external

Bindings for core::io::external namespace

class pyrosetta.rosetta.core.io.external.PsiPredInterface

Bases: pybind11_object

run_psipred(self: pyrosetta.rosetta.core.io.external.PsiPredInterface, pose: pyrosetta.rosetta.core.pose.Pose, blueprint_ss: str) → pyrosetta.rosetta.core.io.external.PsiPredResult

Runs psipred, as specified by “cmd” on the fasta file “fasta_filename”, and returns the psipred filename

if cached psipred output has already been saved for the AA sequence of pose, the cached output will be returned.

C++: core::io::external::PsiPredInterface::run_psipred(const class core::pose::Pose &, const std::string &) –> struct core::io::external::PsiPredResult

run_psipred_prob(self: pyrosetta.rosetta.core.io.external.PsiPredInterface, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t

C++: core::io::external::PsiPredInterface::run_psipred_prob(const class core::pose::Pose &) –> class utility::vector1<class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >, class std::allocator<class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > > >

class pyrosetta.rosetta.core.io.external.PsiPredResult

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.io.external.PsiPredResult, : pyrosetta.rosetta.core.io.external.PsiPredResult) → pyrosetta.rosetta.core.io.external.PsiPredResult

C++: core::io::external::PsiPredResult::operator=(const struct core::io::external::PsiPredResult &) –> struct core::io::external::PsiPredResult &

property nres

property pred_ss

property psipred2_confidence

property psipred_prob

pyrosetta.rosetta.core.io.external.generate_prob(psipred_result: pyrosetta.rosetta.core.io.external.PsiPredResult, desired_ss: str) → pyrosetta.rosetta.utility.vector1_double

generates scores for each residue based on psipred confidence and the desired secondary structure

C++: core::io::external::generate_prob(const struct core::io::external::PsiPredResult &, std::string) –> class utility::vector1<double, class std::allocator<double> >

pyrosetta.rosetta.core.io.external.nonmatching_residues(blueprint_ss: str, pred_ss: str) → pyrosetta.rosetta.utility.vector1_unsigned_long

finds which positions in the blueprint and predicted secondary structure string don’t match

returns a vector of the residue numbers

C++: core::io::external::nonmatching_residues(const std::string &, const std::string &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >