protein_interface_design

Bindings for protocols::protein_interface_design namespace

class pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue

Bases: pybind11_object

class FavorNativeResidue changes a pose object so that its residue identities at the initialization of FavorNativeResidue are kept in memory. If the res_type_constraint score term is set to a value other than 0, an energy bonus will be assigned if the residue doesn’t change. This is useful e.g., in design based on a native scaffold where we want a barrier to mutation.

assign(self: pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue, : pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue) → pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue

C++: protocols::protein_interface_design::FavorNativeResidue::operator=(const class protocols::protein_interface_design::FavorNativeResidue &) –> class protocols::protein_interface_design::FavorNativeResidue &

class pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue

Bases: pybind11_object

class FavorNonNativeResidue changes a pose object so that its residue identities at the initialization of FavorNonNativeResidue are kept in memory. If the res_type_constraint score term is set to a value other than 0, an energy bonus will be assigned if the residue changes. This is useful if we want to encourage mutation. A negative score would discourage mutation.

assign(self: pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue, : pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue) → pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue

C++: protocols::protein_interface_design::FavorNonNativeResidue::operator=(const class protocols::protein_interface_design::FavorNonNativeResidue &) –> class protocols::protein_interface_design::FavorNonNativeResidue &

pyrosetta.rosetta.protocols.protein_interface_design.MinimizeInterface(*args, **kwargs)

Overloaded function.

  1. MinimizeInterface(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, min_bb: pyrosetta.rosetta.utility.vector1_bool, min_sc: pyrosetta.rosetta.utility.vector1_bool, min_rb: pyrosetta.rosetta.utility.vector1_bool, optimize_foldtree: bool, target_residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

  2. MinimizeInterface(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, min_bb: pyrosetta.rosetta.utility.vector1_bool, min_sc: pyrosetta.rosetta.utility.vector1_bool, min_rb: pyrosetta.rosetta.utility.vector1_bool, optimize_foldtree: bool, target_residues: pyrosetta.rosetta.utility.vector1_unsigned_long, simultaneous_minimization: bool) -> None

utility function for minimizing sidechain in rigid-body dof, the interface sc, and bb in the entire protein.

C++: protocols::protein_interface_design::MinimizeInterface(class core::pose::Pose &, class std::shared_ptr<const class core::scoring::ScoreFunction>, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &, const bool, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

class pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputter

Bases: PDBJobInputter

assign(self: pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputter, : pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputter) → pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputter

C++: protocols::protein_interface_design::ParserJobInputter::operator=(const class protocols::protein_interface_design::ParserJobInputter &) –> class protocols::protein_interface_design::ParserJobInputter &

fill_jobs(self: pyrosetta.rosetta.protocols.jd2.PDBJobInputter, jobs: protocols::jd2::JobsContainer) → None

this function determines what jobs exist from -s/-l

C++: protocols::jd2::PDBJobInputter::fill_jobs(class protocols::jd2::JobsContainer &) –> void

get_self_ptr(self: pyrosetta.rosetta.protocols.jd2.JobInputter) → pyrosetta.rosetta.protocols.jd2.JobInputter

Get self owning pointers.

C++: protocols::jd2::JobInputter::get_self_ptr() –> class std::shared_ptr<class protocols::jd2::JobInputter>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.jd2.JobInputter) → pyrosetta.rosetta.std.weak_ptr_protocols_jd2_JobInputter_t

Get self weak pointers.

C++: protocols::jd2::JobInputter::get_self_weak_ptr() –> class std::weak_ptr<class protocols::jd2::JobInputter>

input_source(self: pyrosetta.rosetta.protocols.jd2.PDBJobInputter) → pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum
Return the type of input source that the PDBJobInputter is currently

using.

Always PDB_FILE.

C++: protocols::jd2::PDBJobInputter::input_source() const –> enum protocols::jd2::JobInputterInputSource::Enum

static job_inputter_input_source_to_string(source: pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum) → str
call this with input_source() to get the input source of a

particular job inputter

C++: protocols::jd2::JobInputter::job_inputter_input_source_to_string(enum protocols::jd2::JobInputterInputSource::Enum) –> std::string

pose_from_job(self: pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputter, pose: pyrosetta.rosetta.core.pose.Pose, job: pyrosetta.rosetta.protocols.jd2.Job) → None

this function is responsible for filling the pose reference with the pose indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference. This implementation uses pose_from_pdb

C++: protocols::protein_interface_design::ParserJobInputter::pose_from_job(class core::pose::Pose &, class std::shared_ptr<class protocols::jd2::Job>) –> void

update_jobs_list(self: pyrosetta.rosetta.protocols.jd2.JobInputter, jobs: protocols::jd2::JobsContainer) → None

This function is only called by certain JobInputters to update the jobs list after it has already been created.

An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back.

C++: protocols::jd2::JobInputter::update_jobs_list(class std::shared_ptr<class protocols::jd2::JobsContainer>) –> void

updates_jobs_list(self: pyrosetta.rosetta.protocols.jd2.JobInputter) → bool

Does this type of JobInputter update the jobs list?

False by default. Override this function in derived classes to make it true.

C++: protocols::jd2::JobInputter::updates_jobs_list() const –> bool

class pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputterCreator

Bases: JobInputterCreator

assign(self: pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputterCreator, : pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputterCreator) → pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputterCreator

C++: protocols::protein_interface_design::ParserJobInputterCreator::operator=(const class protocols::protein_interface_design::ParserJobInputterCreator &) –> class protocols::protein_interface_design::ParserJobInputterCreator &

create_JobInputter(self: pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputterCreator) → pyrosetta.rosetta.protocols.jd2.JobInputter

C++: protocols::protein_interface_design::ParserJobInputterCreator::create_JobInputter() const –> class std::shared_ptr<class protocols::jd2::JobInputter>

keyname(self: pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputterCreator) → str

C++: protocols::protein_interface_design::ParserJobInputterCreator::keyname() const –> std::string

class pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader, : pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader) → pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader

C++: protocols::protein_interface_design::PatchdockReader::operator=(const class protocols::protein_interface_design::PatchdockReader &) –> class protocols::protein_interface_design::PatchdockReader &

clear_internals(self: pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader) → None

C++: protocols::protein_interface_design::PatchdockReader::clear_internals() –> void

from_entry(*args, **kwargs)

Overloaded function.

  1. from_entry(self: pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader, f: int) -> None

C++: protocols::protein_interface_design::PatchdockReader::from_entry(const unsigned long) –> void

  1. from_entry(self: pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader) -> int

C++: protocols::protein_interface_design::PatchdockReader::from_entry() const –> unsigned long

number_of_patchdock_entries(self: pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader) → int

C++: protocols::protein_interface_design::PatchdockReader::number_of_patchdock_entries() –> unsigned long

patchdock_entry_num(*args, **kwargs)

Overloaded function.

  1. patchdock_entry_num(self: pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader) -> int

C++: protocols::protein_interface_design::PatchdockReader::patchdock_entry_num() const –> unsigned long

  1. patchdock_entry_num(self: pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader, s: int) -> None

C++: protocols::protein_interface_design::PatchdockReader::patchdock_entry_num(const unsigned long) –> void

patchdock_fname(*args, **kwargs)

Overloaded function.

  1. patchdock_fname(self: pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader) -> str

C++: protocols::protein_interface_design::PatchdockReader::patchdock_fname() const –> std::string

  1. patchdock_fname(self: pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader, s: str) -> None

C++: protocols::protein_interface_design::PatchdockReader::patchdock_fname(const std::string &) –> void

random_entry(*args, **kwargs)

Overloaded function.

  1. random_entry(self: pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader) -> bool

C++: protocols::protein_interface_design::PatchdockReader::random_entry() const –> bool

  1. random_entry(self: pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader, b: bool) -> None

C++: protocols::protein_interface_design::PatchdockReader::random_entry(const bool) –> void

read_patchdock(self: pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader, input_tag: str, native_tag: str) → None

C++: protocols::protein_interface_design::PatchdockReader::read_patchdock(std::string &, std::string &) –> void

read_patchdock_entry(self: pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader) → pyrosetta.rosetta.protocols.protein_interface_design.Transformation

C++: protocols::protein_interface_design::PatchdockReader::read_patchdock_entry() –> struct protocols::protein_interface_design::Transformation

read_poses(*args, **kwargs)

Overloaded function.

  1. read_poses(self: pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader, input_pose: pyrosetta.rosetta.core.pose.Pose, input_tag: str) -> None

if no native is read

C++: protocols::protein_interface_design::PatchdockReader::read_poses(class core::pose::Pose &, std::string &) –> void

  1. read_poses(self: pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader, input_pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, input_tag: str, native_tag: str) -> None

reads input and native poses from file. If patchdock flags are used will read the patchdock transformation

and transform the input pose accordingly

C++: protocols::protein_interface_design::PatchdockReader::read_poses(class core::pose::Pose &, class core::pose::Pose &, std::string &, std::string &) –> void

to_entry(*args, **kwargs)

Overloaded function.

  1. to_entry(self: pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader, t: int) -> None

C++: protocols::protein_interface_design::PatchdockReader::to_entry(const unsigned long) –> void

  1. to_entry(self: pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader) -> int

C++: protocols::protein_interface_design::PatchdockReader::to_entry() const –> unsigned long

transform_pose(self: pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader, pose: pyrosetta.rosetta.core.pose.Pose, chain: int, t: pyrosetta.rosetta.protocols.protein_interface_design.Transformation) → None

C++: protocols::protein_interface_design::PatchdockReader::transform_pose(class core::pose::Pose &, const unsigned long, const struct protocols::protein_interface_design::Transformation &) –> void

class pyrosetta.rosetta.protocols.protein_interface_design.ReportPSSMDifferences

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.protein_interface_design.ReportPSSMDifferences, : pyrosetta.rosetta.protocols.protein_interface_design.ReportPSSMDifferences) → pyrosetta.rosetta.protocols.protein_interface_design.ReportPSSMDifferences

C++: protocols::protein_interface_design::ReportPSSMDifferences::operator=(const class protocols::protein_interface_design::ReportPSSMDifferences &) –> class protocols::protein_interface_design::ReportPSSMDifferences &

calculate(self: pyrosetta.rosetta.protocols.protein_interface_design.ReportPSSMDifferences, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → float

C++: protocols::protein_interface_design::ReportPSSMDifferences::calculate(const class core::pose::Pose &, const class core::pose::Pose &, const class std::shared_ptr<const class core::pack::task::PackerTask> &) –> double

load_pssm_data(self: pyrosetta.rosetta.protocols.protein_interface_design.ReportPSSMDifferences, native_filename: str) → bool

C++: protocols::protein_interface_design::ReportPSSMDifferences::load_pssm_data(const std::string &) –> bool

pssm_(self: pyrosetta.rosetta.protocols.protein_interface_design.ReportPSSMDifferences) → pyrosetta.rosetta.utility.vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t

C++: protocols::protein_interface_design::ReportPSSMDifferences::pssm_() const –> const class utility::vector1<struct std::pair<enum core::chemical::AA, class utility::vector1<double, class std::allocator<double> > >, class std::allocator<struct std::pair<enum core::chemical::AA, class utility::vector1<double, class std::allocator<double> > > > > &

res_name1(self: pyrosetta.rosetta.protocols.protein_interface_design.ReportPSSMDifferences) → pyrosetta.rosetta.std.map_unsigned_long_std_string

C++: protocols::protein_interface_design::ReportPSSMDifferences::res_name1() const –> const class std::map<unsigned long, std::string, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, std::string > > > &

class pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences

Bases: pybind11_object

Class ReportSequenceDifferences takes in two poses and provides information on the sequence changes between them, including the residue energies associated with those changes.

assign(self: pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences, : pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences) → pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences

C++: protocols::protein_interface_design::ReportSequenceDifferences::operator=(const class protocols::protein_interface_design::ReportSequenceDifferences &) –> class protocols::protein_interface_design::ReportSequenceDifferences &

calculate(self: pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::protein_interface_design::ReportSequenceDifferences::calculate(const class core::pose::Pose &, const class core::pose::Pose &) –> void

get_res_energy(self: pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences, num: int) → pyrosetta.rosetta.std.map_unsigned_long_double

C++: protocols::protein_interface_design::ReportSequenceDifferences::get_res_energy(const unsigned long) const –> const class std::map<unsigned long, double, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, double> > > *

report(self: pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences, out: pyrosetta.rosetta.std.ostream) → None

C++: protocols::protein_interface_design::ReportSequenceDifferences::report(std::ostream &) const –> void

res_name1(self: pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences) → pyrosetta.rosetta.std.map_unsigned_long_std_string

C++: protocols::protein_interface_design::ReportSequenceDifferences::res_name1() const –> const class std::map<unsigned long, std::string, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, std::string > > > &

res_name2(self: pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences) → pyrosetta.rosetta.std.map_unsigned_long_std_string

C++: protocols::protein_interface_design::ReportSequenceDifferences::res_name2() const –> const class std::map<unsigned long, std::string, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, std::string > > > &

class pyrosetta.rosetta.protocols.protein_interface_design.Revert

Bases: pybind11_object

class Revert takes in ‘wt’ and ‘designed’ poses and attempts to revert all substitutions in the design to their wt identities. Each substitution is tried separately in the context of the designed protein and reversions that don’t adversely affect ddg are made. If the energy of the residue in the design is higher than 0, but the reversion did not succeed, Revert will attempt an Ala substitution.

apply(self: pyrosetta.rosetta.protocols.protein_interface_design.Revert, pose_wt: pyrosetta.rosetta.core.pose.Pose, pose_des: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::protein_interface_design::Revert::apply(class core::pose::Pose &, class core::pose::Pose &) const –> void

assign(self: pyrosetta.rosetta.protocols.protein_interface_design.Revert, : pyrosetta.rosetta.protocols.protein_interface_design.Revert) → pyrosetta.rosetta.protocols.protein_interface_design.Revert

C++: protocols::protein_interface_design::Revert::operator=(const class protocols::protein_interface_design::Revert &) –> class protocols::protein_interface_design::Revert &

pyrosetta.rosetta.protocols.protein_interface_design.SymMinimizeInterface(*args, **kwargs)

Overloaded function.

  1. SymMinimizeInterface(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, min_bb: pyrosetta.rosetta.utility.vector1_bool, min_sc: pyrosetta.rosetta.utility.vector1_bool, min_rb: pyrosetta.rosetta.utility.vector1_bool) -> None

  2. SymMinimizeInterface(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, min_bb: pyrosetta.rosetta.utility.vector1_bool, min_sc: pyrosetta.rosetta.utility.vector1_bool, min_rb: pyrosetta.rosetta.utility.vector1_bool, simultaneous_minimization: bool) -> None

C++: protocols::protein_interface_design::SymMinimizeInterface(class core::pose::Pose &, class std::shared_ptr<const class core::scoring::ScoreFunction>, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &, const bool) –> void

class pyrosetta.rosetta.protocols.protein_interface_design.Transformation

Bases: pybind11_object

property alpha
property beta
property gamma
property translation
pyrosetta.rosetta.protocols.protein_interface_design.best_bbcst_residues(pose: pyrosetta.rosetta.core.pose.Pose, chain: int, n_return: int) → pyrosetta.rosetta.utility.vector1_unsigned_long
evaluate backbone_stub_constraints for each residue in a chain and return a vector with the top n_return residue numbers by cst score

note that this function is NOT guaranteed to return n_return residues! It will return the best n<=n_return

C++: protocols::protein_interface_design::best_bbcst_residues(const class core::pose::Pose &, const unsigned long, const unsigned long) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.protein_interface_design.best_cutpoint(pose: pyrosetta.rosetta.core.pose.Pose, prev_u: int, prev_d: int, u: int, d: int) → int

utility function for stub_based_atom_tree. tries to find an optimal cutpoint in a pose given two different boundaries.

C++: protocols::protein_interface_design::best_cutpoint(class core::pose::Pose &, const unsigned long, const unsigned long, const unsigned long, const unsigned long) –> unsigned long

pyrosetta.rosetta.protocols.protein_interface_design.find_lowest_constraint_energy_residue(pose: pyrosetta.rosetta.core.pose.Pose, chain: int, resi: int, lowest_energy: float) → None

C++: protocols::protein_interface_design::find_lowest_constraint_energy_residue(const class core::pose::Pose &, const unsigned long, unsigned long &, double &) –> void

pyrosetta.rosetta.protocols.protein_interface_design.find_nearest_residue(*args, **kwargs)

Overloaded function.

  1. find_nearest_residue(pose: pyrosetta.rosetta.core.pose.Pose, target_chain: int, res: int) -> int

  2. find_nearest_residue(pose: pyrosetta.rosetta.core.pose.Pose, target_chain: int, res: int, atom: str) -> int

find nearest residue on target_chain to res

C++: protocols::protein_interface_design::find_nearest_residue(const class core::pose::Pose &, const unsigned long, const unsigned long, const std::string &) –> unsigned long

pyrosetta.rosetta.protocols.protein_interface_design.get_bbcsts(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::protein_interface_design::get_bbcsts(const class core::pose::Pose &) –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

pyrosetta.rosetta.protocols.protein_interface_design.hbonded(*args, **kwargs)

Overloaded function.

  1. hbonded(pose: pyrosetta.rosetta.core.pose.Pose, target_residue: int, binders: pyrosetta.rosetta.std.set_unsigned_long_t, bb: bool, sc: bool, energy_thres: float) -> pyrosetta.rosetta.std.list_unsigned_long_t

  2. hbonded(pose: pyrosetta.rosetta.core.pose.Pose, target_residue: int, binders: pyrosetta.rosetta.std.set_unsigned_long_t, bb: bool, sc: bool, energy_thres: float, bb_bb: bool) -> pyrosetta.rosetta.std.list_unsigned_long_t

  3. hbonded(pose: pyrosetta.rosetta.core.pose.Pose, target_residue: int, binders: pyrosetta.rosetta.std.set_unsigned_long_t, bb: bool, sc: bool, energy_thres: float, bb_bb: bool, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.std.list_unsigned_long_t

utility function for finding hbonding partners among a list of potential binder residues to a specific target

C++: protocols::protein_interface_design::hbonded(const class core::pose::Pose &, const unsigned long, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, const bool, const bool, const double, const bool, class std::shared_ptr<class core::scoring::ScoreFunction>) –> class std::list<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.protein_interface_design.hbonded_atom(*args, **kwargs)

Overloaded function.

  1. hbonded_atom(pose: pyrosetta.rosetta.core.pose.Pose, target_residue: int, target_atom: str, binders: pyrosetta.rosetta.std.set_unsigned_long_t, bb: bool, sc: bool, energy_thres: float) -> pyrosetta.rosetta.std.list_unsigned_long_t

  2. hbonded_atom(pose: pyrosetta.rosetta.core.pose.Pose, target_residue: int, target_atom: str, binders: pyrosetta.rosetta.std.set_unsigned_long_t, bb: bool, sc: bool, energy_thres: float, bb_bb: bool) -> pyrosetta.rosetta.std.list_unsigned_long_t

  3. hbonded_atom(pose: pyrosetta.rosetta.core.pose.Pose, target_residue: int, target_atom: str, binders: pyrosetta.rosetta.std.set_unsigned_long_t, bb: bool, sc: bool, energy_thres: float, bb_bb: bool, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.std.list_unsigned_long_t

utility function for finding hbonding partners among a list of potential binder residues to a specific target

C++: protocols::protein_interface_design::hbonded_atom(const class core::pose::Pose &, const unsigned long, const std::string &, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, const bool, const bool, const double, const bool, class std::shared_ptr<class core::scoring::ScoreFunction>) –> class std::list<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.protein_interface_design.make_hotspot_foldtree(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.kinematics.FoldTree

C++: protocols::protein_interface_design::make_hotspot_foldtree(const class core::pose::Pose &) –> class core::kinematics::FoldTree

pyrosetta.rosetta.protocols.protein_interface_design.optimal_connection_point(residue_type: str) → str
what is the optimal connection point for an atom tree, given a residue type (puts the connection point

at the beginning of a functional group

C++: protocols::protein_interface_design::optimal_connection_point(const std::string &) –> std::string

pyrosetta.rosetta.protocols.protein_interface_design.remove_coordinate_constraints_from_pose(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

removes ALL coordinate constraints from a pose. returns the constraints that were removed

C++: protocols::protein_interface_design::remove_coordinate_constraints_from_pose(class core::pose::Pose &) –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

pyrosetta.rosetta.protocols.protein_interface_design.star_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.kinematics.FoldTree

C++: protocols::protein_interface_design::star_fold_tree(class core::pose::Pose &) –> class core::kinematics::FoldTree

pyrosetta.rosetta.protocols.protein_interface_design.sum_total_residue_energy(pose: pyrosetta.rosetta.core.pose.Pose, resid: int) → float

C++: protocols::protein_interface_design::sum_total_residue_energy(const class core::pose::Pose &, const unsigned long) –> double