calibur¶

Bindings for protocols::cluster::calibur namespace

class pyrosetta.rosetta.protocols.cluster.calibur.ADJ_LIST_MODE¶

Bases: pybind11_object

Members:

MATRIX

LIST

LITE

LIST = <ADJ_LIST_MODE.LIST: 1>¶

LITE = <ADJ_LIST_MODE.LITE: 2>¶

MATRIX = <ADJ_LIST_MODE.MATRIX: 0>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.cluster.calibur.AdjacentList¶

Bases: pybind11_object

add(self: pyrosetta.rosetta.protocols.cluster.calibur.AdjacentList, n: int, d: float, ifNeigh: bool) → None¶: C++: protocols::cluster::calibur::AdjacentList::add(int, double, bool) –> void

property dist¶

getD(self: pyrosetta.rosetta.protocols.cluster.calibur.AdjacentList, n: int) → float¶: C++: protocols::cluster::calibur::AdjacentList::getD(int) const –> double

property neigh¶

property num_neighbors_¶

remove(self: pyrosetta.rosetta.protocols.cluster.calibur.AdjacentList, n: int) → None¶: C++: protocols::cluster::calibur::AdjacentList::remove(int) –> void

property reverse_index_¶

property which_¶

class pyrosetta.rosetta.protocols.cluster.calibur.Clustering¶

Bases: pybind11_object

property CLU_RADIUS¶

property EST_THRESHOLD¶

property FILTER_MODE¶

property PDBs_¶

property THRESHOLD¶

property adjacent_lists_¶

allocateSpaceForRMSD(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, len: int) → None¶: C++: protocols::cluster::calibur::Clustering::allocateSpaceForRMSD(int) –> void

assign(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, : pyrosetta.rosetta.protocols.cluster.calibur.Clustering) → pyrosetta.rosetta.protocols.cluster.calibur.Clustering¶: C++: protocols::cluster::calibur::Clustering::operator=(const class protocols::cluster::calibur::Clustering &) –> class protocols::cluster::calibur::Clustering &

property autoAdjustPercentile¶

auxClustering(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering) → None¶: C++: protocols::cluster::calibur::Clustering::auxClustering() –> void

property bestClusMargin¶

property bestClusSize¶

buildAdjacentLists(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering) → None¶: C++: protocols::cluster::calibur::Clustering::buildAdjacentLists() –> void

cluster(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering) → None¶: C++: protocols::cluster::calibur::Clustering::cluster() –> void

destroyRandomDecoys(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, : pyrosetta.rosetta.std.vector_std_string, : pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_cluster_calibur_Stru_t) → None¶: C++: protocols::cluster::calibur::Clustering::destroyRandomDecoys(const class std::vector<std::string, class std::allocator<std::string > > &, const class std::vector<class std::shared_ptr<class protocols::cluster::calibur::Stru>, class std::allocator<class std::shared_ptr<class protocols::cluster::calibur::Stru> > > &) –> void

estD(*args, **kwargs)¶

Overloaded function.

estD(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, i: int, j: int) -> float

C++: protocols::cluster::calibur::Clustering::estD(int, int) –> double

estD(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, a: pyrosetta.rosetta.protocols.cluster.calibur.Stru, b: pyrosetta.rosetta.protocols.cluster.calibur.Stru) -> float

C++: protocols::cluster::calibur::Clustering::estD(const class protocols::cluster::calibur::Stru &, const class protocols::cluster::calibur::Stru &) –> double

estimateDist(*args, **kwargs)¶

Overloaded function.

estimateDist(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, : pyrosetta.rosetta.std.vector_std_string, : int, : int, : float, : float, : float, : float, : float) -> None

C++: protocols::cluster::calibur::Clustering::estimateDist(const class std::vector<std::string, class std::allocator<std::string > > &, int, int, double, double &, double &, double &, double &) –> void

estimateDist(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, : pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_cluster_calibur_Stru_t, : float, : float, : float, : float, : float) -> None

C++: protocols::cluster::calibur::Clustering::estimateDist(const class std::vector<class std::shared_ptr<class protocols::cluster::calibur::Stru>, class std::allocator<class std::shared_ptr<class protocols::cluster::calibur::Stru> > > &, double, double &, double &, double &, double &) –> void

eucD(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, i: int, j: int) → float¶: C++: protocols::cluster::calibur::Clustering::eucD(int, int) –> double

findDecoyWithMostNeighbors(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering) → int¶: C++: protocols::cluster::calibur::Clustering::findDecoyWithMostNeighbors() –> int

findLargestClusters(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering) → None¶: C++: protocols::cluster::calibur::Clustering::findLargestClusters() –> void

getPDBs(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, : pyrosetta.rosetta.std.vector_std_string, : pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_cluster_calibur_Stru_t, : pyrosetta.rosetta.std.vector_int, : int) → None¶: C++: protocols::cluster::calibur::Clustering::getPDBs(class std::vector<std::string, class std::allocator<std::string > > &, class std::vector<class std::shared_ptr<class protocols::cluster::calibur::Stru>, class std::allocator<class std::shared_ptr<class protocols::cluster::calibur::Stru> > > &, const class std::vector<int, class std::allocator<int> > &, int) –> void

getRandomDecoyNames(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, : pyrosetta.rosetta.std.vector_std_string, : int) → pyrosetta.rosetta.std.vector_std_string¶: C++: protocols::cluster::calibur::Clustering::getRandomDecoyNames(const class std::vector<std::string, class std::allocator<std::string > > &, int) –> class std::vector<std::string, class std::allocator<std::string > >

getThresholdAndDecoys(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering) → None¶: C++: protocols::cluster::calibur::Clustering::getThresholdAndDecoys() –> void

get_neighbor_list(*args, **kwargs)¶

Overloaded function.

get_neighbor_list(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, : pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_cluster_calibur_Stru_t, : pyrosetta.rosetta.std.vector_std_string, : int, nbors: pyrosetta.rosetta.std.vector_std_vector_double_t) -> None

C++: protocols::cluster::calibur::Clustering::get_neighbor_list(const class std::vector<class std::shared_ptr<class protocols::cluster::calibur::Stru>, class std::allocator<class std::shared_ptr<class protocols::cluster::calibur::Stru> > > &, const class std::vector<std::string, class std::allocator<std::string > > &, int, class std::vector<class std::vector<double, class std::allocator<double> >, class std::allocator<class std::vector<double, class std::allocator<double> > > > &) –> void

get_neighbor_list(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, : pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_cluster_calibur_Stru_t, : int, : float, : float, nbors: pyrosetta.rosetta.std.vector_std_vector_double_t) -> None

C++: protocols::cluster::calibur::Clustering::get_neighbor_list(const class std::vector<class std::shared_ptr<class protocols::cluster::calibur::Stru>, class std::allocator<class std::shared_ptr<class protocols::cluster::calibur::Stru> > > &, int, double &, double &, class std::vector<class std::vector<double, class std::allocator<double> >, class std::allocator<class std::vector<double, class std::allocator<double> > > > &) –> void

get_threshold(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, nbors: pyrosetta.rosetta.std.vector_std_vector_double_t, : int, : int, : int, : int, : float, : float) → float¶: C++: protocols::cluster::calibur::Clustering::get_threshold(const class std::vector<class std::vector<double, class std::allocator<double> >, class std::allocator<class std::vector<double, class std::allocator<double> > > > &, int, int, int, int, double, double) –> double

initRef(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, index: int) → None¶: C++: protocols::cluster::calibur::Clustering::initRef(int *) –> void

initialize(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, filename: str, threshold: float) → None¶: C++: protocols::cluster::calibur::Clustering::initialize(const std::string &, double) –> void

listAdjacentLists(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering) → None¶: C++: protocols::cluster::calibur::Clustering::listAdjacentLists() –> void

property mCen¶

property mCluCen¶

property mD2C¶

property mFinalClusters¶

property mFinalDecoy¶

property mInputFileName¶

property mLen¶

property mRemainingSize¶

property n_pdbs_¶

property names_¶

property num_neighbors_¶

property pref_ref_use_first_few_decoys¶

property pref_use_scud¶

property pref_use_sig¶

readDecoyNames(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering) → None¶: C++: protocols::cluster::calibur::Clustering::readDecoyNames() –> void

readDecoys(*args, **kwargs)¶

Overloaded function.

readDecoys(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, : pyrosetta.rosetta.std.vector_std_string, : pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_cluster_calibur_Stru_t) -> None

C++: protocols::cluster::calibur::Clustering::readDecoys(const class std::vector<std::string, class std::allocator<std::string > > &, const class std::vector<class std::shared_ptr<class protocols::cluster::calibur::Stru>, class std::allocator<class std::shared_ptr<class protocols::cluster::calibur::Stru> > > &) –> void

readDecoys(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, : pyrosetta.rosetta.std.vector_std_string) -> pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_cluster_calibur_Stru_t

C++: protocols::cluster::calibur::Clustering::readDecoys(const class std::vector<std::string, class std::allocator<std::string > > &) –> class std::vector<class std::shared_ptr<class protocols::cluster::calibur::Stru>, class std::allocator<class std::shared_ptr<class protocols::cluster::calibur::Stru> > >

realignDecoys(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, ref: int) → None¶: C++: protocols::cluster::calibur::Clustering::realignDecoys(int) –> void

refBound(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, i: int, j: int, lower: float, upper: float) → None¶: C++: protocols::cluster::calibur::Clustering::refBound(int, int, double &, double &) –> void

property references_¶

reinitialize(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, : pyrosetta.rosetta.std.vector_std_string, : pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_cluster_calibur_Stru_t, threshold: float) → None¶: C++: protocols::cluster::calibur::Clustering::reinitialize(const class std::vector<std::string, class std::allocator<std::string > > &, const class std::vector<class std::shared_ptr<class protocols::cluster::calibur::Stru>, class std::allocator<class std::shared_ptr<class protocols::cluster::calibur::Stru> > > &, const double) –> void

property remaining_list_¶

property remaining_list_index_¶

removeDecoys(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, adj: pyrosetta.rosetta.protocols.cluster.calibur.AdjacentList) → None¶: C++: protocols::cluster::calibur::Clustering::removeDecoys(class protocols::cluster::calibur::AdjacentList &) –> void

showClusters(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, : int) → None¶: C++: protocols::cluster::calibur::Clustering::showClusters(int) –> void

property spaceAllocatedForRMSD¶

superimposeAndReplace(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, coor1: pyrosetta.rosetta.std.vector_double, coor2: pyrosetta.rosetta.std.vector_double) → None¶: C++: protocols::cluster::calibur::Clustering::superimposeAndReplace(class std::vector<double, class std::allocator<double> > &, class std::vector<double, class std::allocator<double> > &) –> void

trueD(*args, **kwargs)¶

Overloaded function.

trueD(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, a: pyrosetta.rosetta.protocols.cluster.calibur.Stru, b: pyrosetta.rosetta.protocols.cluster.calibur.Stru) -> float

C++: protocols::cluster::calibur::Clustering::trueD(const class protocols::cluster::calibur::Stru &, const class protocols::cluster::calibur::Stru &) –> double

trueD(self: pyrosetta.rosetta.protocols.cluster.calibur.Clustering, i: int, j: int) -> float

C++: protocols::cluster::calibur::Clustering::trueD(int, int) –> double

property xFactor¶

property xPercentile¶

class pyrosetta.rosetta.protocols.cluster.calibur.EST_THRESHOLD_MODE¶

Bases: pybind11_object

Members:

PERCENT_EDGES

MIN_AVG_DIST_BASED

MOST_FREQ_BASED

ROSETTA

SAMPLED_ROSETTA

USER_SPECIFIED

MIN_AVG_DIST_BASED = <EST_THRESHOLD_MODE.MIN_AVG_DIST_BASED: 1>¶

MOST_FREQ_BASED = <EST_THRESHOLD_MODE.MOST_FREQ_BASED: 2>¶

PERCENT_EDGES = <EST_THRESHOLD_MODE.PERCENT_EDGES: 0>¶

ROSETTA = <EST_THRESHOLD_MODE.ROSETTA: 3>¶

SAMPLED_ROSETTA = <EST_THRESHOLD_MODE.SAMPLED_ROSETTA: 4>¶

USER_SPECIFIED = <EST_THRESHOLD_MODE.USER_SPECIFIED: 5>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.cluster.calibur.INPUT_FILE_TYPE¶

Bases: pybind11_object

Members:

UNKNOWN

SILENT_FILE

PDB_LIST

PDB_LIST = <INPUT_FILE_TYPE.PDB_LIST: 1>¶

SILENT_FILE = <INPUT_FILE_TYPE.SILENT_FILE: 0>¶

UNKNOWN = <INPUT_FILE_TYPE.UNKNOWN: -1>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.cluster.calibur.PreloadedPDB¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.cluster.calibur.PreloadedPDB, : pyrosetta.rosetta.protocols.cluster.calibur.PreloadedPDB) → pyrosetta.rosetta.protocols.cluster.calibur.PreloadedPDB¶: C++: protocols::cluster::calibur::PreloadedPDB::operator=(const class protocols::cluster::calibur::PreloadedPDB &) –> class protocols::cluster::calibur::PreloadedPDB &

property filename2PDB¶

getSimPDB(self: pyrosetta.rosetta.protocols.cluster.calibur.PreloadedPDB, pdbfilename: str) → protocols::cluster::calibur::SimPDB¶: C++: protocols::cluster::calibur::PreloadedPDB::getSimPDB(const std::string &) –> class std::shared_ptr<class protocols::cluster::calibur::SimPDB>

loadPDBFromList(self: pyrosetta.rosetta.protocols.cluster.calibur.PreloadedPDB, pdblistfilename: str) → None¶: C++: protocols::cluster::calibur::PreloadedPDB::loadPDBFromList(const std::string &) –> void

loadSilentFile(self: pyrosetta.rosetta.protocols.cluster.calibur.PreloadedPDB, silentfilename: str) → None¶: C++: protocols::cluster::calibur::PreloadedPDB::loadSilentFile(const std::string &) –> void

property mNumDecoy¶

property names_¶

property num_residue_¶

pyrosetta.rosetta.protocols.cluster.calibur.RMSD(coords1: pyrosetta.rosetta.std.vector_double, coords2: pyrosetta.rosetta.std.vector_double, n: int) → float¶: C++: protocols::cluster::calibur::RMSD(class std::vector<double, class std::allocator<double> > &, class std::vector<double, class std::allocator<double> > &, int) –> double

class pyrosetta.rosetta.protocols.cluster.calibur.SimPDB¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.cluster.calibur.SimPDB, : pyrosetta.rosetta.protocols.cluster.calibur.SimPDB) → pyrosetta.rosetta.protocols.cluster.calibur.SimPDB¶: C++: protocols::cluster::calibur::SimPDB::operator=(const class protocols::cluster::calibur::SimPDB &) –> class protocols::cluster::calibur::SimPDB &

property calpha_vector_¶

property num_residue_¶

property protein_file_name_¶

read(self: pyrosetta.rosetta.protocols.cluster.calibur.SimPDB) → None¶: C++: protocols::cluster::calibur::SimPDB::read() –> void

class pyrosetta.rosetta.protocols.cluster.calibur.Stru¶

Bases: pybind11_object

property calpha_vector_¶

dist(*args, **kwargs)¶

Overloaded function.

dist(self: pyrosetta.rosetta.protocols.cluster.calibur.Stru, x: float, y: float, z: float, zz: float) -> float

C++: protocols::cluster::calibur::Stru::dist(double, double, double, const double *) –> double

dist(self: pyrosetta.rosetta.protocols.cluster.calibur.Stru, x: float, y: float, z: float) -> float

C++: protocols::cluster::calibur::Stru::dist(double, double, double) –> double

property mPDB¶

property signature_¶

pyrosetta.rosetta.protocols.cluster.calibur.center_residues(calpha_vector: pyrosetta.rosetta.std.vector_double, num_residue_: int) → None¶: C++: protocols::cluster::calibur::center_residues(class std::vector<double, class std::allocator<double> > &, int) –> void

pyrosetta.rosetta.protocols.cluster.calibur.cubic_roots1(a2: float, a1: float, a0: float, z: float) → None¶: C++: protocols::cluster::calibur::cubic_roots1(double, double, double, double *) –> void

pyrosetta.rosetta.protocols.cluster.calibur.cubic_roots2(a2: float, a1: float, a0: float, z: float) → None¶

This is faster but leaves no option for obtaining imaginary roots.: (After “-O” in GCC, the speed gain is not much, only ~4%)

C++: protocols::cluster::calibur::cubic_roots2(double, double, double, double *) –> void

pyrosetta.rosetta.protocols.cluster.calibur.fast_rmsd(coords1: pyrosetta.rosetta.std.vector_double, coords2: pyrosetta.rosetta.std.vector_double, n: int) → float¶: C++: protocols::cluster::calibur::fast_rmsd(class std::vector<double, class std::allocator<double> > &, class std::vector<double, class std::allocator<double> > &, int) –> double

pyrosetta.rosetta.protocols.cluster.calibur.filetype(filename: str) → pyrosetta.rosetta.protocols.cluster.calibur.INPUT_FILE_TYPE¶: C++: protocols::cluster::calibur::filetype(const std::string &) –> enum protocols::cluster::calibur::INPUT_FILE_TYPE

pyrosetta.rosetta.protocols.cluster.calibur.num_lines_in_file(filename: str) → int¶: C++: protocols::cluster::calibur::num_lines_in_file(const std::string &) –> unsigned int

pyrosetta.rosetta.protocols.cluster.calibur.toFloat(aString: str) → float¶: C++: protocols::cluster::calibur::toFloat(const std::string &) –> double

pyrosetta.rosetta.protocols.cluster.calibur.toInt(aString: str) → int¶: C++: protocols::cluster::calibur::toInt(const std::string &) –> int