Simple class for identifying CDR clusters of an antibody or protein structure. More...
#include <CDRClusterMatcher.hh>
Public Member Functions | |
| CDRClusterMatcher () | |
| ~CDRClusterMatcher () override | |
| CDRClusterOP | get_cdr_cluster (core::pose::Pose const &pose, CDRNameEnum const cdr, core::Size start, const core::Size end) const |
| Get the cluster of an antibody CDR region, defined between start and end of the pose. Should it give out an OP or not? It's a small class... I don't have any idea... More... | |
| CDRClusterOP | get_closest_cluster (core::pose::Pose const &pose, core::Size const start, core::Size const end) const |
| Get the closest cluster of a region. Used to detect CDR-like regions in normal proteins. More... | |
| bool | allow_rama_mismatches () const |
| skip first grouping Cis and Trans for clusters in which a Cis/Trans designation currently does not exist. Default False More... | |
| void | allow_rama_mismatches (bool const allow) |
| Set to skip first grouping Cis and Trans for clusters in which a Cis/Trans designation currently does not exist. Default False. More... | |
Private Member Functions | |
| void | load_center_data () |
| std::map< std::string, utility::vector1< core::Real > > | get_pose_angles (core::pose::Pose const &pose, core::Size const start, core::Size const end) const |
Private Attributes | |
| std::string | center_cluster_db_path_ |
| utility::vector1< ClusterData > | cluster_data_ |
| bool | allow_rama_mismatches_ |
| skip first grouping Cis and Trans for clusters in which a Cis/Trans designation currently does not exist. More... | |
Detailed Description
Simple class for identifying CDR clusters of an antibody or protein structure.
Main interface is through CDRClusterSet/AntibodyInfo. That is where AntibodyNumbering can be used to access specific CDRs and numbering scheme transformations.
Constructor & Destructor Documentation
◆ CDRClusterMatcher()
| protocols::antibody::clusters::CDRClusterMatcher::CDRClusterMatcher | ( | ) |
◆ ~CDRClusterMatcher()
|
overridedefault |
Member Function Documentation
◆ allow_rama_mismatches() [1/2]
|
inline |
skip first grouping Cis and Trans for clusters in which a Cis/Trans designation currently does not exist. Default False
References allow_rama_mismatches_.
◆ allow_rama_mismatches() [2/2]
|
inline |
Set to skip first grouping Cis and Trans for clusters in which a Cis/Trans designation currently does not exist. Default False.
References allow_rama_mismatches_.
◆ get_cdr_cluster()
| CDRClusterOP protocols::antibody::clusters::CDRClusterMatcher::get_cdr_cluster | ( | core::pose::Pose const & | pose, |
| CDRNameEnum const | cdr, | ||
| core::Size | start, | ||
| const core::Size | end | ||
| ) | const |
Get the cluster of an antibody CDR region, defined between start and end of the pose. Should it give out an OP or not? It's a small class... I don't have any idea...
References protocols::antibody::clusters::calculate_dihedral_distance(), protocols::antibody::clusters::ClusterData::cdr, protocols::antibody::clusters::ClusterData::cis_trans_conf, core::kinematics::distance(), core::sequence::end, protocols::antibody::clusters::get_pose_cis_trans_conformation(), protocols::antibody::clusters::ClusterData::length, protocols::mean_field::min(), protocols::antibody::clusters::NA, protocols::antibody::clusters::ClusterData::phis, protocols::antibody::clusters::ClusterData::psis, protocols::loops::start, and protocols::antibody::clusters::TR().
◆ get_closest_cluster()
| CDRClusterOP protocols::antibody::clusters::CDRClusterMatcher::get_closest_cluster | ( | core::pose::Pose const & | pose, |
| core::Size const | start, | ||
| core::Size const | end | ||
| ) | const |
Get the closest cluster of a region. Used to detect CDR-like regions in normal proteins.
References protocols::antibody::clusters::calculate_dihedral_distance(), protocols::antibody::clusters::ClusterData::cis_trans_conf, core::kinematics::distance(), core::sequence::end, protocols::antibody::clusters::get_pose_cis_trans_conformation(), protocols::antibody::l1, protocols::antibody::clusters::ClusterData::length, protocols::mean_field::min(), protocols::antibody::clusters::NA, protocols::antibody::clusters::ClusterData::phis, protocols::antibody::clusters::ClusterData::psis, protocols::loops::start, and protocols::antibody::clusters::TR().
◆ get_pose_angles()
|
private |
References core::sequence::end, core::pose::Pose::phi(), core::pose::Pose::psi(), and protocols::loops::start.
◆ load_center_data()
|
private |
References protocols::antibody::clusters::ClusterData::cdr, protocols::antibody::clusters::ClusterData::cis_trans_conf, protocols::antibody::clusters::ClusterData::cluster, protocols::antibody::clusters::ClusterData::length, protocols::antibody::clusters::ClusterData::phis, protocols::antibody::clusters::ClusterData::psis, and protocols::sparta::split().
Member Data Documentation
◆ allow_rama_mismatches_
|
private |
skip first grouping Cis and Trans for clusters in which a Cis/Trans designation currently does not exist.
Referenced by allow_rama_mismatches().
◆ center_cluster_db_path_
|
private |
◆ cluster_data_
|
private |
The documentation for this class was generated from the following files:
- src/protocols/antibody/clusters/CDRClusterMatcher.hh
- src/protocols/antibody/clusters/CDRClusterMatcher.cc
