mainchain_potential

Bindings for protocols::mainchain_potential namespace

class pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotential

Bases: pybind11_object

A generator for mainchain potentials. Inputs are a noncanonical residue type with an already-generated sidechain potential; outputs are a potential file suitable for use by the RamaPrePro scoreterm.

assign(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotential, : pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotential) → pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotential

C++: protocols::mainchain_potential::GenerateMainchainPotential::operator=(const class protocols::mainchain_potential::GenerateMainchainPotential &) –> class protocols::mainchain_potential::GenerateMainchainPotential &

clone(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotential) → pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotential

Clone function: make a copy of this object and return an owning pointer to the copy.

C++: protocols::mainchain_potential::GenerateMainchainPotential::clone() const –> class std::shared_ptr<class protocols::mainchain_potential::GenerateMainchainPotential>

run(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotential) → None

Entry point into protocol execution.

C++: protocols::mainchain_potential::GenerateMainchainPotential::run() –> void

write_last_generated_to_disk(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotential) → None

Write the last generated mainchain potential to disk. The output filename is given in the

options_ object.

If we’re writing individual scoretables for individual scoreterms, that happens here, too.

C++: protocols::mainchain_potential::GenerateMainchainPotential::write_last_generated_to_disk() const –> void

class pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions

Bases: pybind11_object

Options container for the generator for mainchain potentials.

assign(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions, : pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions) → pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::operator=(const class protocols::mainchain_potential::GenerateMainchainPotentialOptions &) –> class protocols::mainchain_potential::GenerateMainchainPotentialOptions &

clone(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions) → pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions

Clone function: create a copy of this object, and return an owning pointer to the copy.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::clone() const –> class std::shared_ptr<class protocols::mainchain_potential::GenerateMainchainPotentialOptions>

dimensions(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions) → pyrosetta.rosetta.utility.vector1_unsigned_long

Access the vector of the number of points in each dimension for a given residue type. (Const-access)/

The length of this vector must match the number of mainchain dihedral DoFs for which we’re generating a mainchain potential.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::dimensions() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

do_minimization(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions) → bool

Get whether we’re minimizing each rotamer.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::do_minimization() const –> bool

get_scorefxn_filename(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions) → str

Name of the scorefunction that we’ll use. An empty string indicates that the default should be used.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::get_scorefxn_filename() const –> const std::string &

kbt(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions) → float

Get the Boltzmann temperature.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::kbt() const –> const double &

mainchain_torsions_covered(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions) → pyrosetta.rosetta.utility.vector1_unsigned_long

Get which mainchain torsions are covered.

If this is an empty vector, it indicates that all mainchain torsions are covered.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::mainchain_torsions_covered() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

make_pre_proline_potential(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions) → bool

Get whether we’re generating a pre-proline potential.

If true, then we generate a potential for a position before a proline, sarcosine, or other N-substituted building block (e.g. a peptoid). If false, then the next residue’s nitrogen is unsubstituted.

Determines the patch applied to the C-terminus.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::make_pre_proline_potential() const –> bool

minimization_threshold(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions) → float

Get the minimization threshold.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::minimization_threshold() const –> const double &

minimization_type(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions) → str

Get the minimization type.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::minimization_type() const –> const std::string &

output_filename(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions) → str

Get the mainchain potential filename to write.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::output_filename() const –> const std::string &

static register_options() → None

Static function used to register releavnt options.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::register_options() –> void

residue_name(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions) → str

Get the name of the residue type for which we’ll be generating a mainchain potential.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::residue_name() const –> const std::string &

set_dimensions(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions, dimensions_in: pyrosetta.rosetta.utility.vector1_int) → None

Set the vector of number of points in each dimension for the mainchain potential that we’re generating.

This takes a vector of ints, not Sizes, because that’s what comes from the global options system.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_dimensions(const class utility::vector1<int, class std::allocator<int> > &) –> void

set_do_minimization(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions, setting: bool) → None

Set whether we’re minimizing each rotamer.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_do_minimization(const bool) –> void

set_kbt(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions, kbt_in: float) → None

Set the Boltzmann temperature.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_kbt(const double &) –> void

set_mainchain_torsions_covered(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions, mainchain_torsions_in: pyrosetta.rosetta.utility.vector1_int) → None

Set which mainchain torsions are covered.

If this is an empty vector, it indicates that all mainchain torsions are covered. This takes a vector of ints, not Sizes, because that’s what comes from the global options sytem.

Pass this an empty vector to set the default (all mainchain torsions for the residue type.)

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_mainchain_torsions_covered(const class utility::vector1<int, class std::allocator<int> > &) –> void

set_make_pre_proline_potential(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions, setting: bool) → None

Set whether we’re generating a pre-proline potential.

If true, then we generate a potential for a position before a proline, sarcosine, or other N-substituted building block (e.g. a peptoid). If false, then the next residue’s nitrogen is unsubstituted.

Determines the patch applied to the C-terminus.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_make_pre_proline_potential(const bool) –> void

set_minimization_threshold(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions, threshold_in: float) → None

Set the minimization threshold.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_minimization_threshold(const double &) –> void

set_minimization_type(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions, type_in: str) → None

Set the minimization type.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_minimization_type(const std::string &) –> void

set_output_filename(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions, filename_in: str) → None

Set the mainchain potential filename to write.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_output_filename(const std::string &) –> void

set_residue_name(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions, name_in: str) → None

Set the name of the residue type for which we’ll be generating a mainchain potential.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_residue_name(const std::string &) –> void

set_scorefxn_filename(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions, filename_in: str) → None

Set name of the scorefunction that we’ll use. An empty string indicates that the default should be used.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_scorefxn_filename(const std::string &) –> void

set_symmetrize_output(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions, setting: bool) → None

Set whether the output should be made symmetric.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_symmetrize_output(const bool) –> void

set_write_potentials_for_individual_scoreterms(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions, setting: bool) → None

Set whether we are writing mainchain potentials for individual scoreterms.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_write_potentials_for_individual_scoreterms(const bool) –> void

symmetrize_output(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions) → bool

Should the output be made symmetric?

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::symmetrize_output() const –> bool

write_potentials_for_individual_scoreterms(self: pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions) → bool

Are we writing mainchain potentials for individual scoreterms?

Default false.

C++: protocols::mainchain_potential::GenerateMainchainPotentialOptions::write_potentials_for_individual_scoreterms() const –> bool