clusters¶

Bindings for protocols::antibody::clusters namespace

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

Bases: 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_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_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

CDRClusterEnum_start = <CDRClusterEnum.H1_10_1: 1>¶

CDRClusterEnum_stop = <CDRClusterEnum.L3_11_cis7_1: 115>¶

CDRClusterEnum_total = <CDRClusterEnum.NA: 116>¶

H1_10_1 = <CDRClusterEnum.H1_10_1: 1>¶

H1_12_1 = <CDRClusterEnum.H1_12_1: 2>¶

H1_13_1 = <CDRClusterEnum.H1_13_1: 3>¶

H1_13_10 = <CDRClusterEnum.H1_13_10: 12>¶

H1_13_11 = <CDRClusterEnum.H1_13_11: 13>¶

H1_13_2 = <CDRClusterEnum.H1_13_2: 4>¶

H1_13_3 = <CDRClusterEnum.H1_13_3: 5>¶

H1_13_4 = <CDRClusterEnum.H1_13_4: 6>¶

H1_13_5 = <CDRClusterEnum.H1_13_5: 7>¶

H1_13_6 = <CDRClusterEnum.H1_13_6: 8>¶

H1_13_7 = <CDRClusterEnum.H1_13_7: 9>¶

H1_13_8 = <CDRClusterEnum.H1_13_8: 10>¶

H1_13_9 = <CDRClusterEnum.H1_13_9: 11>¶

H1_13_cis9_1 = <CDRClusterEnum.H1_13_cis9_1: 14>¶

H1_14_1 = <CDRClusterEnum.H1_14_1: 15>¶

H1_15_1 = <CDRClusterEnum.H1_15_1: 16>¶

H1_16_1 = <CDRClusterEnum.H1_16_1: 17>¶

H2_10_1 = <CDRClusterEnum.H2_10_1: 22>¶

H2_10_2 = <CDRClusterEnum.H2_10_2: 23>¶

H2_10_3 = <CDRClusterEnum.H2_10_3: 24>¶

H2_10_4 = <CDRClusterEnum.H2_10_4: 25>¶

H2_10_5 = <CDRClusterEnum.H2_10_5: 26>¶

H2_10_6 = <CDRClusterEnum.H2_10_6: 27>¶

H2_10_7 = <CDRClusterEnum.H2_10_7: 28>¶

H2_10_8 = <CDRClusterEnum.H2_10_8: 29>¶

H2_10_9 = <CDRClusterEnum.H2_10_9: 30>¶

H2_12_1 = <CDRClusterEnum.H2_12_1: 31>¶

H2_15_1 = <CDRClusterEnum.H2_15_1: 32>¶

H2_8_1 = <CDRClusterEnum.H2_8_1: 18>¶

H2_9_1 = <CDRClusterEnum.H2_9_1: 19>¶

H2_9_2 = <CDRClusterEnum.H2_9_2: 20>¶

H2_9_3 = <CDRClusterEnum.H2_9_3: 21>¶

H3_10_1 = <CDRClusterEnum.H3_10_1: 34>¶

H3_10_2 = <CDRClusterEnum.H3_10_2: 60>¶

H3_10_3 = <CDRClusterEnum.H3_10_3: 66>¶

H3_10_cis5_1 = <CDRClusterEnum.H3_10_cis5_1: 62>¶

H3_11_1 = <CDRClusterEnum.H3_11_1: 35>¶

H3_11_2 = <CDRClusterEnum.H3_11_2: 44>¶

H3_12_1 = <CDRClusterEnum.H3_12_1: 36>¶

H3_12_2 = <CDRClusterEnum.H3_12_2: 40>¶

H3_12_cis9_1 = <CDRClusterEnum.H3_12_cis9_1: 45>¶

H3_13_1 = <CDRClusterEnum.H3_13_1: 33>¶

H3_13_2 = <CDRClusterEnum.H3_13_2: 37>¶

H3_13_3 = <CDRClusterEnum.H3_13_3: 48>¶

H3_13_cis7_1 = <CDRClusterEnum.H3_13_cis7_1: 61>¶

H3_13_cis8_1 = <CDRClusterEnum.H3_13_cis8_1: 74>¶

H3_14_1 = <CDRClusterEnum.H3_14_1: 38>¶

H3_14_2 = <CDRClusterEnum.H3_14_2: 63>¶

H3_14_3 = <CDRClusterEnum.H3_14_3: 42>¶

H3_14_4 = <CDRClusterEnum.H3_14_4: 73>¶

H3_14_cis7_1 = <CDRClusterEnum.H3_14_cis7_1: 68>¶

H3_15_1 = <CDRClusterEnum.H3_15_1: 65>¶

H3_15_2 = <CDRClusterEnum.H3_15_2: 41>¶

H3_16_1 = <CDRClusterEnum.H3_16_1: 50>¶

H3_16_2 = <CDRClusterEnum.H3_16_2: 39>¶

H3_17_1 = <CDRClusterEnum.H3_17_1: 56>¶

H3_18_1 = <CDRClusterEnum.H3_18_1: 69>¶

H3_18_2 = <CDRClusterEnum.H3_18_2: 53>¶

H3_19_1 = <CDRClusterEnum.H3_19_1: 49>¶

H3_20_1 = <CDRClusterEnum.H3_20_1: 67>¶

H3_21_1 = <CDRClusterEnum.H3_21_1: 54>¶

H3_22_1 = <CDRClusterEnum.H3_22_1: 75>¶

H3_24_1 = <CDRClusterEnum.H3_24_1: 70>¶

H3_26_1 = <CDRClusterEnum.H3_26_1: 71>¶

H3_5_1 = <CDRClusterEnum.H3_5_1: 43>¶

H3_5_2 = <CDRClusterEnum.H3_5_2: 59>¶

H3_6_1 = <CDRClusterEnum.H3_6_1: 52>¶

H3_7_1 = <CDRClusterEnum.H3_7_1: 47>¶

H3_7_2 = <CDRClusterEnum.H3_7_2: 64>¶

H3_7_3 = <CDRClusterEnum.H3_7_3: 58>¶

H3_7_cis4_1 = <CDRClusterEnum.H3_7_cis4_1: 51>¶

H3_8_1 = <CDRClusterEnum.H3_8_1: 55>¶

H3_8_2 = <CDRClusterEnum.H3_8_2: 72>¶

H3_9_1 = <CDRClusterEnum.H3_9_1: 46>¶

H3_9_2 = <CDRClusterEnum.H3_9_2: 57>¶

L1_10_1 = <CDRClusterEnum.L1_10_1: 76>¶

L1_10_2 = <CDRClusterEnum.L1_10_2: 77>¶

L1_11_1 = <CDRClusterEnum.L1_11_1: 78>¶

L1_11_2 = <CDRClusterEnum.L1_11_2: 79>¶

L1_11_3 = <CDRClusterEnum.L1_11_3: 80>¶

L1_12_1 = <CDRClusterEnum.L1_12_1: 81>¶

L1_12_2 = <CDRClusterEnum.L1_12_2: 82>¶

L1_12_3 = <CDRClusterEnum.L1_12_3: 83>¶

L1_13_1 = <CDRClusterEnum.L1_13_1: 84>¶

L1_13_2 = <CDRClusterEnum.L1_13_2: 85>¶

L1_14_1 = <CDRClusterEnum.L1_14_1: 86>¶

L1_14_2 = <CDRClusterEnum.L1_14_2: 87>¶

L1_15_1 = <CDRClusterEnum.L1_15_1: 88>¶

L1_15_2 = <CDRClusterEnum.L1_15_2: 89>¶

L1_16_1 = <CDRClusterEnum.L1_16_1: 90>¶

L1_17_1 = <CDRClusterEnum.L1_17_1: 91>¶

L2_12_1 = <CDRClusterEnum.L2_12_1: 97>¶

L2_12_2 = <CDRClusterEnum.L2_12_2: 98>¶

L2_8_1 = <CDRClusterEnum.L2_8_1: 92>¶

L2_8_2 = <CDRClusterEnum.L2_8_2: 93>¶

L2_8_3 = <CDRClusterEnum.L2_8_3: 94>¶

L2_8_4 = <CDRClusterEnum.L2_8_4: 95>¶

L2_8_5 = <CDRClusterEnum.L2_8_5: 96>¶

L3_10_1 = <CDRClusterEnum.L3_10_1: 99>¶

L3_10_cis7_8_1 = <CDRClusterEnum.L3_10_cis7_8_1: 114>¶

L3_10_cis8_1 = <CDRClusterEnum.L3_10_cis8_1: 113>¶

L3_11_1 = <CDRClusterEnum.L3_11_1: 100>¶

L3_11_cis7_1 = <CDRClusterEnum.L3_11_cis7_1: 115>¶

L3_12_1 = <CDRClusterEnum.L3_12_1: 101>¶

L3_13_1 = <CDRClusterEnum.L3_13_1: 102>¶

L3_7_1 = <CDRClusterEnum.L3_7_1: 103>¶

L3_8_1 = <CDRClusterEnum.L3_8_1: 104>¶

L3_8_2 = <CDRClusterEnum.L3_8_2: 105>¶

L3_8_cis6_1 = <CDRClusterEnum.L3_8_cis6_1: 106>¶

L3_9_1 = <CDRClusterEnum.L3_9_1: 107>¶

L3_9_2 = <CDRClusterEnum.L3_9_2: 108>¶

L3_9_cis6_1 = <CDRClusterEnum.L3_9_cis6_1: 109>¶

L3_9_cis7_1 = <CDRClusterEnum.L3_9_cis7_1: 110>¶

L3_9_cis7_2 = <CDRClusterEnum.L3_9_cis7_2: 111>¶

L3_9_cis7_3 = <CDRClusterEnum.L3_9_cis7_3: 112>¶

NA = <CDRClusterEnum.NA: 116>¶

property name¶

property value¶

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

Bases: 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 std::string &) 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 std::string &) 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.CDRClusterFeatures¶

Bases: FeaturesReporter

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

check_relevant_residues(*args, **kwargs)¶

Overloaded function.

check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) → bool¶: C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() → str¶: C++: protocols::antibody::clusters::CDRClusterFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) → None¶: C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

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

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) → pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T¶: C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Specify specific CDRs to load and analyze, with cdr_definition and scheme

C++: protocols::antibody::clusters::CDRClusterFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::antibody::clusters::CDRClusterFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) → int¶: C++: protocols::antibody::clusters::CDRClusterFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) → str¶

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_cdrs_to_use(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures, cdrs: pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRNameEnum) → None¶

Limit CDRs being analyzed.

C++: protocols::antibody::clusters::CDRClusterFeatures::set_cdrs_to_use(class utility::vector1<enum protocols::antibody::CDRNameEnum, class std::allocator<enum protocols::antibody::CDRNameEnum> >) –> void

set_numbering_scheme(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures, numbering_scheme: pyrosetta.rosetta.protocols.antibody.AntibodyNumberingSchemeEnum) → None¶

set the numbering scheme used by the pose.

C++: protocols::antibody::clusters::CDRClusterFeatures::set_numbering_scheme(const enum protocols::antibody::AntibodyNumberingSchemeEnum &) –> void

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) → None¶: C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures) → str¶: C++: protocols::antibody::clusters::CDRClusterFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) → None¶: C++: protocols::antibody::clusters::CDRClusterFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

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

Bases: FeaturesReporterCreator

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

create_features_reporter(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeaturesCreator) → pyrosetta.rosetta.protocols.features.FeaturesReporter¶: C++: protocols::antibody::clusters::CDRClusterFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::antibody::clusters::CDRClusterFeaturesCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

type_name(self: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeaturesCreator) → str¶: C++: protocols::antibody::clusters::CDRClusterFeaturesCreator::type_name() const –> std::string

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

Bases: 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_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_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 &

property cdr¶

property cis_trans_conf¶

property cluster¶

property length¶

property phis¶

property psis¶

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