upstream¶

Bindings for protocols::match::upstream namespace

class pyrosetta.rosetta.protocols.match.upstream.BuildSet¶

Bases: pybind11_builtins.pybind11_object

Still sketchy on this class. It holds all of the data needed for describing the geometry of the downstream partner relative to the upstream partner for a single residue type. This class holds the data for deciding which base rotamers to consider, how each base rotamer should be expanded to produce a full set of chi rotamers, and how to orient the downstream partner relative to this rotamer. It also holds the UpstreamResTypeGeometry object for the restype being built.

algorithm(self: pyrosetta.rosetta.protocols.match.upstream.BuildSet) → protocols::match::downstream::DownstreamAlgorithm¶: C++: protocols::match::upstream::BuildSet::algorithm() –> class protocols::match::downstream::DownstreamAlgorithm &

assign(self: pyrosetta.rosetta.protocols.match.upstream.BuildSet, rhs: pyrosetta.rosetta.protocols.match.upstream.BuildSet) → pyrosetta.rosetta.protocols.match.upstream.BuildSet¶: C++: protocols::match::upstream::BuildSet::operator=(const class protocols::match::upstream::BuildSet &) –> class protocols::match::upstream::BuildSet &

atom_radius(self: pyrosetta.rosetta.protocols.match.upstream.BuildSet, atomno: int) → pyrosetta.rosetta.protocols.match.ProbeRadius¶: C++: protocols::match::upstream::BuildSet::atom_radius(unsigned long) const –> enum protocols::match::ProbeRadius

backbone_only(self: pyrosetta.rosetta.protocols.match.upstream.BuildSet) → bool¶: C++: protocols::match::upstream::BuildSet::backbone_only() const –> bool

check_fa_dun(self: pyrosetta.rosetta.protocols.match.upstream.BuildSet) → bool¶: C++: protocols::match::upstream::BuildSet::check_fa_dun() const –> bool

fa_dun_cutoff(self: pyrosetta.rosetta.protocols.match.upstream.BuildSet) → float¶: C++: protocols::match::upstream::BuildSet::fa_dun_cutoff() const –> double

has_algorithm(self: pyrosetta.rosetta.protocols.match.upstream.BuildSet) → bool¶: C++: protocols::match::upstream::BuildSet::has_algorithm() –> bool

has_restype(self: pyrosetta.rosetta.protocols.match.upstream.BuildSet) → bool¶

accessors

C++: protocols::match::upstream::BuildSet::has_restype() const –> bool

nbonds_from_bb_atom(self: pyrosetta.rosetta.protocols.match.upstream.BuildSet, atom_index: int) → int¶: C++: protocols::match::upstream::BuildSet::nbonds_from_bb_atom(unsigned long) const –> unsigned long

probability_limit(self: pyrosetta.rosetta.protocols.match.upstream.BuildSet) → float¶: C++: protocols::match::upstream::BuildSet::probability_limit() const –> double

restype(self: pyrosetta.rosetta.protocols.match.upstream.BuildSet) → pyrosetta.rosetta.core.chemical.ResidueType¶: C++: protocols::match::upstream::BuildSet::restype() const –> const class core::chemical::ResidueType &

restype_geometry(self: pyrosetta.rosetta.protocols.match.upstream.BuildSet) → protocols::match::upstream::UpstreamResTypeGeometry¶: C++: protocols::match::upstream::BuildSet::restype_geometry() const –> const class protocols::match::upstream::UpstreamResTypeGeometry &

sample_strategy_for_chi(self: pyrosetta.rosetta.protocols.match.upstream.BuildSet, chi: int) → pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData¶: C++: protocols::match::upstream::BuildSet::sample_strategy_for_chi(unsigned long) const –> const class protocols::match::upstream::SampleStrategyData &

set_downstream_algorithm(self: pyrosetta.rosetta.protocols.match.upstream.BuildSet, : protocols::match::downstream::DownstreamAlgorithm) → None¶: C++: protocols::match::upstream::BuildSet::set_downstream_algorithm(class std::shared_ptr<class protocols::match::downstream::DownstreamAlgorithm>) –> void

set_fa_dun_cutoff(self: pyrosetta.rosetta.protocols.match.upstream.BuildSet, cutoff: float) → None¶: C++: protocols::match::upstream::BuildSet::set_fa_dun_cutoff(double) –> void

set_residue_type(*args, **kwargs)¶

Overloaded function.

set_residue_type(self: pyrosetta.rosetta.protocols.match.upstream.BuildSet, restype: pyrosetta.rosetta.core.chemical.ResidueType) -> None
set_residue_type(self: pyrosetta.rosetta.protocols.match.upstream.BuildSet, restype: pyrosetta.rosetta.core.chemical.ResidueType, backbone_only: bool) -> None

initialization

C++: protocols::match::upstream::BuildSet::set_residue_type(class std::shared_ptr<const class core::chemical::ResidueType>, bool) –> void

set_sample_strategy_for_chi(self: pyrosetta.rosetta.protocols.match.upstream.BuildSet, chi: int, data: pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData) → None¶: C++: protocols::match::upstream::BuildSet::set_sample_strategy_for_chi(unsigned long, const class protocols::match::upstream::SampleStrategyData &) –> void

class pyrosetta.rosetta.protocols.match.upstream.ChiStrategy¶

Bases: pybind11_builtins.pybind11_object

Members:

no_samples

follow_EX_flags

rotameric_chi_mimic_EX_flags

rotameric_chi_step_by_value

rotameric_chi_step_wi_sd_range

rotameric_chi_partition_sd_range

nonrotameric_chi_sample_wi_nrchi_bin

nonrotameric_chi_sample_wi_nrchi_bin_to_lower_boundary

class pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler¶

Bases: pyrosetta.rosetta.protocols.match.upstream.ProteinSCSampler

Basic class for sidechain sampling that pulls data from the Dunbrack rotamer library. The samples that are returned are the basic rotamers and do not include any expansions by the “ex” flags.

assign(self: pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler, : pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler) → pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler¶: C++: protocols::match::upstream::DunbrackSCSampler::operator=(const class protocols::match::upstream::DunbrackSCSampler &) –> class protocols::match::upstream::DunbrackSCSampler &

desymmeterize(self: pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler) → bool¶: C++: protocols::match::upstream::DunbrackSCSampler::desymmeterize() const –> bool

samples(self: pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler, bb_conf: pyrosetta.rosetta.protocols.match.upstream.ScaffoldBuildPoint, restype: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData¶: C++: protocols::match::upstream::DunbrackSCSampler::samples(const class protocols::match::upstream::ScaffoldBuildPoint &, const class core::chemical::ResidueType &) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

set_desymmeterize(self: pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler, setting: bool) → None¶

Should amino acids that are symmetric about their final chi torsion: be treated as if they actually are not symmetric? This can be useful if you want to set a constraint to one side of the amino acid and a second constraint to the other side. E.g., let’s say you want OD1 on ASP to contact one thing 1, and OD2 to contact thing 2. If you were to specify the constraint to atom type OOC, then you wouldn’t be able to prevent the case where OD1 contacted both things. This functionality can be activated in the matcher constraint file by adding DESYMMETERIZE to the ALGORITHM_INFO:: block in a matcher constraint file. E.g. <APL NOTE: FILL IN THE REST OF THE COMMENTS HERE>

C++: protocols::match::upstream::DunbrackSCSampler::set_desymmeterize(bool) –> void

class pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData¶

Bases: pybind11_builtins.pybind11_object

This class holds all of the data associated with the logic for generating extra samples for a particular chi angle. There are tons of ways concievable to build extra rotamers; the data in this class is intended to group all of that data into one place. This class is not responsible for building extra rotamer samples; that responsibility is given to class FullChiSampleSet.

n_samples_per_side_of_nrchi_bin(self: pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData) → int¶: C++: protocols::match::upstream::SampleStrategyData::n_samples_per_side_of_nrchi_bin() const –> unsigned long

n_samples_wi_sd_range(self: pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData) → int¶: C++: protocols::match::upstream::SampleStrategyData::n_samples_wi_sd_range() const –> unsigned long

nrchi_prob_minimum_for_extra_samples(self: pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData) → float¶: C++: protocols::match::upstream::SampleStrategyData::nrchi_prob_minimum_for_extra_samples() const –> double

sample_level(self: pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData) → pyrosetta.rosetta.core.pack.task.ExtraRotSample¶: C++: protocols::match::upstream::SampleStrategyData::sample_level() const –> enum core::pack::task::ExtraRotSample

sd_range(self: pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData) → float¶: C++: protocols::match::upstream::SampleStrategyData::sd_range() const –> double

set_n_samples_per_side_of_nrchi_bin(self: pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData, setting: int) → None¶: C++: protocols::match::upstream::SampleStrategyData::set_n_samples_per_side_of_nrchi_bin(unsigned long) –> void

set_n_samples_wi_sd_range(self: pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData, setting: int) → None¶: C++: protocols::match::upstream::SampleStrategyData::set_n_samples_wi_sd_range(unsigned long) –> void

set_nrchi_prob_minimum_for_extra_samples(self: pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData, setting: float) → None¶: C++: protocols::match::upstream::SampleStrategyData::set_nrchi_prob_minimum_for_extra_samples(double) –> void

set_sample_level(self: pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData, setting: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None¶: C++: protocols::match::upstream::SampleStrategyData::set_sample_level(enum core::pack::task::ExtraRotSample) –> void

set_sd_range(self: pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData, setting: float) → None¶: C++: protocols::match::upstream::SampleStrategyData::set_sd_range(double) –> void

set_step_size(self: pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData, setting: float) → None¶: C++: protocols::match::upstream::SampleStrategyData::set_step_size(double) –> void

set_strategy(self: pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData, : pyrosetta.rosetta.protocols.match.upstream.ChiStrategy) → None¶: C++: protocols::match::upstream::SampleStrategyData::set_strategy(enum protocols::match::upstream::ChiStrategy) –> void

step_size(self: pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData) → float¶: C++: protocols::match::upstream::SampleStrategyData::step_size() const –> double

strategy(self: pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData) → pyrosetta.rosetta.protocols.match.upstream.ChiStrategy¶: C++: protocols::match::upstream::SampleStrategyData::strategy() const –> enum protocols::match::upstream::ChiStrategy

class pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry¶

Bases: pybind11_builtins.pybind11_object

A simple class that describes the geometry for a particular residue type. It describes the coordinate frame geometry for the fourth atom defining each chi dihedral. The fourth atom is called the “chi tip” atom, as it’s at the tip of the growing kinematic chain when building chi i. This class also describes the location of the atoms controlled by each chi which are not the chi-tip atoms; it measures their location in the coordinate frame of the chi-tip atom.

To generate the coordinate of the chi-tip atom, the stored coordinate frame is multiplied by the coordinate frame at the third atom after that coordinate frame has been multipled by the chi-angle-z-axis rotation HT.

CA_atom_id(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → int¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::CA_atom_id() const –> unsigned long

CB_atom_id(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → int¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::CB_atom_id() const –> unsigned long

C_atom_id(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → int¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::C_atom_id() const –> unsigned long

HA_atom_id(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → int¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::HA_atom_id() const –> unsigned long

H_atom_id(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → int¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::H_atom_id() const –> unsigned long

N_atom_id(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → int¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::N_atom_id() const –> unsigned long

O_atom_id(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → int¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::O_atom_id() const –> unsigned long

assign(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry, : pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::operator=(const class protocols::match::upstream::UpstreamResTypeGeometry &) –> class protocols::match::upstream::UpstreamResTypeGeometry &

atom_controlled_by_any_chi(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry, atomno: int) → bool¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::atom_controlled_by_any_chi(unsigned long) const –> bool

atom_has_nonchi_coordinate(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry, restype_atomid: int) → bool¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::atom_has_nonchi_coordinate(unsigned long) const –> bool

atom_is_chitip(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry, atomno: int) → bool¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::atom_is_chitip(unsigned long) const –> bool

chitip_atom(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry, chi: int) → int¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::chitip_atom(unsigned long) const –> unsigned long

chitip_atoms(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::chitip_atoms() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

controlling_chi_for_atom(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::controlling_chi_for_atom() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

coordinate_for_nonchi_atom_in_ideal_frame(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry, restype_atomid: int) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::coordinate_for_nonchi_atom_in_ideal_frame(unsigned long) const –> const class numeric::xyzVector<double> &

has_CA_atom(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → bool¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::has_CA_atom() const –> bool

has_CB_atom(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → bool¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::has_CB_atom() const –> bool

has_C_atom(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → bool¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::has_C_atom() const –> bool

has_HA_atom(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → bool¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::has_HA_atom() const –> bool

has_H_atom(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → bool¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::has_H_atom() const –> bool

has_N_atom(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → bool¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::has_N_atom() const –> bool

has_O_atom(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → bool¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::has_O_atom() const –> bool

ht_for_chitip_atom(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry, chi: int) → pyrosetta.rosetta.numeric.HomogeneousTransform_double_t¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::ht_for_chitip_atom(unsigned long) const –> const class numeric::HomogeneousTransform<double> &

ht_for_chitip_atoms(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → pyrosetta.rosetta.utility.vector1_numeric_HomogeneousTransform_double_t¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::ht_for_chitip_atoms() const –> const class utility::vector1<class numeric::HomogeneousTransform<double>, class std::allocator<class numeric::HomogeneousTransform<double> > > &

initialize_from_residue_type(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry, : pyrosetta.rosetta.core.chemical.ResidueType) → None¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(const class core::chemical::ResidueType &) –> void

n_nonchitip_atoms_for_chi(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry, chi: int) → int¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::n_nonchitip_atoms_for_chi(unsigned long) const –> unsigned long

name(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → str¶

the name of the residue type used to generate this geometry

C++: protocols::match::upstream::UpstreamResTypeGeometry::name() const –> const std::string &

natoms(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → int¶

the number of atoms in this residue type

C++: protocols::match::upstream::UpstreamResTypeGeometry::natoms() const –> unsigned long

nchi(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → int¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::nchi() const –> unsigned long

nonchitip_atom(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry, chi: int, which_nonchitip_atom_for_chi: int) → int¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::nonchitip_atom(unsigned long, unsigned long) const –> unsigned long

nonchitip_atoms(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::nonchitip_atoms() const –> const class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &

point_for_nonchitip_atom(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry, atom: int) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

Convenience function: get the coordinate in the chitip frame: for a particular atom. The atom must be a non-chitip atom that is not part of the backbone (it must be controlled by a chi angle).

C++: protocols::match::upstream::UpstreamResTypeGeometry::point_for_nonchitip_atom(unsigned long) –> const class numeric::xyzVector<double> &

points_for_nonchitip_atoms(*args, **kwargs)¶

Overloaded function.

points_for_nonchitip_atoms(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) -> pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t

C++: protocols::match::upstream::UpstreamResTypeGeometry::points_for_nonchitip_atoms() const –> const class utility::vector1<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >, class std::allocator<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > > > &

points_for_nonchitip_atoms(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry, chi: int) -> pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

C++: protocols::match::upstream::UpstreamResTypeGeometry::points_for_nonchitip_atoms(unsigned long) const –> const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &

pre_chitip_transform(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry, chi: int) → pyrosetta.rosetta.numeric.HomogeneousTransform_double_t¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::pre_chitip_transform(unsigned long) const –> const class numeric::HomogeneousTransform<double> &

which_point_for_atom(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::match::upstream::UpstreamResTypeGeometry::which_point_for_atom() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &