Classes
class	CDRCluster
	Simple class to hold and access CDRCluster info for a region of the pose. More...

class	CDRClusterEnumManager
	Interface to this class is in AntibodyInfo. Should be a singleton. More...

class	CDRClusterFeatures

class	CDRClusterFeaturesCreator

struct	ClusterData
	Holds data for each cluster type. More...

class	CDRClusterMatcher
	Simple class for identifying CDR clusters of an antibody or protein structure. More...

class	CDRClusterSet
	Class that can determine a CDR Cluster, hold that information, and give it out when asked. More...

class	BasicCDRClusterSet
	Basic container class for CDRClusterSet, with some extra information. More...

Typedefs
typedef utility::pointer::shared_ptr< CDRCluster >	CDRClusterOP

typedef utility::pointer::shared_ptr< CDRCluster const >	CDRClusterCOP

typedef utility::pointer::shared_ptr< CDRClusterEnumManager >	CDRClusterEnumManagerOP

typedef utility::pointer::shared_ptr< CDRClusterEnumManager const >	CDRClusterEnumManagerCOP

typedef utility::pointer::shared_ptr< CDRClusterFeatures >	CDRClusterFeaturesOP

typedef utility::pointer::shared_ptr< CDRClusterFeatures const >	CDRClusterFeaturesCOP

typedef utility::pointer::shared_ptr< CDRClusterMatcher >	CDRClusterMatcherOP

typedef utility::pointer::shared_ptr< CDRClusterMatcher const >	CDRClusterMatcherCOP

typedef utility::pointer::shared_ptr< CDRClusterSet >	CDRClusterSetOP

typedef utility::pointer::shared_ptr< CDRClusterSet const >	CDRClusterSetCOP

typedef utility::pointer::shared_ptr< BasicCDRClusterSet >	BasicCDRClusterSetOP

typedef utility::pointer::shared_ptr< BasicCDRClusterSet const >	BasicCDRClusterSetCOP

Enumerations
enum	CDRClusterEnum { H1_10_1 = 1 , H1_12_1 , H1_13_1 , H1_13_2 , H1_13_3 , H1_13_4 , H1_13_5 , H1_13_6 , H1_13_7 , H1_13_8 , H1_13_9 , H1_13_10 , H1_13_11 , H1_13_cis9_1 , H1_14_1 , H1_15_1 , H1_16_1 , H2_8_1 , H2_9_1 , H2_9_2 , H2_9_3 , H2_10_1 , H2_10_2 , H2_10_3 , H2_10_4 , H2_10_5 , H2_10_6 , H2_10_7 , H2_10_8 , H2_10_9 , H2_12_1 , H2_15_1 , H3_13_1 , H3_10_1 , H3_11_1 , H3_12_1 , H3_13_2 , H3_14_1 , H3_16_2 , H3_12_2 , H3_15_2 , H3_14_3 , H3_5_1 , H3_11_2 , H3_12_cis9_1 , H3_9_1 , H3_7_1 , H3_13_3 , H3_19_1 , H3_16_1 , H3_7_cis4_1 , H3_6_1 , H3_18_2 , H3_21_1 , H3_8_1 , H3_17_1 , H3_9_2 , H3_7_3 , H3_5_2 , H3_10_2 , H3_13_cis7_1 , H3_10_cis5_1 , H3_14_2 , H3_7_2 , H3_15_1 , H3_10_3 , H3_20_1 , H3_14_cis7_1 , H3_18_1 , H3_24_1 , H3_26_1 , H3_8_2 , H3_14_4 , H3_13_cis8_1 , H3_22_1 , L1_10_1 , L1_10_2 , L1_11_1 , L1_11_2 , L1_11_3 , L1_12_1 , L1_12_2 , L1_12_3 , L1_13_1 , L1_13_2 , L1_14_1 , L1_14_2 , L1_15_1 , L1_15_2 , L1_16_1 , L1_17_1 , L2_8_1 , L2_8_2 , L2_8_3 , L2_8_4 , L2_8_5 , L2_12_1 , L2_12_2 , L3_10_1 , L3_11_1 , L3_12_1 , L3_13_1 , L3_7_1 , L3_8_1 , L3_8_2 , L3_8_cis6_1 , L3_9_1 , L3_9_2 , L3_9_cis6_1 , L3_9_cis7_1 , L3_9_cis7_2 , L3_9_cis7_3 , L3_10_cis8_1 , L3_10_cis7_8_1 , L3_11_cis7_1 , NA , CDRClusterEnum_start = H1_10_1 , CDRClusterEnum_stop = L3_11_cis7_1 , CDRClusterEnum_total = NA }

Functions
static basic::Tracer	TR ("protocols.antibody.clusters")

void	add_cluster_comments_to_pose (core::pose::Pose &pose, AntibodyInfoCOP ab_info)

std::string	get_pose_cis_trans_conformation (core::pose::Pose const &pose, core::Size const start, core::Size const end)

core::Real	calculate_dihedral_distance (vector1< Real > cluster_phis, vector1< Real > pose_phis, vector1< Real > cluster_psis, vector1< Real > pose_psis)

bool	check_if_pose_renumbered_for_clusters (core::pose::Pose const &pose)
	Very basic way to check to make sure pose residues are North_AHO (North, et al) scheme, which allows the clustering. More...

CDRClusterEnum	get_cluster_from_cache_or_ab_info (AntibodyInfoCOP ab_info, core::pose::Pose const &pose, CDRNameEnum const cdr)

core::Real	calculate_dihedral_distance (utility::vector1< core::Real > cluster_phis, utility::vector1< core::Real > pose_phis, utility::vector1< core::Real > cluster_psis, utility::vector1< core::Real > pose_psis)
	Calculates the dihedral distance used to match cluster centers. More...

Typedef Documentation

◆ BasicCDRClusterSetCOP

typedef utility::pointer::shared_ptr< BasicCDRClusterSet const > protocols::antibody::clusters::BasicCDRClusterSetCOP

◆ BasicCDRClusterSetOP

typedef utility::pointer::shared_ptr< BasicCDRClusterSet > protocols::antibody::clusters::BasicCDRClusterSetOP

◆ CDRClusterCOP

typedef utility::pointer::shared_ptr< CDRCluster const > protocols::antibody::clusters::CDRClusterCOP

◆ CDRClusterEnumManagerCOP

typedef utility::pointer::shared_ptr< CDRClusterEnumManager const > protocols::antibody::clusters::CDRClusterEnumManagerCOP

◆ CDRClusterEnumManagerOP

typedef utility::pointer::shared_ptr< CDRClusterEnumManager > protocols::antibody::clusters::CDRClusterEnumManagerOP

◆ CDRClusterFeaturesCOP

typedef utility::pointer::shared_ptr< CDRClusterFeatures const > protocols::antibody::clusters::CDRClusterFeaturesCOP

◆ CDRClusterFeaturesOP

typedef utility::pointer::shared_ptr< CDRClusterFeatures > protocols::antibody::clusters::CDRClusterFeaturesOP

◆ CDRClusterMatcherCOP

typedef utility::pointer::shared_ptr< CDRClusterMatcher const > protocols::antibody::clusters::CDRClusterMatcherCOP

◆ CDRClusterMatcherOP

typedef utility::pointer::shared_ptr< CDRClusterMatcher > protocols::antibody::clusters::CDRClusterMatcherOP

◆ CDRClusterOP

typedef utility::pointer::shared_ptr< CDRCluster > protocols::antibody::clusters::CDRClusterOP

◆ CDRClusterSetCOP

typedef utility::pointer::shared_ptr< CDRClusterSet const > protocols::antibody::clusters::CDRClusterSetCOP

◆ CDRClusterSetOP

typedef utility::pointer::shared_ptr< CDRClusterSet > protocols::antibody::clusters::CDRClusterSetOP

Enumeration Type Documentation

◆ CDRClusterEnum

enum protocols::antibody::clusters::CDRClusterEnum

Identified antibody CDR Clusters See North, Lehmann, Dunbrack. (2011). JMB 406(2): 228-256. More clusters will be added as the PDB grows.

Enumerator
H1_10_1
H1_12_1
H1_13_1
H1_13_2
H1_13_3
H1_13_4
H1_13_5
H1_13_6
H1_13_7
H1_13_8
H1_13_9
H1_13_10
H1_13_11
H1_13_cis9_1
H1_14_1
H1_15_1
H1_16_1
H2_8_1
H2_9_1
H2_9_2
H2_9_3
H2_10_1
H2_10_2
H2_10_3
H2_10_4
H2_10_5
H2_10_6
H2_10_7
H2_10_8
H2_10_9
H2_12_1
H2_15_1
H3_13_1
H3_10_1
H3_11_1
H3_12_1
H3_13_2
H3_14_1
H3_16_2
H3_12_2
H3_15_2
H3_14_3
H3_5_1
H3_11_2
H3_12_cis9_1
H3_9_1
H3_7_1
H3_13_3
H3_19_1
H3_16_1
H3_7_cis4_1
H3_6_1
H3_18_2
H3_21_1
H3_8_1
H3_17_1
H3_9_2
H3_7_3
H3_5_2
H3_10_2
H3_13_cis7_1
H3_10_cis5_1
H3_14_2
H3_7_2
H3_15_1
H3_10_3
H3_20_1
H3_14_cis7_1
H3_18_1
H3_24_1
H3_26_1
H3_8_2
H3_14_4
H3_13_cis8_1
H3_22_1
L1_10_1
L1_10_2
L1_11_1
L1_11_2
L1_11_3
L1_12_1
L1_12_2
L1_12_3
L1_13_1
L1_13_2
L1_14_1
L1_14_2
L1_15_1
L1_15_2
L1_16_1
L1_17_1
L2_8_1
L2_8_2
L2_8_3
L2_8_4
L2_8_5
L2_12_1
L2_12_2
L3_10_1
L3_11_1
L3_12_1
L3_13_1
L3_7_1
L3_8_1
L3_8_2
L3_8_cis6_1
L3_9_1
L3_9_2
L3_9_cis6_1
L3_9_cis7_1
L3_9_cis7_2
L3_9_cis7_3
L3_10_cis8_1
L3_10_cis7_8_1
L3_11_cis7_1
NA
CDRClusterEnum_start
CDRClusterEnum_stop
CDRClusterEnum_total

Function Documentation

◆ add_cluster_comments_to_pose()

void protocols::antibody::clusters::add_cluster_comments_to_pose	(	core::pose::Pose &	pose,
		AntibodyInfoCOP	ab_info
	)

References core::pose::add_comment(), core::pose::datacache::CacheableDataType::CDR_CLUSTER_INFO, core::pose::Pose::data(), protocols::antibody::clusters::BasicCDRClusterSet::get_cluster(), core::pose::setPoseExtraScore(), and core::id::to_string().

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

◆ calculate_dihedral_distance() [1/2]

core::Real protocols::antibody::clusters::calculate_dihedral_distance	(	utility::vector1< core::Real >	cluster_phis,
		utility::vector1< core::Real >	pose_phis,
		utility::vector1< core::Real >	cluster_psis,
		utility::vector1< core::Real >	pose_psis
	)

Calculates the dihedral distance used to match cluster centers.

◆ calculate_dihedral_distance() [2/2]

core::Real protocols::antibody::clusters::calculate_dihedral_distance	(	vector1< Real >	cluster_phis,
		vector1< Real >	pose_phis,
		vector1< Real >	cluster_psis,
		vector1< Real >	pose_psis
	)

References PI.

Referenced by protocols::antibody::clusters::CDRClusterMatcher::get_cdr_cluster(), and protocols::antibody::clusters::CDRClusterMatcher::get_closest_cluster().

◆ check_if_pose_renumbered_for_clusters()

bool protocols::antibody::clusters::check_if_pose_renumbered_for_clusters ( core::pose::Pose const & pose )

Very basic way to check to make sure pose residues are North_AHO (North, et al) scheme, which allows the clustering.

If any of these anchor residues that are checked are missing, it will return false.

References core::pose::has_chain(), core::conformation::Residue::name1(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and TR().

◆ get_cluster_from_cache_or_ab_info()

CDRClusterEnum protocols::antibody::clusters::get_cluster_from_cache_or_ab_info	(	AntibodyInfoCOP	ab_info,
		core::pose::Pose const &	pose,
		CDRNameEnum const	cdr
	)

References core::pose::datacache::CacheableDataType::CDR_CLUSTER_INFO, core::pose::Pose::data(), and protocols::antibody::clusters::BasicCDRClusterSet::get_cluster().

Referenced by protocols::antibody::design::MutateFrameworkForCluster::has_framework_dependant_cluster().

◆ get_pose_cis_trans_conformation()

std::string protocols::antibody::clusters::get_pose_cis_trans_conformation	(	core::pose::Pose const &	pose,
		core::Size const	start,
		core::Size const	end
	)

References core::sequence::end, core::pose::Pose::omega(), and protocols::loops::start.