protocols::antibody::clusters Namespace Reference

Classes
class	BasicCDRClusterSet
	Basic container class for CDRClusterSet, with some extra information. 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")
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)
	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...
CDRClusterEnum	get_cluster_from_cache_or_ab_info (AntibodyInfoCOP ab_info, core::pose::Pose const &pose, CDRNameEnum const cdr)

Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

Enumeration Type Documentation

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

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(), basic::datacache::BasicDataCache::get(), protocols::antibody::clusters::BasicCDRClusterSet::get_cluster(), basic::datacache::BasicDataCache::has(), and utility::to_string().

Referenced by protocols::antibody::design::AntibodyDesignMover::apply(), protocols::antibody::design::AntibodyDesignProtocol::apply(), and protocols::antibody::design::AntibodyDesignProtocol::output_ensemble().

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.

References PI, and numeric::NumericTraits< class >::pi().

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

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::pose::Pose::pdb_info(), core::pose::Pose::residue(), and TR().

Referenced by protocols::antibody::design::AntibodyDesignMover::apply(), and protocols::antibody::design::AntibodyDesignProtocol::apply().

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(), basic::datacache::BasicDataCache::get(), protocols::antibody::clusters::BasicCDRClusterSet::get_cluster(), and basic::datacache::BasicDataCache::has().

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

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::pose::Pose::omega().

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

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

static

Referenced by check_if_pose_renumbered_for_clusters(), protocols::antibody::clusters::CDRClusterMatcher::get_cdr_cluster(), and protocols::antibody::clusters::CDRClusterSet::set_cacheable_cluster_data_to_pose().