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Rosetta Protocols
2014.35
|
Namespaces | |
clusters | |
design | |
Classes | |
class | Ab_TemplateInfo |
Specifically for AntibodyModeling protocol templates. Not for general use. More... | |
class | AntibodyEnumManager |
Interface to this class is in AntibodyInfo. More... | |
class | AntibodyFeatures |
Collects data on an antibody including CDRs, interfaces of L_H, L_A, H_A, and LH_A (this can be set), and other metrics. More... | |
class | AntibodyFeaturesCreator |
creator for the HBondParameterFeatures class More... | |
class | AntibodyInfo |
This class is used to get all relevant information you would need when dealing with an antibody. More... | |
class | AntibodyModelerProtocol |
struct | AntibodyNumbering |
class | AntibodyNumberingParser |
Class responsible for reading database Numbering Scheme definitions and their transforms from the database. More... | |
class | CDRsMinPackMin |
class | CloseOneCDRLoop |
Closes only one CDR onto a framework. More... | |
struct | FrameWork |
class | GraftCDRLoopsProtocol |
class | GraftedStemOptimizer |
Grafts only one CDR onto a framework. More... | |
class | GraftOneCDRLoop |
Grafts only one CDR onto a framework. More... | |
class | H3CterInsert |
H3 CDR, Fragment Insertion and CCD. More... | |
class | H3PerturbCCD |
class | H3RefineCCD |
class | LHRepulsiveRamp |
class | LHRepulsiveRampLegacy |
class | LHSnugFitLegacy |
class | ModelCDRH3 |
Ab initio modeling of CDR H3 loop. More... | |
struct | ParatopeMetric |
Convenience struct for passing around paratope data, including individual data for cdrs. CDRs not present default to 0. Templates are used mainly to have Size/ Real or string values. More... | |
class | PDBLandmark |
Class that was once a struct; Used for matching pdb information between numbering schemes and cdr definitions. More... | |
class | RefineBetaBarrel |
class | RefineOneCDRLoop |
class | RefineOneCDRLoopCentroid |
class | SnugDock |
MoveSet step of Snugdock as described in: More... | |
class | SnugDockProtocol |
Functions | |
std::ostream & | operator<< (std::ostream &out, const Ab_TemplateInfo &ab_t_info) |
scoring::ScoreFunctionCOP | get_Pack_ScoreFxn (void) |
scoring::ScoreFunctionCOP | get_Dock_ScoreFxn (void) |
scoring::ScoreFunctionCOP | get_LoopCentral_ScoreFxn (void) |
scoring::ScoreFunctionCOP | get_LoopHighRes_ScoreFxn (void) |
std::ostream & | operator<< (std::ostream &out, const AntibodyInfo &ab_info) |
std::ostream & | operator<< (std::ostream &out, const AntibodyModelerProtocol &ab_m) |
std::ostream & | operator<< (std::ostream &out, const CDRsMinPackMin &ab_m_2) |
std::ostream & | operator<< (std::ostream &out, const GraftCDRLoopsProtocol &ab_m_2) |
vector1< Real > | vl_vh_orientation_coords (const core::pose::Pose &pose_in, const AntibodyInfo &ab_info) |
calculate the VH_VL packing angle from 2 sheet definitions on each antibody chain More... | |
std::pair< core::Real, core::Real > | kink_dihedral (const core::pose::Pose &pose, const protocols::antibody::AntibodyInfo &ab_info, bool debug) |
core::Real | kink_bb_Hbond (const core::pose::Pose &pose, const protocols::antibody::AntibodyInfo &ab_info) |
core::Real | kink_RD_Hbond (const core::pose::Pose &pose, const protocols::antibody::AntibodyInfo &ab_info) |
core::Real | kink_Trp_Hbond (const core::pose::Pose &pose, const protocols::antibody::AntibodyInfo &ab_info) |
std::pair< ParatopeMetric < core::Real >, ParatopeMetric < core::Real > > | paratope_sasa (const core::pose::Pose &pose, const AntibodyInfo &ab_info) |
calculate the SASA of the antibody paratope. Returns all and hydrophobic components. More... | |
core::SSize | pose_charge (core::pose::Pose const &pose) |
calculate the net charge of the antibody More... | |
ParatopeMetric< core::SSize > | paratope_charge (core::pose::Pose const &pose, const protocols::antibody::AntibodyInfo &abinfo) |
calculate the net charge of the paratope More... | |
core::Real | cdr_energy (core::pose::Pose const &pose, AntibodyInfoCOP ab_info, core::scoring::ScoreFunctionCOP scorefxn, CDRNameEnum const &cdr) |
calculate dSASA of the paratope and antigen using result of InterfaceAnalyzerMover More... | |
core::Real | cdr_CN_anchor_distance (core::pose::Pose const &pose, AntibodyInfoCOP ab_info, CDRNameEnum const &cdr) |
Calculate the distance between the carbon and nitrogen of each residue before and after the CDR respectively. More... | |
std::ostream & | operator<< (std::ostream &out, SnugDock const &) |
std::ostream & | operator<< (std::ostream &out, SnugDockProtocol const &snugdockprotocol) |
void | simple_one_loop_fold_tree (pose::Pose &pose_in, loops::Loop const &loop) |
void | simple_fold_tree (pose::Pose &pose_in, Size jumppoint1, Size cutpoint, Size jumppoint2) |
std::string | setup_LH_A_foldtree (AntibodyInfoCOP ab_info, core::pose::Pose &pose) |
Setup LH_A foldtree. Return dock_chains string. More... | |
std::string | setup_A_LH_foldtree (AntibodyInfoCOP ab_info, core::pose::Pose &pose) |
Setup A_LH foldtree. Return dock_chains string. More... | |
bool | CDR_H3_filter_legacy_code_with_old_rule (const pose::Pose &pose_in, loops::Loop &input_loop, bool is_camelid) |
tests if a loop has H3 like base charachteristics More... | |
bool | CDR_H3_cter_filter (const pose::Pose &pose_in, AntibodyInfoOP ab_info) |
core::pack::task::TaskFactoryOP | setup_packer_task (core::pose::Pose &pose_in) |
Very specific packertask,. More... | |
bool | cutpoints_separation (core::pose::Pose &pose, AntibodyInfoOP &antibody_info) |
return false if any cdr cutpoint is broken More... | |
Real | cutpoint_separation (pose::Pose &pose_in, Size cutpoint) |
Real | global_loop_rmsd (const pose::Pose &pose_in, const pose::Pose &native_pose, loops::LoopsOP current_loop) |
void | align_to_native (core::pose::Pose &pose, core::pose::Pose const &native_pose, AntibodyInfoOP const ab_info, AntibodyInfoOP const native_ab_info, std::string const &request_chain="LH") |
align current Fv to native.Fv More... | |
std::map< CDRNameEnum, bool > | add_harmonic_cluster_constraints (AntibodyInfoOP ab_info, pose::Pose &pose) |
Adds dihedral harmonic constraints to Pose CDRs using cluster info in AntibodyInfo. More... | |
std::map< CDRNameEnum, bool > | add_harmonic_cluster_constraints (AntibodyInfoOP ab_info, pose::Pose &pose, utility::vector1< core::scoring::constraints::ConstraintCOP > constraints) |
Same as above, but adds constraints to the vector so they can be identified and removed from the pose if needed. More... | |
bool | add_harmonic_cluster_constraint (AntibodyInfoCOP ab_info, pose::Pose &pose, CDRClusterEnum const cluster) |
Adds a harmonic constraint to a Pose CDR based on cluster type. More... | |
bool | add_harmonic_cluster_constraint (AntibodyInfoCOP ab_info, pose::Pose &pose, CDRClusterEnum const cluster, utility::vector1< core::scoring::constraints::ConstraintCOP > constraints) |
Same as above, but adds constraints to the vector so they can be identified and removed from the pose if needed. More... | |
std::string | get_harmonic_cluster_constraint_filename (AntibodyInfoCOP ab_info, CDRClusterEnum const cluster) |
Gets the cluster constraint name. Returns NA if not found. More... | |
Variables | |
static basic::Tracer | TR ("protocols.antibody.AntibodyNumberingParser") |
typedef utility::pointer::owning_ptr< Ab_TemplateInfo const > protocols::antibody::Ab_TemplateInfoCOP |
typedef utility::pointer::owning_ptr< AntibodyEnumManager const > protocols::antibody::AntibodyEnumManagerCOP |
typedef utility::pointer::owning_ptr< AntibodyEnumManager > protocols::antibody::AntibodyEnumManagerOP |
typedef utility::pointer::owning_ptr< AntibodyFeatures const > protocols::antibody::AntibodyFeaturesCOP |
typedef utility::pointer::owning_ptr< AntibodyModelerProtocol const > protocols::antibody::AntibodyModelerProtocolCOP |
typedef utility::pointer::owning_ptr< AntibodyModelerProtocol > protocols::antibody::AntibodyModelerProtocolOP |
typedef utility::pointer::owning_ptr< AntibodyNumberingParser const > protocols::antibody::AntibodyNumberingParserCOP |
typedef utility::pointer::owning_ptr< AntibodyNumberingParser > protocols::antibody::AntibodyNumberingParserOP |
typedef utility::pointer::owning_ptr< CloseOneCDRLoop const > protocols::antibody::CloseOneCDRLoopCOP |
typedef utility::pointer::owning_ptr< GraftCDRLoopsProtocol const > protocols::antibody::GraftCDRLoopsProtocolCOP |
typedef utility::pointer::owning_ptr< GraftCDRLoopsProtocol > protocols::antibody::GraftCDRLoopsProtocolOP |
typedef utility::pointer::owning_ptr<const GraftedStemOptimizer> protocols::antibody::GraftedStemOptimizerCOP |
typedef utility::pointer::owning_ptr< GraftedStemOptimizer > protocols::antibody::GraftedStemOptimizerOP |
typedef utility::pointer::owning_ptr< LHRepulsiveRamp const > protocols::antibody::LHRepulsiveRampCOP |
typedef utility::pointer::owning_ptr< LHRepulsiveRampLegacy const > protocols::antibody::LHRepulsiveRampLegacyCOP |
typedef utility::pointer::owning_ptr< LHRepulsiveRampLegacy > protocols::antibody::LHRepulsiveRampLegacyOP |
typedef utility::pointer::owning_ptr< LHSnugFitLegacy const > protocols::antibody::LHSnugFitLegacyCOP |
typedef utility::pointer::owning_ptr< RefineBetaBarrel const > protocols::antibody::RefineBetaBarrelCOP |
typedef utility::pointer::owning_ptr< RefineOneCDRLoopCentroid const > protocols::antibody::RefineOneCDRLoopCentroidCOP |
typedef utility::pointer::owning_ptr< RefineOneCDRLoopCentroid > protocols::antibody::RefineOneCDRLoopCentroidOP |
typedef utility::pointer::owning_ptr< RefineOneCDRLoop const > protocols::antibody::RefineOneCDRLoopCOP |
typedef utility::pointer::owning_ptr< SnugDockProtocol const > protocols::antibody::SnugDockProtocolCOP |
Main enumerator for AntibodyNumbering.
Enumerator | |
---|---|
cdr_start | |
cdr_end | |
CDRLandmarkEnum_total |
bool protocols::antibody::add_harmonic_cluster_constraint | ( | AntibodyInfoCOP | ab_info, |
pose::Pose & | pose, | ||
CDRClusterEnum const | cluster | ||
) |
Adds a harmonic constraint to a Pose CDR based on cluster type.
Currently requires North_AHO numbering.
References core::pose::Pose::add_constraints(), cst, core::scoring::constraints::ConstraintSet::get_all_constraints(), get_harmonic_cluster_constraint_filename(), and TR.
Referenced by protocols::antibody::design::AntibodyGraftDesignMover::graft_cdr(), and protocols::antibody::design::AntibodySeqDesignMover::setup_constraints().
bool protocols::antibody::add_harmonic_cluster_constraint | ( | AntibodyInfoCOP | ab_info, |
pose::Pose & | pose, | ||
CDRClusterEnum const | cluster, | ||
utility::vector1< core::scoring::constraints::ConstraintCOP > | constraints | ||
) |
Same as above, but adds constraints to the vector so they can be identified and removed from the pose if needed.
Returns true or false depending on success
References core::pose::Pose::add_constraints(), cst, core::scoring::constraints::ConstraintSet::get_all_constraints(), get_harmonic_cluster_constraint_filename(), NA, and TR.
Referenced by add_harmonic_cluster_constraints().
std::map< CDRNameEnum, bool > protocols::antibody::add_harmonic_cluster_constraints | ( | AntibodyInfoOP | ab_info, |
pose::Pose & | pose | ||
) |
Adds dihedral harmonic constraints to Pose CDRs using cluster info in AntibodyInfo.
Currently requires North_AHO numbering. Returns map of success/failure
References add_harmonic_cluster_constraint().
std::map< CDRNameEnum, bool > protocols::antibody::add_harmonic_cluster_constraints | ( | AntibodyInfoOP | ab_info, |
pose::Pose & | pose, | ||
utility::vector1< core::scoring::constraints::ConstraintCOP > | constraints | ||
) |
Same as above, but adds constraints to the vector so they can be identified and removed from the pose if needed.
Returns map of success/failure
References add_harmonic_cluster_constraint().
void protocols::antibody::align_to_native | ( | core::pose::Pose & | pose, |
core::pose::Pose const & | native_pose, | ||
AntibodyInfoOP const | ab_info, | ||
AntibodyInfoOP const | native_ab_info, | ||
std::string const & | reqeust_chain | ||
) |
align current Fv to native.Fv
References core::id::BOGUS_ATOM_ID, core::pose::initialize_atomid_map(), core::pose::Pose::sequence(), protocols::loops::start, and core::scoring::superimpose_pose().
Referenced by protocols::antibody::GraftCDRLoopsProtocol::apply(), and protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2().
core::Real protocols::antibody::cdr_CN_anchor_distance | ( | core::pose::Pose const & | pose, |
AntibodyInfoCOP | ab_info, | ||
CDRNameEnum const & | cdr | ||
) |
Calculate the distance between the carbon and nitrogen of each residue before and after the CDR respectively.
References numeric::xyzVector< class >::distance(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().
Referenced by protocols::antibody::AntibodyFeatures::report_cdr_metrics_features().
core::Real protocols::antibody::cdr_energy | ( | core::pose::Pose const & | pose, |
AntibodyInfoCOP | ab_info, | ||
core::scoring::ScoreFunctionCOP | scorefxn, | ||
CDRNameEnum const & | cdr | ||
) |
calculate dSASA of the paratope and antigen using result of InterfaceAnalyzerMover
calculate dSASA of the paratope using data held in PerResidueInterfaceData returned from InterfaceAnalyzerMover calculate dSASA of a cdr and antigen using InterfaceAnalyzerMover. Returns all and hydrophobic components. calculate dSASA of a cdr using data held in PerResidueInterfaceData returned from InterfaceAnalyzerMover. Calculates energy of cdr by decomposing scorefxn into pair and then summing. This means it includes hbonding components, etc.
References cdr_end, cdr_start, core::pose::Pose::energies(), options, and core::scoring::Energies::residue_total_energy().
Referenced by protocols::antibody::AntibodyFeatures::report_cdr_metrics_features().
bool protocols::antibody::CDR_H3_cter_filter | ( | const pose::Pose & | pose_in, |
AntibodyInfoOP | ab_info | ||
) |
References Aroop, protocols::frag_picker::CA, numeric::dihedral_degrees(), Extended, h3, Kinked, core::conformation::Residue::name3(), core::pose::Pose::residue(), protocols::loops::start, protocols::loops::stop, TR, and core::conformation::Residue::xyz().
Referenced by protocols::antibody::H3CterInsert::apply(), protocols::antibody::H3PerturbCCD::apply(), protocols::antibody::RefineOneCDRLoop::apply(), and protocols::antibody::H3RefineCCD::apply().
bool protocols::antibody::CDR_H3_filter_legacy_code_with_old_rule | ( | const pose::Pose & | pose_in, |
loops::Loop & | input_loop, | ||
bool | is_camelid | ||
) |
tests if a loop has H3 like base charachteristics
CDR_H3_filter
[in] | pose | full actual protein loop_begin: seq numbered loop begin corresponding to pose size: size of loop to compute loop_end |
References protocols::frag_picker::CA, numeric::dihedral_degrees(), core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::loops::Loop::start(), protocols::loops::start, protocols::loops::Loop::stop(), protocols::loops::stop, TR, and core::conformation::Residue::xyz().
core::Real protocols::antibody::cutpoint_separation | ( | core::pose::Pose & | pose_in, |
Size | cutpoint | ||
) |
Compute the separation at the cutpoint. The N-C distance of the peptide bond which should be formed at the cutpoint. A closed loop is assumed to have a gap < 1.9 Ang
References C, N, core::pose::Pose::residue(), and core::conformation::Residue::xyz().
Referenced by cutpoints_separation().
bool protocols::antibody::cutpoints_separation | ( | core::pose::Pose & | pose, |
AntibodyInfoOP & | antibody_info | ||
) |
return false if any cdr cutpoint is broken
References cutpoint_separation().
Referenced by protocols::antibody::ModelCDRH3::apply(), and protocols::antibody::H3RefineCCD::apply().
scoring::ScoreFunctionCOP protocols::antibody::get_Dock_ScoreFxn | ( | void | ) |
std::string protocols::antibody::get_harmonic_cluster_constraint_filename | ( | AntibodyInfoCOP | ab_info, |
CDRClusterEnum const | cluster | ||
) |
Gets the cluster constraint name. Returns NA if not found.
References utility::file::file_exists(), basic::database::full_name(), path, and TR.
Referenced by add_harmonic_cluster_constraint().
scoring::ScoreFunctionCOP protocols::antibody::get_LoopCentral_ScoreFxn | ( | void | ) |
scoring::ScoreFunctionCOP protocols::antibody::get_LoopHighRes_ScoreFxn | ( | void | ) |
References protocols::forge::methods::overlap_chainbreak().
scoring::ScoreFunctionCOP protocols::antibody::get_Pack_ScoreFxn | ( | void | ) |
core::Real protocols::antibody::global_loop_rmsd | ( | const pose::Pose & | pose_in, |
const pose::Pose & | native_pose, | ||
loops::LoopsOP | current_loop | ||
) |
core::Real protocols::antibody::kink_bb_Hbond | ( | const core::pose::Pose & | pose, |
const protocols::antibody::AntibodyInfo & | ab_info | ||
) |
References D, protocols::antibody::AntibodyInfo::kink_anion_residue(), protocols::antibody::AntibodyInfo::kink_cation_residue(), core::conformation::Residue::name3(), norm(), core::pose::Pose::residue(), TR, and core::conformation::Residue::xyz().
Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2(), and protocols::antibody::AntibodyFeatures::report_ab_H3_kink_metrics_features().
std::pair< core::Real, core::Real > protocols::antibody::kink_dihedral | ( | const core::pose::Pose & | pose, |
const protocols::antibody::AntibodyInfo & | ab_info, | ||
bool | debug | ||
) |
References dihedral(), protocols::antibody::AntibodyInfo::kink_begin(), core::conformation::Residue::name1(), q, core::pose::Pose::residue(), TR, and core::conformation::Residue::xyz().
Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2(), and protocols::antibody::AntibodyFeatures::report_ab_H3_kink_metrics_features().
core::Real protocols::antibody::kink_RD_Hbond | ( | const core::pose::Pose & | pose, |
const protocols::antibody::AntibodyInfo & | ab_info | ||
) |
References Ca, protocols::antibody::AntibodyInfo::kink_anion_atoms(), protocols::antibody::AntibodyInfo::kink_cation_atoms(), and norm().
Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2(), and protocols::antibody::AntibodyFeatures::report_ab_H3_kink_metrics_features().
core::Real protocols::antibody::kink_Trp_Hbond | ( | const core::pose::Pose & | pose, |
const protocols::antibody::AntibodyInfo & | ab_info | ||
) |
References protocols::antibody::AntibodyInfo::kink_begin(), protocols::antibody::AntibodyInfo::kink_trp(), core::conformation::Residue::name3(), norm(), core::pose::Pose::residue(), TR, W, and core::conformation::Residue::xyz().
Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2(), and protocols::antibody::AntibodyFeatures::report_ab_H3_kink_metrics_features().
std::ostream& protocols::antibody::operator<< | ( | std::ostream & | out, |
const Ab_TemplateInfo & | ab_t_info | ||
) |
References protocols::antibody::Ab_TemplateInfo::H1_t_name_, protocols::antibody::Ab_TemplateInfo::H1_t_pose_, protocols::antibody::Ab_TemplateInfo::H2_t_name_, protocols::antibody::Ab_TemplateInfo::H2_t_pose_, protocols::antibody::Ab_TemplateInfo::H3_t_name_, protocols::antibody::Ab_TemplateInfo::H3_t_pose_, protocols::antibody::Ab_TemplateInfo::L1_t_name_, protocols::antibody::Ab_TemplateInfo::L1_t_pose_, protocols::antibody::Ab_TemplateInfo::L2_t_name_, protocols::antibody::Ab_TemplateInfo::L2_t_pose_, protocols::antibody::Ab_TemplateInfo::L3_t_name_, protocols::antibody::Ab_TemplateInfo::L3_t_pose_, protocols::antibody::Ab_TemplateInfo::load_H1_, protocols::antibody::Ab_TemplateInfo::load_H2_, protocols::antibody::Ab_TemplateInfo::load_H3_, protocols::antibody::Ab_TemplateInfo::load_L1_, protocols::antibody::Ab_TemplateInfo::load_L2_, and protocols::antibody::Ab_TemplateInfo::load_L3_.
std::ostream& protocols::antibody::operator<< | ( | std::ostream & | out, |
const CDRsMinPackMin & | ab_m_2 | ||
) |
std::ostream& protocols::antibody::operator<< | ( | std::ostream & | out, |
SnugDockProtocol const & | snugdockprotocol | ||
) |
std::ostream& protocols::antibody::operator<< | ( | std::ostream & | out, |
SnugDock const & | |||
) |
std::ostream& protocols::antibody::operator<< | ( | std::ostream & | out, |
const GraftCDRLoopsProtocol & | ab_m_2 | ||
) |
References protocols::antibody::GraftCDRLoopsProtocol::camelid_, protocols::antibody::GraftCDRLoopsProtocol::graft_h1_, protocols::antibody::GraftCDRLoopsProtocol::graft_h2_, protocols::antibody::GraftCDRLoopsProtocol::graft_h3_, protocols::antibody::GraftCDRLoopsProtocol::graft_l1_, protocols::antibody::GraftCDRLoopsProtocol::graft_l2_, and protocols::antibody::GraftCDRLoopsProtocol::graft_l3_.
std::ostream& protocols::antibody::operator<< | ( | std::ostream & | out, |
const AntibodyModelerProtocol & | ab_m | ||
) |
References protocols::antibody::AntibodyModelerProtocol::camelid_, protocols::antibody::AntibodyModelerProtocol::cter_insert_, protocols::antibody::AntibodyModelerProtocol::h3_filter_, protocols::antibody::AntibodyModelerProtocol::h3_filter_tolerance_, protocols::antibody::AntibodyModelerProtocol::h3_perturb_type_, protocols::antibody::AntibodyModelerProtocol::h3_refine_type_, protocols::antibody::AntibodyModelerProtocol::LH_repulsive_ramp_, protocols::antibody::AntibodyModelerProtocol::model_h3_, protocols::antibody::AntibodyModelerProtocol::refine_h3_, and protocols::antibody::AntibodyModelerProtocol::snugfit_.
std::ostream& protocols::antibody::operator<< | ( | std::ostream & | out, |
const AntibodyInfo & | ab_info | ||
) |
References protocols::antibody::clusters::CDRClusterEnumManager::cdr_cluster_enum_to_string(), protocols::antibody::AntibodyInfo::cdr_cluster_manager_, protocols::antibody::AntibodyInfo::enum_manager_, protocols::antibody::AntibodyInfo::get_CDR_cluster(), protocols::antibody::AntibodyInfo::get_CDR_loop(), protocols::antibody::AntibodyInfo::get_CDR_name(), protocols::antibody::AntibodyInfo::get_CDR_sequence_with_stem(), protocols::antibody::AntibodyEnumManager::h3_base_type_enum_to_string(), protocols::antibody::AntibodyInfo::is_camelid(), protocols::loops::Loop::length(), protocols::antibody::AntibodyInfo::predicted_H3_base_type_, start_cdr_loop, and protocols::antibody::AntibodyInfo::total_cdr_loops_.
ParatopeMetric< core::SSize > protocols::antibody::paratope_charge | ( | core::pose::Pose const & | pose, |
const protocols::antibody::AntibodyInfo & | ab_info | ||
) |
calculate the net charge of the paratope
References protocols::antibody::ParatopeMetric< T >::cdr, protocols::antibody::AntibodyInfo::get_CDR_loop(), protocols::antibody::AntibodyInfo::get_CDR_name(), protocols::antibody::AntibodyInfo::get_total_num_CDRs(), core::conformation::Residue::name3(), core::pose::Pose::residue(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and TR.
Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2(), protocols::antibody::AntibodyFeatures::report_features(), and protocols::antibody::AntibodyFeatures::write_ab_metrics_schema_to_db().
std::pair< ParatopeMetric< core::Real >, ParatopeMetric< core::Real > > protocols::antibody::paratope_sasa | ( | const core::pose::Pose & | pose, |
const protocols::antibody::AntibodyInfo & | ab_info | ||
) |
calculate the SASA of the antibody paratope. Returns all and hydrophobic components.
References protocols::antibody::ParatopeMetric< T >::cdr, protocols::antibody::AntibodyInfo::get_CDR_loop(), protocols::antibody::AntibodyInfo::get_CDR_name(), protocols::antibody::AntibodyInfo::get_total_num_CDRs(), protocols::antibody::ParatopeMetric< T >::paratope, core::pose::Pose::residue(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and TR.
Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2(), and protocols::antibody::AntibodyFeatures::report_features().
core::SSize protocols::antibody::pose_charge | ( | core::pose::Pose const & | pose | ) |
calculate the net charge of the antibody
References core::conformation::Residue::name3(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().
Referenced by protocols::antibody::AntibodyFeatures::report_ab_metrics_features().
std::string protocols::antibody::setup_A_LH_foldtree | ( | AntibodyInfoCOP | ab_info, |
core::pose::Pose & | pose | ||
) |
Setup A_LH foldtree. Return dock_chains string.
References protocols::docking::setup_foldtree().
std::string protocols::antibody::setup_LH_A_foldtree | ( | AntibodyInfoCOP | ab_info, |
core::pose::Pose & | pose | ||
) |
Setup LH_A foldtree. Return dock_chains string.
References protocols::docking::setup_foldtree().
core::pack::task::TaskFactoryOP protocols::antibody::setup_packer_task | ( | core::pose::Pose & | pose_in | ) |
Very specific packertask,.
Ubound rotamer options, repack only, protein only, no disulfides.
References core::pack::task::TaskFactory::clear(), core::pack::dunbrack::load_unboundrot(), TR, and unboundrot.
Referenced by protocols::antibody::H3RefineCCD::apply(), protocols::antibody::RefineBetaBarrel::finalize_setup(), protocols::antibody::GraftCDRLoopsProtocol::finalize_setup(), protocols::antibody::LHRepulsiveRampLegacy::finalize_setup(), protocols::antibody::H3RefineCCD::finalize_setup(), protocols::antibody::GraftedStemOptimizer::get_stem_taskfactory(), protocols::antibody::AntibodyInfo::get_TaskFactory_AllCDRs(), and protocols::antibody::AntibodyInfo::get_TaskFactory_OneCDR().
void protocols::antibody::simple_fold_tree | ( | pose::Pose & | pose_in, |
Size | jumppoint1, | ||
Size | cutpoint, | ||
Size | jumppoint2 | ||
) |
References core::kinematics::FoldTree::clear(), core::pose::Pose::fold_tree(), nres, protocols::make_rot_lib::PEPTIDE, core::pose::Pose::total_residue(), and TR.
Referenced by protocols::antibody::RefineOneCDRLoop::apply(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants(), and protocols::antibody::H3RefineCCD::finalize_setup().
void protocols::antibody::simple_one_loop_fold_tree | ( | pose::Pose & | pose_in, |
loops::Loop const & | loop | ||
) |
References core::kinematics::FoldTree::clear(), protocols::loops::Loop::cut(), core::pose::Pose::fold_tree(), nres, protocols::make_rot_lib::PEPTIDE, protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::pose::Pose::total_residue(), and TR.
Referenced by protocols::antibody::CloseOneCDRLoop::apply(), protocols::antibody::ModelCDRH3::apply(), protocols::antibody::H3PerturbCCD::apply(), and protocols::antibody::RefineOneCDRLoopCentroid::loop_centroid_relax().
utility::vector1< core::Real > protocols::antibody::vl_vh_orientation_coords | ( | const core::pose::Pose & | pose_in, |
const AntibodyInfo & | ab_info | ||
) |
calculate the VH_VL packing angle from 2 sheet definitions on each antibody chain
vector is made up of: vl_vh_distance opening_angle opposite_angle packing_angle
References numeric::angle_degrees(), numeric::dihedral_degrees(), numeric::xyzVector< class >::distance(), numeric::first_principal_component(), protocols::antibody::AntibodyInfo::get_PackingAngleResidues(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().
Referenced by protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2(), and protocols::antibody::AntibodyFeatures::report_ab_metrics_features().
|
static |
Referenced by protocols::antibody::RefineBetaBarrel::apply(), protocols::antibody::SnugDockProtocol::apply(), protocols::antibody::GraftCDRLoopsProtocol::apply(), protocols::antibody::AntibodyModelerProtocol::apply(), protocols::antibody::H3CterInsert::apply(), protocols::antibody::design::ResidueProbDesignOperation::apply(), protocols::antibody::ModelCDRH3::apply(), protocols::antibody::RefineOneCDRLoopCentroid::apply(), protocols::antibody::H3PerturbCCD::apply(), protocols::antibody::LHRepulsiveRamp::apply(), protocols::antibody::SnugDock::apply(), protocols::antibody::LHRepulsiveRampLegacy::apply(), protocols::antibody::RefineOneCDRLoop::apply(), protocols::antibody::H3RefineCCD::apply(), protocols::antibody::design::AntibodyDesignMover::apply(), protocols::antibody::design::AntibodyGraftDesignMover::apply(), protocols::antibody::design::AntibodySeqDesignMover::apply(), protocols::antibody::AntibodyFeatures::calculate_cdr_contacts_nres(), protocols::antibody::AntibodyFeatures::calculate_residue_atomic_contacts(), protocols::antibody::AntibodyNumberingParser::debug_print(), protocols::antibody::AntibodyInfo::detect_and_set_camelid_CDR_H3_stem_type(), protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type(), protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type_new_rule(), protocols::antibody::GraftCDRLoopsProtocol::display_constraint_residues(), protocols::antibody::AntibodyModelerProtocol::display_constraint_residues(), protocols::antibody::design::AntibodyDesignModeler::dock_A_LH_high_res(), protocols::antibody::design::AntibodyDesignModeler::dock_A_LH_low_res(), protocols::antibody::design::AntibodyDesignModeler::dock_H_L_high_res(), protocols::antibody::design::AntibodyDesignModeler::dock_H_L_low_res(), protocols::antibody::design::AntibodyDesignModeler::dock_high_res(), protocols::antibody::design::AntibodyDesignModeler::dock_L_H_high_res(), protocols::antibody::design::AntibodyDesignModeler::dock_L_H_low_res(), protocols::antibody::design::AntibodyDesignModeler::dock_LH_A_high_res(), protocols::antibody::design::AntibodyDesignModeler::dock_LH_A_low_res(), protocols::antibody::design::AntibodyDesignModeler::dock_low_res(), protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_jd2(), protocols::antibody::design::AntibodyGraftDesignMover::extend_native_cdrs(), protocols::antibody::RefineOneCDRLoopCentroid::finalize_setup(), protocols::antibody::CDRsMinPackMin::finalize_setup(), protocols::antibody::RefineBetaBarrel::finalize_setup(), protocols::antibody::GraftCDRLoopsProtocol::finalize_setup(), protocols::antibody::LHRepulsiveRampLegacy::finalize_setup(), protocols::antibody::AntibodyModelerProtocol::finalize_setup(), protocols::antibody::design::AntibodyGraftDesignMover::fix_pdb_info(), protocols::antibody::AntibodyInfo::get_landmark_resnum(), protocols::antibody::AntibodyInfo::get_MoveMap_for_AllCDRsSideChains_and_H3backbone(), protocols::antibody::design::AntibodyGraftDesignMover::graft_cdr(), protocols::antibody::AntibodyInfo::identify_CDR_from_a_sequence(), protocols::antibody::GraftCDRLoopsProtocol::init_from_options(), protocols::antibody::AntibodyModelerProtocol::init_from_options(), protocols::antibody::design::AntibodyDatabaseManager::load_cdr_design_data(), protocols::antibody::design::AntibodyDatabaseManager::load_cdrs_for_grafting(), protocols::antibody::design::ConservativeDesignOperation::load_data_from_db(), protocols::antibody::design::AntibodyDesignModeler::minimize_cdrs(), protocols::antibody::design::AntibodyDesignModeler::minimize_cdrs_and_neighbor_sc(), protocols::antibody::design::AntibodyDesignModeler::minimize_interface(), protocols::antibody::design::AntibodyDesignMover::model_post_graft(), protocols::antibody::design::AntibodyDesignMover::output_ensemble(), protocols::antibody::AntibodyFeatures::parse_my_tag(), protocols::antibody::H3PerturbCCD::read_and_store_fragments(), protocols::antibody::AntibodyNumberingParser::read_cdr_definition_file(), protocols::antibody::design::DesignInstructionsParser::read_cdr_graft_instructions(), protocols::antibody::H3CterInsert::read_H3_cter_fragment(), protocols::antibody::AntibodyNumberingParser::read_numbering_scheme_file(), protocols::antibody::design::AntibodyDesignModeler::relax_cdrs(), protocols::antibody::design::AntibodyDesignModeler::relax_cdrs_and_neighbor_sc(), protocols::antibody::design::AntibodyDesignModeler::relax_interface(), protocols::antibody::design::AntibodySeqDesignMover::remove_conservative_design_residues_from_prob_set(), protocols::antibody::design::AntibodyDesignModeler::repack_antibody_interface(), protocols::antibody::design::AntibodyDesignModeler::repack_antigen_ab_interface(), protocols::antibody::design::AntibodyDesignModeler::repack_antigen_interface(), protocols::antibody::design::AntibodyDesignModeler::repack_CDRs(), protocols::antibody::design::AntibodyDesignModeler::repack_CDRs_and_neighbors(), protocols::antibody::AntibodyFeatures::report_features(), protocols::antibody::design::AntibodyGraftDesignMover::run_basic_mc_algorithm(), protocols::antibody::design::AntibodyGraftDesignMover::run_deterministic_graft_algorithm(), protocols::antibody::AntibodyModelerProtocol::set_default(), protocols::antibody::GraftCDRLoopsProtocol::set_default(), protocols::antibody::RefineOneCDRLoopCentroid::set_default(), protocols::antibody::AntibodyInfo::set_default(), protocols::antibody::AntibodyInfo::setup_CDR_clusters(), protocols::antibody::AntibodyInfo::setup_CDRsInfo(), protocols::antibody::design::AntibodySeqDesignMover::setup_constraints(), protocols::antibody::SnugDockProtocol::setup_objects(), protocols::antibody::SnugDock::setup_objects(), and protocols::antibody::design::AntibodySeqDesignMover::setup_task_factory().