...
 
core::pack::task::operation::RestrictResidueToRepackingOP disable_design_cdr (AntibodyInfoCOP ab_info, CDRNameEnum cdr, const core::pose::Pose &pose)
 Get a Restrict operation to turn OFF design for particular CDRs. More...
 
core::pack::task::operation::RestrictResidueToRepackingOP disable_conserved_framework_positions (AntibodyInfoCOP ab_info, const core::pose::Pose &pose)
 Disable design for conserved framework positions. TODO: Needs to be expanded to read positions from database. More...
 
core::pack::task::operation::RestrictResidueToRepackingOP disable_h3_stem_positions (AntibodyInfoCOP ab_info, const core::pose::Pose &pose, core::Size nter_stem=2, core::Size cter_stem=3)
 Disable design of the first 2 and last 3 residues of the H3 CDR (North CDR definitions - kink determinants) More...
 
AntibodyCDRSetOptions get_cdr_set_options ()
 Get default options. More...
 
AntibodyCDRSetOptions get_cdr_set_options (std::string instruction_file)
 Get options from an instruction file. More...
 
AntibodyCDRGraftDesignOptions get_graft_design_options ()
 Get default options. More...
 
AntibodyCDRGraftDesignOptions get_graft_design_options (std::string instruction_file)
 Get options from an instruction file. More...
 
AntibodyCDRSeqDesignOptions get_seq_design_options ()
 Get default options. More...
 
AntibodyCDRSeqDesignOptions get_seq_design_options (std::string instruction_file)
 Get options from an instruction file. More...
 
std::map< core::Size, std::map
< core::chemical::AA,
core::Real > > 
get_cluster_profile_probability_data (AntibodyInfoCOP ab_info, const core::pose::Pose &pose, utility::vector1< bool > const &cdrs, utility::vector1< bool > &no_data_cdrs, const core::Size prob_cutoff=10, const bool use_outliers=false, const bool force_north_db=false, const bool ignore_light_chain_=false)
 Get probability data for a given set of CDRs. Will fill in the no_data_cdrs;. More...
 
std::map< core::Size, std::map
< core::chemical::AA,
core::Real > > 
get_cluster_profile_probability_data (AntibodyInfoCOP ab_info, const core::pose::Pose &pose, AntibodyCDRSeqDesignOptions const &seq_design_options, utility::vector1< bool > &no_data_cdrs, const core::Size prob_cutoff, const bool use_outliers, const bool force_north_db, const bool ignore_light_chain)
 
std::map< core::Size,
core::chemical::AA
transform_sequence_to_mutation_set (AntibodyInfoCOP ab_info, core::pose::Pose const &pose, CDRNameEnum const cdr, std::string const &sequence)
 Transforms a sequence to a mutation set used by the AddCDRProfileSetsOperation. Assumes that the sequence is the same length as the CDR. Forces use of North CDR definitions. More...
 
void set_native_cdr_sequence (AntibodyInfoCOP ab_info, CDRNameEnum cdr, core::pose::Pose &pose)
 Set the native CDR sequence into the pose datacache If none is set in the pose, will add it. More...
 
std::string get_native_sequence (core::pose::Pose const &pose, AntibodyInfo const &ab_info)
 
bool has_native_sequence (core::pose::Pose const &pose)
 
utility::vector1
< utility::vector1< core::Size > > 
get_all_graft_permutations (utility::vector1< utility::vector1< core::Size > > permutations, utility::vector1< core::Size > totals, core::Size const n)
 Gets all possible graft permutations. More...
 
utility::vector1< boolget_resnums_from_strings_with_ranges (core::pose::Pose const &pose, utility::vector1< std::string > const &pdb_residues)
 Get a boolean vector of resnums with ranges, where a - indicates range. Parses strings for PDB resnums such as 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code. Example: 1A-10A or 1A-10A:I. More...
 
utility::vector1< PDBNumberingget_pdb_numbering_from_strings (utility::vector1< std::string > const &pdb_residues)
 Get PDBNumbering from a vector of strings: Example: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code. More...
 
utility::vector1< boolget_resnum_from_pdb_numbering (core::pose::Pose const &pose, utility::vector1< PDBNumbering >const &pdb_residues)
 Get a boolean vector from a string of PDBNumbering. No error checking. Use with caution. More...
 

Typedef Documentation

typedef utility::pointer::shared_ptr< AntibodyDesignMover const > protocols::antibody::design::AntibodyDesignMoverCOP
typedef utility::pointer::shared_ptr< CDRSeqDesignOptions const > protocols::antibody::design::CDRSeqDesignOptionsCOP
typedef utility::pointer::shared_ptr< NativeAntibodySeq const> protocols::antibody::design::NativeAntibodySeqCOP

Enumeration Type Documentation

Enumerator
generalized_monte_carlo 
even_cluster_monte_carlo 
even_length_cluster_monte_carlo 
deterministic_graft 
DesignProtocolEnum_total 
Enumerator
relax 
centroid_relax 
minimize 
minimize_cartesian 
dualspace 
repack 
backrub_protocol 
no_min 
MinTypeEnum_total 
Enumerator
seq_design_profiles 
seq_design_conservative 
seq_design_profile_sets 
seq_design_profile_sets_combined 
seq_design_basic 
seq_design_none 
SeqDesignStrategyEnum_total 

Function Documentation

void protocols::antibody::design::add_loops_from_bool_vector ( loops::Loops &  loops,
utility::vector1< bool residues,
bool  add_cutpoints 
)
void protocols::antibody::design::attributes_for_get_ab_design_global_scorefxn ( utility::tag::AttributeList &  attlist)

adds the required attribute to the AttributeList for XMLSchema generation

References core::scoring::attributes_for_parse_score_function().

Referenced by protocols::antibody::design::AntibodyDesignMover::provide_xml_schema().

void protocols::antibody::design::attributes_for_get_ab_design_min_scorefxn ( utility::tag::AttributeList &  attlist)

adds the required attribute to the AttributeList for XMLSchema generation

Referenced by protocols::antibody::design::AntibodyDesignMover::provide_xml_schema().

std::pair< bool, core::Size > protocols::antibody::design::check_cb ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  residues 
)

Check for severe peptide bond issues. Return pair of chainbreak, and position of wonky peptide bond.

References protocols::loops::has_severe_pep_bond_geom_issues(), and core::pose::Pose::size().

Referenced by protocols::antibody::AntibodyCDRGrafter::apply_to_cdr(), and protocols::antibody::design::AntibodyDesignMover::run_graft().

std::pair< bool, core::Size > protocols::antibody::design::check_cb ( core::pose::Pose const &  pose,
protocols::loops::Loops const &  loops 
)

Check for severe peptide bond issues. Return pair of chainbreak, and position of wonky peptide bond.

References protocols::loops::has_severe_pep_bond_geom_issues().

CDRSeqDesignOptionsOP protocols::antibody::design::deep_copy ( CDRSeqDesignOptions const &  source)
inline
AntibodyDesignProtocolEnum protocols::antibody::design::design_protocol_to_enum ( std::string const &  design_type)
std::string protocols::antibody::design::design_protocol_to_string ( AntibodyDesignProtocolEnum const  design_type)
core::pack::task::operation::RestrictResidueToRepackingOP protocols::antibody::design::disable_conserved_framework_positions ( AntibodyInfoCOP  ab_info,
const core::pose::Pose pose 
)

Disable design for conserved framework positions. TODO: Needs to be expanded to read positions from database.

References protocols::antibody::AHO_Scheme, and core::pose::has_chain().

Referenced by protocols::antibody::design::AntibodySeqDesignTFCreator::add_extra_restrict_operations().

core::pack::task::operation::RestrictResidueToRepackingOP protocols::antibody::design::disable_design_antigen ( AntibodyInfoCOP  ab_info,
const core::pose::Pose pose 
)

Disable design of the antigen residues.

References protocols::antibody::antigen_region, and disable_design_region().

core::pack::task::operation::RestrictResidueToRepackingOP protocols::antibody::design::disable_design_cdr ( AntibodyInfoCOP  ab_info,
CDRNameEnum  cdr,
const core::pose::Pose pose 
)
core::pack::task::operation::RestrictResidueToRepackingOP protocols::antibody::design::disable_design_cdrs ( AntibodyInfoCOP  ab_info,
const core::pose::Pose pose 
)

Get a Restrict operation to turn OFF design for all CDRs.

References protocols::antibody::cdr_region, and disable_design_region().

core::pack::task::operation::RestrictResidueToRepackingOP protocols::antibody::design::disable_design_framework ( AntibodyInfoCOP  ab_info,
const core::pose::Pose pose,
bool  cdr4_as_framework 
)

Disable design of the framework residues.

References disable_design_region(), and protocols::antibody::framework_region.

core::pack::task::operation::RestrictResidueToRepackingOP protocols::antibody::design::disable_design_region ( AntibodyInfoCOP  ab_info,
const core::pose::Pose pose,
AntibodyRegionEnum  region,
bool  cdr4_as_framework 
)
core::pack::task::operation::RestrictResidueToRepackingOP protocols::antibody::design::disable_h3_stem_positions ( AntibodyInfoCOP  ab_info,
const core::pose::Pose pose,
core::Size  nter_stem,
core::Size  cter_stem 
)

Disable design of the first 2 and last 3 residues of the H3 CDR (North CDR definitions - kink determinants)

References protocols::antibody::AHO_Scheme.

Referenced by protocols::antibody::design::AntibodySeqDesignTFCreator::add_extra_restrict_operations().

core::scoring::ScoreFunctionOP protocols::antibody::design::get_ab_design_dock_high_scorefxn ( )
core::scoring::ScoreFunctionOP protocols::antibody::design::get_ab_design_dock_low_scorefxn ( )
core::scoring::ScoreFunctionOP protocols::antibody::design::get_ab_design_global_scorefxn ( )
core::scoring::ScoreFunctionOP protocols::antibody::design::get_ab_design_global_scorefxn ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)

Get Global Scorefxn from RS; XSD companion function: attributes_for_get_ab_design_global_scorefxn.

References core::scoring::atom_pair_constraint, core::scoring::dihedral_constraint, core::scoring::get_score_function(), and core::scoring::parse_score_function().

core::scoring::ScoreFunctionOP protocols::antibody::design::get_ab_design_min_scorefxn ( )
core::scoring::ScoreFunctionOP protocols::antibody::design::get_ab_design_min_scorefxn ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
utility::vector1<utility::vector1< core::Size > > protocols::antibody::design::get_all_graft_permutations ( utility::vector1< utility::vector1< core::Size > >  permutations,
utility::vector1< core::Size totals,
core::Size const  n 
)

Gets all possible graft permutations.

all_permutations is a list of vectors corresponding to cdrs_to_design vector. Essentially, each inner index describes a position in the cdr_set. Indexes correspond to CDRNameEnum, and whose values correspond to the cdr_set index. If the value is 0, it means no cdr in set. Example: <1, 0, 1, 1, 1, 1>. This is a possible combination to try graft, the second CDR, H2 is not part of the combination.

References core::pack::dunbrack::c, and get_all_graft_permutations().

Referenced by get_all_graft_permutations(), and protocols::antibody::design::AntibodyDesignMover::get_cdr_set_index_list().

vector1< vector1< core::Size > > protocols::antibody::design::get_all_graft_permutations ( utility::vector1< utility::vector1< core::Size > >  permutations,
utility::vector1< core::Size totals,
core::Size const  n 
)

Gets all possible graft permutations.

all_permutations is a list of vectors corresponding to cdrs_to_design vector. Essentially, each inner index describes a position in the cdr_set. Indexes correspond to CDRNameEnum, and whose values correspond to the cdr_set index. If the value is 0, it means no cdr in set. Example: <1, 0, 1, 1, 1, 1>. This is a possible combination to try graft, the second CDR, H2 is not part of the combination.

References core::pack::dunbrack::c, and get_all_graft_permutations().

Referenced by get_all_graft_permutations(), and protocols::antibody::design::AntibodyDesignMover::get_cdr_set_index_list().

AntibodyCDRSetOptions protocols::antibody::design::get_cdr_set_options ( )
AntibodyCDRSetOptions protocols::antibody::design::get_cdr_set_options ( std::string  filename)
std::map< core::Size, std::map< core::chemical::AA, core::Real > > protocols::antibody::design::get_cluster_profile_probability_data ( AntibodyInfoCOP  ab_info,
const core::pose::Pose pose,
utility::vector1< bool > const &  cdrs,
utility::vector1< bool > &  no_data_cdrs,
const core::Size  prob_cutoff,
const bool  use_outliers,
const bool  force_north_db,
const bool  ignore_light_chain 
)
std::map< core::Size, std::map< core::chemical::AA, core::Real > > protocols::antibody::design::get_cluster_profile_probability_data ( AntibodyInfoCOP  ab_info,
const core::pose::Pose pose,
AntibodyCDRSeqDesignOptions const &  seq_design_options,
utility::vector1< bool > &  no_data_cdrs,
const core::Size  prob_cutoff,
const bool  use_outliers,
const bool  force_north_db,
const bool  ignore_light_chain 
)
std::string protocols::antibody::design::get_dock_chains_from_ab_dock_chains ( AntibodyInfoCOP  ab_info,
std::string const &  ab_dock_chains 
)
AntibodyCDRGraftDesignOptions protocols::antibody::design::get_graft_design_options ( )
AntibodyCDRGraftDesignOptions protocols::antibody::design::get_graft_design_options ( std::string  filename)
std::string protocols::antibody::design::get_native_sequence ( core::pose::Pose const &  pose,
AntibodyInfo const &  ab_info 
)
PDBNumbering protocols::antibody::design::get_pdb_numbering_from_single_string ( std::string const &  pdb_residue)

These all need better names and they need to be moved to a general place. Make the ResidueKey of PDBInfo a public class:

Get the PDBNumbering from strings such as: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code.

References protocols::antibody::design::PDBNumbering::chain, protocols::antibody::design::PDBNumbering::icode, protocols::antibody::design::PDBNumbering::resnum, and protocols::antibody::TR().

Referenced by get_pdb_numbering_from_strings(), get_resnum_from_single_string(), get_resnum_from_single_string_w_landmark(), and get_resnums_from_strings_with_ranges().

utility::vector1<PDBNumbering> protocols::antibody::design::get_pdb_numbering_from_strings ( utility::vector1< std::string > const &  pdb_residues)

Get PDBNumbering from a vector of strings: Example: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code.

vector1<PDBNumbering> protocols::antibody::design::get_pdb_numbering_from_strings ( vector1< std::string > const &  pdb_residues)
utility::vector1<bool> protocols::antibody::design::get_resnum_from_pdb_numbering ( core::pose::Pose const &  pose,
utility::vector1< PDBNumbering >const &  pdb_residues 
)
vector1<bool> protocols::antibody::design::get_resnum_from_pdb_numbering ( core::pose::Pose const &  pose,
vector1< PDBNumbering > const &  pdb_residues 
)
core::Size protocols::antibody::design::get_resnum_from_single_string ( core::pose::Pose const &  pose,
std::string const &  pdb_residue 
)
core::Size protocols::antibody::design::get_resnum_from_single_string_w_landmark ( AntibodyInfoCOP  ab_info,
core::pose::Pose const &  pose,
std::string const &  pdb_residue,
AntibodyNumberingSchemeEnum const &  scheme 
)
utility::vector1< bool > protocols::antibody::design::get_resnum_from_strings ( core::pose::Pose const &  pose,
utility::vector1< std::string > const &  pdb_residues 
)

get a boolean vector from a vector of strings: Example: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code.

References get_pdb_numbering_from_strings(), and get_resnum_from_pdb_numbering().

utility::vector1<bool> protocols::antibody::design::get_resnums_from_strings_with_ranges ( core::pose::Pose const &  pose,
utility::vector1< std::string > const &  pdb_residues 
)

Get a boolean vector of resnums with ranges, where a - indicates range. Parses strings for PDB resnums such as 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code. Example: 1A-10A or 1A-10A:I.

vector1<bool> protocols::antibody::design::get_resnums_from_strings_with_ranges ( core::pose::Pose const &  pose,
vector1< std::string > const &  pdb_residues 
)
AntibodyCDRSeqDesignOptions protocols::antibody::design::get_seq_design_options ( )
AntibodyCDRSeqDesignOptions protocols::antibody::design::get_seq_design_options ( std::string  filename)
bool protocols::antibody::design::has_native_sequence ( core::pose::Pose const &  pose)
void protocols::antibody::design::insert_cdr_into_antibody ( AntibodyInfoCOP  ab_info,
CDRNameEnum const  cdr,
core::pose::Pose pose,
core::pose::Pose cdr_piece,
core::Size  overhang 
)

Use insert_pose_into_pose to replace the cdr_piece with the current antibody's CDR. No modeling or superposition. For that, use protocols/grafting.

References protocols::antibody::cdr_end, protocols::antibody::cdr_start, protocols::grafting::delete_region(), protocols::grafting::insert_pose_into_pose(), core::pose::Pose::pdb_info(), and core::pose::Pose::size().

SeqDesignStrategyEnum protocols::antibody::design::seq_design_strategy_to_enum ( std::string const &  strategy)
std::string protocols::antibody::design::seq_design_strategy_to_string ( SeqDesignStrategyEnum  strategy)
void protocols::antibody::design::set_native_cdr_sequence ( AntibodyInfoCOP  ab_info,
CDRNameEnum  cdr,
core::pose::Pose pose 
)

Set the native CDR sequence into the pose datacache If none is set in the pose, will add it.

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::NATIVE_ANTIBODY_SEQ, and protocols::antibody::TR().

Referenced by protocols::antibody::design::AntibodyDesignMover::apply_to_cdr().

std::map< core::Size, core::chemical::AA > protocols::antibody::design::transform_sequence_to_mutation_set ( AntibodyInfoCOP  ab_info,
core::pose::Pose const &  pose,
CDRNameEnum const  cdr,
std::string const &  sequence 
)

Transforms a sequence to a mutation set used by the AddCDRProfileSetsOperation. Assumes that the sequence is the same length as the CDR. Forces use of North CDR definitions.

References core::chemical::aa_from_oneletter_code(), protocols::antibody::North, protocols::loops::start, and core::id::to_string().

Referenced by protocols::antibody::task_operations::AddCDRProfileSetsOperation::apply().