clusters¶

Bindings for protocols::antibody::clusters namespace

class pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet¶

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

Basic container class for CDRClusterSet, with some extra information

assign(self: pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet, : pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet) → pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet¶: C++: protocols::antibody::clusters::BasicCDRClusterSet::operator=(const class protocols::antibody::clusters::BasicCDRClusterSet &) –> class protocols::antibody::clusters::BasicCDRClusterSet &

clone(self: pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: protocols::antibody::clusters::BasicCDRClusterSet::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_cluster(self: pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum) → pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster¶

Get the CDRCluster

C++: protocols::antibody::clusters::BasicCDRClusterSet::get_cluster(enum protocols::antibody::CDRNameEnum) const –> class std::shared_ptr<const class protocols::antibody::clusters::CDRCluster>

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t¶: C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

set_cluster(self: pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum, cluster: pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster) → None¶

Set the CDRCluster

C++: protocols::antibody::clusters::BasicCDRClusterSet::set_cluster(enum protocols::antibody::CDRNameEnum, class std::shared_ptr<const class protocols::antibody::clusters::CDRCluster>) –> void

set_clusters(self: pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet, clusters: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_antibody_clusters_CDRCluster_t) → None¶

Get the full set of CDRClusters

C++: protocols::antibody::clusters::BasicCDRClusterSet::set_clusters(const class utility::vector1<class std::shared_ptr<class protocols::antibody::clusters::CDRCluster>, class std::allocator<class std::shared_ptr<class protocols::antibody::clusters::CDRCluster> > >) –> void

class pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster¶

Bases: pybind11_builtins.pybind11_object

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

assign(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster, : pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster) → pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster¶: C++: protocols::antibody::clusters::CDRCluster::operator=(const class protocols::antibody::clusters::CDRCluster &) –> class protocols::antibody::clusters::CDRCluster &

cdr(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster) → pyrosetta.rosetta.protocols.antibody.CDRNameEnum¶: C++: protocols::antibody::clusters::CDRCluster::cdr() const –> enum protocols::antibody::CDRNameEnum

chain(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster) → str¶

return PDB chain

C++: protocols::antibody::clusters::CDRCluster::chain() const –> char

cis_trans_match(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster) → bool¶

Does the closest cluster match at cis_trans positions?: Currently, this should always be True.

C++: protocols::antibody::clusters::CDRCluster::cis_trans_match() const –> bool

clone(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster) → pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster¶: C++: protocols::antibody::clusters::CDRCluster::clone() const –> class std::shared_ptr<class protocols::antibody::clusters::CDRCluster>

cluster(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster) → pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum¶: C++: protocols::antibody::clusters::CDRCluster::cluster() const –> enum protocols::antibody::clusters::CDRClusterEnum

distance(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster) → float¶: C++: protocols::antibody::clusters::CDRCluster::distance() const –> double

end(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster) → int¶

return Rosetta end that was used for construction

C++: protocols::antibody::clusters::CDRCluster::end() const –> unsigned long

length_normalized_distance(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster) → float¶: C++: protocols::antibody::clusters::CDRCluster::length_normalized_distance() const –> double

normalized_distance_in_degrees(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster) → float¶: C++: protocols::antibody::clusters::CDRCluster::normalized_distance_in_degrees() const –> double

pdb_end(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster) → int¶

return PDB end. Useful for CDR length changes in other parts of the antibody when combined with numbering scheme ala AbInfo

C++: protocols::antibody::clusters::CDRCluster::pdb_end() const –> unsigned long

pdb_start(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster) → int¶

return PDB start. Useful for CDR length changes in other parts of the antibody when combined with numbering scheme ala AbInfo

C++: protocols::antibody::clusters::CDRCluster::pdb_start() const –> unsigned long

start(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster) → int¶

return Rosetta start that was used for construction

C++: protocols::antibody::clusters::CDRCluster::start() const –> unsigned long

class pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum¶

Bases: pybind11_builtins.pybind11_object

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

Members:

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

class pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager¶

Bases: pybind11_builtins.pybind11_object

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

assign(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager, : pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager) → pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager¶: C++: protocols::antibody::clusters::CDRClusterEnumManager::operator=(const class protocols::antibody::clusters::CDRClusterEnumManager &) –> class protocols::antibody::clusters::CDRClusterEnumManager &

cdr_cluster_enum_to_string(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager, cluster: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum) → str¶: C++: protocols::antibody::clusters::CDRClusterEnumManager::cdr_cluster_enum_to_string(const enum protocols::antibody::clusters::CDRClusterEnum) const –> std::string

cdr_cluster_is_present(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager, cluster: str) → bool¶: C++: protocols::antibody::clusters::CDRClusterEnumManager::cdr_cluster_is_present(const class std::basic_string<char> &) const –> bool

cdr_cluster_string_to_enum(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager, cluster: str) → pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum¶: C++: protocols::antibody::clusters::CDRClusterEnumManager::cdr_cluster_string_to_enum(const class std::basic_string<char> &) const –> enum protocols::antibody::clusters::CDRClusterEnum

get_recognized_cluster_definitions(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::antibody::clusters::CDRClusterEnumManager::get_recognized_cluster_definitions() const –> class utility::vector1<std::string, class std::allocator<std::string > >

class pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher¶

Bases: pybind11_builtins.pybind11_object

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.

allow_rama_mismatches(*args, **kwargs)¶

Overloaded function.

allow_rama_mismatches(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher) -> bool

skip first grouping Cis and Trans for clusters in which a Cis/Trans designation currently does not exist.: Default False

C++: protocols::antibody::clusters::CDRClusterMatcher::allow_rama_mismatches() const –> bool

allow_rama_mismatches(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher, allow: bool) -> None

Set to skip first grouping Cis and Trans for clusters in which a Cis/Trans designation currently does not exist.: Default False

C++: protocols::antibody::clusters::CDRClusterMatcher::allow_rama_mismatches(const bool) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher, : pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher) → pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher¶: C++: protocols::antibody::clusters::CDRClusterMatcher::operator=(const class protocols::antibody::clusters::CDRClusterMatcher &) –> class protocols::antibody::clusters::CDRClusterMatcher &

get_cdr_cluster(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher, pose: pyrosetta.rosetta.core.pose.Pose, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum, start: int, end: int) → pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster¶

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…

C++: protocols::antibody::clusters::CDRClusterMatcher::get_cdr_cluster(const class core::pose::Pose &, const enum protocols::antibody::CDRNameEnum, unsigned long, const unsigned long) const –> class std::shared_ptr<class protocols::antibody::clusters::CDRCluster>

get_closest_cluster(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher, pose: pyrosetta.rosetta.core.pose.Pose, start: int, end: int) → pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster¶

Get the closest cluster of a region. Used to detect CDR-like regions in normal proteins.

C++: protocols::antibody::clusters::CDRClusterMatcher::get_closest_cluster(const class core::pose::Pose &, const unsigned long, const unsigned long) const –> class std::shared_ptr<class protocols::antibody::clusters::CDRCluster>

class pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet¶

Bases: pybind11_builtins.pybind11_object

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

assign(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet, : pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet) → pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet¶: C++: protocols::antibody::clusters::CDRClusterSet::operator=(const class protocols::antibody::clusters::CDRClusterSet &) –> class protocols::antibody::clusters::CDRClusterSet &

clear(*args, **kwargs)¶

Overloaded function.

clear(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet) -> None

Clear the held cluster data

C++: protocols::antibody::clusters::CDRClusterSet::clear() –> void

clear(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum) -> None

Remove data of CDR using normal numbering.

C++: protocols::antibody::clusters::CDRClusterSet::clear(enum protocols::antibody::CDRNameEnum) –> void

empty(*args, **kwargs)¶

Overloaded function.

empty(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet) -> bool

C++: protocols::antibody::clusters::CDRClusterSet::empty() const –> bool

empty(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum) -> bool

C++: protocols::antibody::clusters::CDRClusterSet::empty(enum protocols::antibody::CDRNameEnum) const –> bool

get_cacheable_cluster_data(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet) → protocols::antibody::clusters::BasicCDRClusterSet¶

Get a new BasicCDRClusterSet with copies of CDRClusters contained in this set.

C++: protocols::antibody::clusters::CDRClusterSet::get_cacheable_cluster_data() const –> class std::shared_ptr<class protocols::antibody::clusters::BasicCDRClusterSet>

get_cluster(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum) → pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum¶: C++: protocols::antibody::clusters::CDRClusterSet::get_cluster(enum protocols::antibody::CDRNameEnum) const –> enum protocols::antibody::clusters::CDRClusterEnum

get_cluster_data(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum) → pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster¶: C++: protocols::antibody::clusters::CDRClusterSet::get_cluster_data(enum protocols::antibody::CDRNameEnum) const –> class std::shared_ptr<const class protocols::antibody::clusters::CDRCluster>

identify_and_set_cdr_cluster(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet, pose: pyrosetta.rosetta.core.pose.Pose, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum) → None¶

Identify the cluster of the CDR, using numbering information held in AntibodyInfo. Replace data if already present.

C++: protocols::antibody::clusters::CDRClusterSet::identify_and_set_cdr_cluster(const class core::pose::Pose &, enum protocols::antibody::CDRNameEnum) –> void

set_cacheable_cluster_data_to_pose(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Set a new BasicCDRClusterSet to a pose with copies of CDRClusters contained in this set.

C++: protocols::antibody::clusters::CDRClusterSet::set_cacheable_cluster_data_to_pose(class core::pose::Pose &) const –> void

set_cluster_data(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum, cluster: pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster) → None¶

Manually set the CDR Cluster

C++: protocols::antibody::clusters::CDRClusterSet::set_cluster_data(enum protocols::antibody::CDRNameEnum, class std::shared_ptr<const class protocols::antibody::clusters::CDRCluster>) –> void

class pyrosetta.rosetta.protocols.antibody.clusters.ClusterData¶

Bases: pybind11_builtins.pybind11_object

Holds data for each cluster type

assign(self: pyrosetta.rosetta.protocols.antibody.clusters.ClusterData, : pyrosetta.rosetta.protocols.antibody.clusters.ClusterData) → pyrosetta.rosetta.protocols.antibody.clusters.ClusterData¶: C++: protocols::antibody::clusters::ClusterData::operator=(const struct protocols::antibody::clusters::ClusterData &) –> struct protocols::antibody::clusters::ClusterData &

pyrosetta.rosetta.protocols.antibody.clusters.add_cluster_comments_to_pose(pose: pyrosetta.rosetta.core.pose.Pose, ab_info: pyrosetta.rosetta.protocols.antibody.AntibodyInfo) → None¶: C++: protocols::antibody::clusters::add_cluster_comments_to_pose(class core::pose::Pose &, class std::shared_ptr<const class protocols::antibody::AntibodyInfo>) –> void

pyrosetta.rosetta.protocols.antibody.clusters.calculate_dihedral_distance(cluster_phis: pyrosetta.rosetta.utility.vector1_double, pose_phis: pyrosetta.rosetta.utility.vector1_double, cluster_psis: pyrosetta.rosetta.utility.vector1_double, pose_psis: pyrosetta.rosetta.utility.vector1_double) → float¶

Calculates the dihedral distance used to match cluster centers.

C++: protocols::antibody::clusters::calculate_dihedral_distance(class utility::vector1<double, class std::allocator<double> >, class utility::vector1<double, class std::allocator<double> >, class utility::vector1<double, class std::allocator<double> >, class utility::vector1<double, class std::allocator<double> >) –> double

pyrosetta.rosetta.protocols.antibody.clusters.check_if_pose_renumbered_for_clusters(pose: pyrosetta.rosetta.core.pose.Pose) → bool¶

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.

C++: protocols::antibody::clusters::check_if_pose_renumbered_for_clusters(const class core::pose::Pose &) –> bool

pyrosetta.rosetta.protocols.antibody.clusters.get_cluster_from_cache_or_ab_info(ab_info: pyrosetta.rosetta.protocols.antibody.AntibodyInfo, pose: pyrosetta.rosetta.core.pose.Pose, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum) → pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum¶: C++: protocols::antibody::clusters::get_cluster_from_cache_or_ab_info(class std::shared_ptr<const class protocols::antibody::AntibodyInfo>, const class core::pose::Pose &, const enum protocols::antibody::CDRNameEnum) –> enum protocols::antibody::clusters::CDRClusterEnum

pyrosetta.rosetta.protocols.antibody.clusters.get_pose_cis_trans_conformation(pose: pyrosetta.rosetta.core.pose.Pose, start: int, end: int) → str¶: C++: protocols::antibody::clusters::get_pose_cis_trans_conformation(const class core::pose::Pose &, const unsigned long, const unsigned long) –> std::string