Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Classes | Typedefs | Enumerations | Functions
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 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

typedef utility::pointer::shared_ptr< BasicCDRClusterSet const > protocols::antibody::clusters::BasicCDRClusterSetCOP
typedef utility::pointer::shared_ptr< CDRCluster const > protocols::antibody::clusters::CDRClusterCOP
typedef utility::pointer::shared_ptr< CDRClusterFeatures const > protocols::antibody::clusters::CDRClusterFeaturesCOP
typedef utility::pointer::shared_ptr< CDRClusterMatcher const > protocols::antibody::clusters::CDRClusterMatcherCOP
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

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 
)
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.

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

CDRClusterEnum protocols::antibody::clusters::get_cluster_from_cache_or_ab_info ( AntibodyInfoCOP  ab_info,
core::pose::Pose const &  pose,
CDRNameEnum const  cdr 
)
std::string protocols::antibody::clusters::get_pose_cis_trans_conformation ( core::pose::Pose const &  pose,
core::Size const  start,
core::Size const  end 
)
static basic::Tracer protocols::antibody::clusters::TR ( "protocols.antibody.clusters"  )
static