Classes
class	BasicCDRClusterSet
	Basic container class for CDRClusterSet. More...

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

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...

struct	ClusterData
	Holds data for each cluster type. 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 thread_local basic::Tracer	TR ("protocols.antibody.clusters")

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)
	Calculates the dihedral distance used to match cluster centers. More...

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...

Typedef Documentation

Enumeration Type Documentation

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

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

Calculates the dihedral distance used to match cluster centers.

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.

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

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

static