cyclic_peptide_predict

Bindings for protocols::cyclic_peptide_predict namespace

class pyrosetta.rosetta.protocols.cyclic_peptide_predict.HIERARCHICAL_HYBRID_JD_MPI_SORT_TYPE

Bases: pybind11_object

Members:

SORT_BY_ENERGIES

SORT_BY_RMSD

SORT_BY_HBONDS

SORT_BY_CIS_PEPTIDE_BONDS

SORT_BY_CIS_PEPTIDE_BONDS = <HIERARCHICAL_HYBRID_JD_MPI_SORT_TYPE.SORT_BY_CIS_PEPTIDE_BONDS: 4>

SORT_BY_ENERGIES = <HIERARCHICAL_HYBRID_JD_MPI_SORT_TYPE.SORT_BY_ENERGIES: 1>

SORT_BY_HBONDS = <HIERARCHICAL_HYBRID_JD_MPI_SORT_TYPE.SORT_BY_HBONDS: 3>

SORT_BY_RMSD = <HIERARCHICAL_HYBRID_JD_MPI_SORT_TYPE.SORT_BY_RMSD: 2>

property name

property value

class pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary

Bases: HierarchicalHybridJD_ResultsSummaryBase

A class for summarizing the result of an MPI-mode job run with the SimpleCycpepPredictApplication.

Vikram K. Mulligan, Baker laboratory (vmullig.edu)

MPI_ranks_handling_message(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase) → pyrosetta.rosetta.utility.vector1_int

Get the list of procs that transmitted this JobResultsSummary.

Whenever a proc sends it to someone else, the receiving proc appends the sender’s rank here. This allows the director node to address an output request to the correct proc.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::MPI_ranks_handling_message() const –> const class utility::vector1<int, class std::allocator<int> > &

add_MPI_rank_handling_message(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase, new_proc: int) → None

Add a proc that handled this message to the list of procs that transmitted this JobResultsSummary.

Whenever a proc sends it to someone else, the receiving proc appends the sender’s rank here. This allows the director node to address an output request to the correct proc.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::add_MPI_rank_handling_message(const int) –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary, : pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary) → pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary::operator=(const class protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary &) –> class protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary &

cis_peptide_bonds(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary) → int

Get the number of cis-peptide bonds of the pose generated by this job.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary::cis_peptide_bonds() const –> unsigned long

clone(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary) → pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase

Clone operator: make a copy of this object and return an OP to the copy.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary::clone() const –> class std::shared_ptr<class protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase>

hbonds(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary) → int

Get the number of hbonds of the pose generated by this job.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary::hbonds() const –> unsigned long

jobindex_on_originating_node(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase) → int

Get the local index of the job on the node on which it was carried out.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::jobindex_on_originating_node() const –> unsigned long

originating_node_MPI_rank(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase) → int

Get the MPI rank of the process that initially carried out this job.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::originating_node_MPI_rank() const –> int

pose_energy(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary) → float

Get the energy of the pose generated by this job.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary::pose_energy() const –> const double &

rmsd(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary) → float

Get the RMSD of the pose generated by this job to native.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary::rmsd() const –> const double &

set_cis_peptide_bonds(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary, val: int) → None

Set the number of cis-peptide bonds of the pose generated by this job.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary::set_cis_peptide_bonds(const unsigned long) –> void

set_hbonds(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary, val: int) → None

Set the number of hbonds of the pose generated by this job.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary::set_hbonds(const unsigned long) –> void

set_jobindex_on_originating_node(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase, index: int) → None

Set the local index of the job on the node on which it was carried out.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::set_jobindex_on_originating_node(const unsigned long) –> void

set_originating_node_MPI_rank(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase, rank: int) → None

Set the MPI rank of the process that initially carried out this job.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::set_originating_node_MPI_rank(const int) –> void

set_pose_energy(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary, val: float) → None

Set the energy of the pose generated by this job.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary::set_pose_energy(const double &) –> void

set_rmsd(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary, val: float) → None

Set the RMSD of the pose generated by this job to native.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary::set_rmsd(const double &) –> void

show(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary, out: pyrosetta.rosetta.std.ostream) → None

Print a summary of this object to a stream.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_PNearToArbitraryStateSummary

Bases: pybind11_object

A class for storing the PNear, Keq, and DeltaG_folding values to an arbitrary state that has been sampled.

Vikram K. Mulligan (vmulligan.org)

Keq(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_PNearToArbitraryStateSummary) → float

Access the PNfolding equilibtrium constant value.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummary::Keq() const –> double

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_PNearToArbitraryStateSummary, : pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_PNearToArbitraryStateSummary) → pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_PNearToArbitraryStateSummary

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummary::operator=(const class protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummary &) –> class protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummary &

clone(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_PNearToArbitraryStateSummary) → pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_PNearToArbitraryStateSummary

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

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummary::clone() const –> class std::shared_ptr<class protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummary>

deltaG_folding(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_PNearToArbitraryStateSummary) → float

Access the Delta-G of folding value.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummary::deltaG_folding() const –> double

jobindex_on_originating_node(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_PNearToArbitraryStateSummary) → int

Access the job index on the originating node.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummary::jobindex_on_originating_node() const –> unsigned long

originating_mpi_node(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_PNearToArbitraryStateSummary) → int

Access the index of the originating MPI node.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummary::originating_mpi_node() const –> unsigned long

pnear(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_PNearToArbitraryStateSummary) → float

Access the PNear value.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummary::pnear() const –> double

class pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_RMSDToBestSummary

Bases: HierarchicalHybridJD_ResultsSummaryBase

A small helper class used by the HierarchicalHybridJDApplication class for transmitting RMSD information up the MPI hierarchy.

Vikram K. Mulligan (vmulligan.org)

MPI_ranks_handling_message(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase) → pyrosetta.rosetta.utility.vector1_int

Get the list of procs that transmitted this JobResultsSummary.

Whenever a proc sends it to someone else, the receiving proc appends the sender’s rank here. This allows the director node to address an output request to the correct proc.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::MPI_ranks_handling_message() const –> const class utility::vector1<int, class std::allocator<int> > &

add_MPI_rank_handling_message(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase, new_proc: int) → None

Add a proc that handled this message to the list of procs that transmitted this JobResultsSummary.

Whenever a proc sends it to someone else, the receiving proc appends the sender’s rank here. This allows the director node to address an output request to the correct proc.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::add_MPI_rank_handling_message(const int) –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_RMSDToBestSummary, : pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_RMSDToBestSummary) → pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_RMSDToBestSummary

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_RMSDToBestSummary::operator=(const class protocols::cyclic_peptide_predict::HierarchicalHybridJD_RMSDToBestSummary &) –> class protocols::cyclic_peptide_predict::HierarchicalHybridJD_RMSDToBestSummary &

clone(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_RMSDToBestSummary) → pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase

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

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_RMSDToBestSummary::clone() const –> class std::shared_ptr<class protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase>

jobindex_on_originating_node(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase) → int

Get the local index of the job on the node on which it was carried out.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::jobindex_on_originating_node() const –> unsigned long

originating_node_MPI_rank(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase) → int

Get the MPI rank of the process that initially carried out this job.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::originating_node_MPI_rank() const –> int

rmsd_to_best(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_RMSDToBestSummary) → float

Get the RMSD to the best structure.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_RMSDToBestSummary::rmsd_to_best() const –> const double &

set_jobindex_on_originating_node(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase, index: int) → None

Set the local index of the job on the node on which it was carried out.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::set_jobindex_on_originating_node(const unsigned long) –> void

set_originating_node_MPI_rank(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase, rank: int) → None

Set the MPI rank of the process that initially carried out this job.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::set_originating_node_MPI_rank(const int) –> void

set_rmsd_to_best(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_RMSDToBestSummary, setting: float) → None

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_RMSDToBestSummary::set_rmsd_to_best(const double &) –> void

class pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase

Bases: pybind11_object

A pure virtual base class for the helper classes used by the HierarchicalHybridJDApplication class for transmitting information up the MPI hierarchy.

Vikram K. Mulligan (vmulligan.org)

MPI_ranks_handling_message(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase) → pyrosetta.rosetta.utility.vector1_int

Get the list of procs that transmitted this JobResultsSummary.

Whenever a proc sends it to someone else, the receiving proc appends the sender’s rank here. This allows the director node to address an output request to the correct proc.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::MPI_ranks_handling_message() const –> const class utility::vector1<int, class std::allocator<int> > &

add_MPI_rank_handling_message(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase, new_proc: int) → None

Add a proc that handled this message to the list of procs that transmitted this JobResultsSummary.

Whenever a proc sends it to someone else, the receiving proc appends the sender’s rank here. This allows the director node to address an output request to the correct proc.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::add_MPI_rank_handling_message(const int) –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase, : pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase) → pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::operator=(const class protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase &) –> class protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase &

clone(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase) → pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase

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

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::clone() const –> class std::shared_ptr<class protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase>

jobindex_on_originating_node(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase) → int

Get the local index of the job on the node on which it was carried out.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::jobindex_on_originating_node() const –> unsigned long

originating_node_MPI_rank(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase) → int

Get the MPI rank of the process that initially carried out this job.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::originating_node_MPI_rank() const –> int

set_jobindex_on_originating_node(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase, index: int) → None

Set the local index of the job on the node on which it was carried out.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::set_jobindex_on_originating_node(const unsigned long) –> void

set_originating_node_MPI_rank(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase, rank: int) → None

Set the MPI rank of the process that initially carried out this job.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::set_originating_node_MPI_rank(const int) –> void

class pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary

Bases: HierarchicalHybridJD_ResultsSummaryBase

A class for storing information about solvent-exposed surface area and for transmitting it up the MPI hierarchy.

Vikram K. Mulligan (vmulligan.org)

MPI_ranks_handling_message(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase) → pyrosetta.rosetta.utility.vector1_int

Get the list of procs that transmitted this JobResultsSummary.

Whenever a proc sends it to someone else, the receiving proc appends the sender’s rank here. This allows the director node to address an output request to the correct proc.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::MPI_ranks_handling_message() const –> const class utility::vector1<int, class std::allocator<int> > &

add_MPI_rank_handling_message(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase, new_proc: int) → None

Add a proc that handled this message to the list of procs that transmitted this JobResultsSummary.

Whenever a proc sends it to someone else, the receiving proc appends the sender’s rank here. This allows the director node to address an output request to the correct proc.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::add_MPI_rank_handling_message(const int) –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary, : pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary) → pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummary::operator=(const class protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummary &) –> class protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummary &

clone(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary) → pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase

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

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummary::clone() const –> class std::shared_ptr<class protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase>

fraction_hydrophobic_sasa(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary) → float

Get the solvent-accessible hydrophobic surface area, as a fraction of the total surface area.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummary::fraction_hydrophobic_sasa() const –> const double &

fraction_polar_sasa(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary) → float

Get the solvent-accessible polar surface area, as a fraction of the total surface area.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummary::fraction_polar_sasa() const –> const double &

hydrophobic_sasa(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary) → float

Get the hydrophobic solvent-accessible surface area, in square Angstroms.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummary::hydrophobic_sasa() const –> const double &

jobindex_on_originating_node(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase) → int

Get the local index of the job on the node on which it was carried out.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::jobindex_on_originating_node() const –> unsigned long

originating_node_MPI_rank(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase) → int

Get the MPI rank of the process that initially carried out this job.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::originating_node_MPI_rank() const –> int

polar_sasa(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary) → float

Get the polar solvent-accessible surface area, in square Angstroms.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummary::polar_sasa() const –> const double &

sasa(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary) → float

Get the total solvent-accessible surface area, in square Angstroms.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummary::sasa() const –> const double &

set(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary, sasa: float, polar_sasa: float, hydrophobic_sasa: float) → None

Set total sasa, polar sasa, and hydrophobic sasa.

Computes fraction_polar_sasa_ and fraction_hydrophobic_sasa_.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummary::set(const double &, const double &, const double &) –> void

set_jobindex_on_originating_node(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase, index: int) → None

Set the local index of the job on the node on which it was carried out.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::set_jobindex_on_originating_node(const unsigned long) –> void

set_originating_node_MPI_rank(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase, rank: int) → None

Set the MPI rank of the process that initially carried out this job.

C++: protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase::set_originating_node_MPI_rank(const int) –> void

class pyrosetta.rosetta.protocols.cyclic_peptide_predict.PNearCalculator

Bases: pybind11_object

A class to compute P_Near and DG_folding.

Vikram K. Mulligan (vmulligan.org)

add_data_point(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.PNearCalculator, energy: float, rmsd: float) → None

Add a data point to the set used to compute PNear.

C++: protocols::cyclic_peptide_predict::PNearCalculator::add_data_point(const double, const double) –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.PNearCalculator, : pyrosetta.rosetta.protocols.cyclic_peptide_predict.PNearCalculator) → pyrosetta.rosetta.protocols.cyclic_peptide_predict.PNearCalculator

C++: protocols::cyclic_peptide_predict::PNearCalculator::operator=(const class protocols::cyclic_peptide_predict::PNearCalculator &) –> class protocols::cyclic_peptide_predict::PNearCalculator &

clone(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.PNearCalculator) → pyrosetta.rosetta.protocols.cyclic_peptide_predict.PNearCalculator

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

C++: protocols::cyclic_peptide_predict::PNearCalculator::clone() const –> class std::shared_ptr<class protocols::cyclic_peptide_predict::PNearCalculator>

compute_pnear_and_dgfolding(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.PNearCalculator, pnear: float, Keq: float, dgfolding: float) → None

Compute PNear and DeltaG_folding given the data points that have been

added previously using add_data_point().

The pnear, Keq, and dgfolding values are overwritten by this operation. (These are the outputs.)

C++: protocols::cyclic_peptide_predict::PNearCalculator::compute_pnear_and_dgfolding(double &, double &, double &) const –> void

class pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type

Bases: pybind11_object

An enum for the cyclization type.

If additional values are added, please add them to the SimpleCycpepPredictApplication::get_cyclization_name_from_type() function.

Members:

SCPA_n_to_c_amide_bond

SCPA_terminal_disulfide

SCPA_thioether_lariat

SCPA_nterm_isopeptide_lariat

SCPA_cterm_isopeptide_lariat

SCPA_sidechain_isopeptide

SCPA_invalid_type

SCPA_number_of_types

SCPA_cterm_isopeptide_lariat = <SCPA_cyclization_type.SCPA_cterm_isopeptide_lariat: 5>

SCPA_invalid_type = <SCPA_cyclization_type.SCPA_invalid_type: 7>

SCPA_n_to_c_amide_bond = <SCPA_cyclization_type.SCPA_n_to_c_amide_bond: 1>

SCPA_nterm_isopeptide_lariat = <SCPA_cyclization_type.SCPA_nterm_isopeptide_lariat: 4>

SCPA_number_of_types = <SCPA_cyclization_type.SCPA_invalid_type: 7>

SCPA_sidechain_isopeptide = <SCPA_cyclization_type.SCPA_sidechain_isopeptide: 6>

SCPA_terminal_disulfide = <SCPA_cyclization_type.SCPA_terminal_disulfide: 2>

SCPA_thioether_lariat = <SCPA_cyclization_type.SCPA_thioether_lariat: 3>

property name

property value

class pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication

Bases: pybind11_object

Application-level code for simple_cycpep_predict application.

Also called by the BOINC minirosetta app.

Vikram K. Mulligan, Baker laboratory (vmullig.edu)

add_entry_to_octahedral_metal_positions(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, res1: int, res2: int, res3: int, res4: int, res5: int, res6: int, metal_type: str) → None

Adds an entry to the octahedral_metal_positions_ vector.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_entry_to_octahedral_metal_positions(const unsigned long, const unsigned long, const unsigned long, const unsigned long, const unsigned long, const unsigned long, const std::string &) –> void

add_entry_to_square_planar_metal_positions(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, res1: int, res2: int, res3: int, res4: int, metal_type: str) → None

Adds an entry to the square_planar_metal_positions_ vector.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_entry_to_square_planar_metal_positions(const unsigned long, const unsigned long, const unsigned long, const unsigned long, const std::string &) –> void

add_entry_to_square_pyramidal_metal_positions(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, res1: int, res2: int, res3: int, res4: int, res5: int, metal_type: str) → None

Adds an entry to the square_pyramidal_metal_positions_ vector.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_entry_to_square_pyramidal_metal_positions(const unsigned long, const unsigned long, const unsigned long, const unsigned long, const unsigned long, const std::string &) –> void

add_entry_to_tetrahedral_metal_positions(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, res1: int, res2: int, res3: int, res4: int, metal_type: str) → None

Adds an entry to the tetrahedral_metal_positions_ vector.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_entry_to_tetrahedral_metal_positions(const unsigned long, const unsigned long, const unsigned long, const unsigned long, const std::string &) –> void

add_entry_to_trigonal_planar_metal_positions(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, res1: int, res2: int, res3: int, metal_type: str) → None

Adds an entry to the trigonal_planar_metal_positions_ vector.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_entry_to_trigonal_planar_metal_positions(const unsigned long, const unsigned long, const unsigned long, const std::string &) –> void

add_entry_to_trigonal_pyramidal_metal_positions(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, res1: int, res2: int, res3: int, metal_type: str) → None

Adds an entry to the trigonal_pyramidal_metal_positions_ vector.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_entry_to_trigonal_pyramidal_metal_positions(const unsigned long, const unsigned long, const unsigned long, const std::string &) –> void

align_and_calculate_rmsd(*args, **kwargs)

Overloaded function.

1. align_and_calculate_rmsd(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose) -> float

2. align_and_calculate_rmsd(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, skip_seq_comparison: bool) -> float

Align pose to native_pose, and return the RMSD between the two poses.

Assumes that the pose has already been de-permuted (i.e. the native and the pose line up). Only uses alpha-amino acids for the alignment, currently.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::align_and_calculate_rmsd(class core::pose::Pose &, const class core::pose::Pose &, const bool) const –> double

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, : pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) → pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::operator=(const class protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication &) –> class protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication &

disable_cis_pro_sampling(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) → None

Set cis proline sampling OFF.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::disable_cis_pro_sampling() –> void

disable_total_energy_cutoff(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) → None

Sets use_total_energy_cutoff_ to ‘false’.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::disable_total_energy_cutoff() –> void

static get_cyclization_name_from_type(type: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type) → str

Given a cyclization name string, return its type enum.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_cyclization_name_from_type(const enum protocols::cyclic_peptide_predict::SCPA_cyclization_type) –> std::string

static get_cyclization_type_from_name(name: str) → pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type

Given a cyclization type enum, return its name string.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_cyclization_type_from_name(const std::string &) –> enum protocols::cyclic_peptide_predict::SCPA_cyclization_type

initialize_from_options(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) → None

Initialize the application.

Initializes using the option system.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::initialize_from_options() –> void

static register_options() → None

Register the set of options that this application uses (for the help menu).

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::register_options() –> void

reset_octahedral_metal_positions(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) → None

Resets the octahedral_metal_positions_ vector.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::reset_octahedral_metal_positions() –> void

reset_square_planar_metal_positions(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) → None

Resets the square_planar_metal_positions_ vector.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::reset_square_planar_metal_positions() –> void

reset_square_pyramidal_metal_positions(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) → None

Resets the square_pyramidal_metal_positions_ vector.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::reset_square_pyramidal_metal_positions() –> void

reset_tetrahedral_metal_positions(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) → None

Resets the tetrahedral_metal_positions_ vector.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::reset_tetrahedral_metal_positions() –> void

reset_trigonal_planar_metal_positions(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) → None

Resets the trigonal_planar_metal_positions_ vector.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::reset_trigonal_planar_metal_positions() –> void

reset_trigonal_pyramidal_metal_positions(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) → None

Resets the trigonal_pyramidal_metal_positions_ vector.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::reset_trigonal_pyramidal_metal_positions() –> void

run(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) → None

Actually run the application.

The initialize_from_options() function must be called before calling this. (Called by default constructor.)

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::run() const –> void

set_D_alpha_compfile_contents(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, contents_in: str) → None

Allows external code to set the file contents for the D-alpha aa_composition file.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_D_alpha_compfile_contents(const std::string &) –> void

set_D_beta_compfile_contents(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, contents_in: str) → None

Allows external code to set the file contents for the D-beta aa_composition file.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_D_beta_compfile_contents(const std::string &) –> void

set_L_alpha_compfile_contents(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, contents_in: str) → None

Allows external code to set the file contents for the L-alpha aa_composition file.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_L_alpha_compfile_contents(const std::string &) –> void

set_L_beta_compfile_contents(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, contents_in: str) → None

Allows external code to set the file contents for the L-beta aa_composition file.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_L_beta_compfile_contents(const std::string &) –> void

set_abba_bins_binfile(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, binfile_in: str) → None

Set the bin transitions file.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_abba_bins_binfile(const std::string &) –> void

set_allowed_residues_by_position(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, allowed_canonicals: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t, allowed_noncanonicals: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t) → None

Allows external code to set the allowed residues by position, so that this needn’t be read directly

from disk.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_allowed_residues_by_position(const class std::map<unsigned long, class utility::vector1<std::string, class std::allocator<std::string > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<std::string, class std::allocator<std::string > > > > > &, const class std::map<unsigned long, class utility::vector1<std::string, class std::allocator<std::string > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<std::string, class std::allocator<std::string > > > > > &) –> void

set_already_completed_job_count(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, count_in: int) → None

Set the number of jobs that this process has already completed.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_already_completed_job_count(const unsigned long) –> void

set_angle_length_relax_rounds(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, rounds_in: int) → None

Set the number of rounds of relaxation with flexible

bond angles and bond lengths.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_angle_length_relax_rounds(const unsigned long) –> void

set_angle_relax_rounds(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, rounds_in: int) → None

Set the number of rounds of relaxation with flexible

bond angles.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_angle_relax_rounds(const unsigned long) –> void

set_cartesian_relax_rounds(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, rounds_in: int) → None

Set the number of rounds of Cartesian relaxation.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_cartesian_relax_rounds(const unsigned long) –> void

set_cyclization_type(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, type_in: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type) → None

Set the cyclization type.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_cyclization_type(const enum protocols::cyclic_peptide_predict::SCPA_cyclization_type) –> void

set_my_rank(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, rank_in: int) → None

If called by MPI code, the rank of the current process can be stored here.

Used for output of job summaries.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_my_rank(const int) –> void

set_native(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, native: pyrosetta.rosetta.core.pose.Pose) → None

Allows external code to provide a native, so that the SimpleCycpepPredictApplication doesn’t have to read

directly from disk.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_native(class std::shared_ptr<const class core::pose::Pose>) –> void

set_nstruct(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, nstruct_in: int) → None

Allows external code to override the number of structures that this should generate (otherwise

set by options system.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_nstruct(const unsigned long) –> void

set_octahedral_metal_positions_from_string_vector(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, vect: pyrosetta.rosetta.utility.vector1_std_string) → None

Given an input vector of strings of the form “res1,res2,res3,res4,metal_name”, parse this and populate

the octahedral_metal_positions_ vector.

Resets the octahedral_metal_positions_ vector.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_octahedral_metal_positions_from_string_vector(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_sample_cis_pro_frequency(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, freq_in: float) → None

Set the frequency with which we sample cis proline.

Implicitly sets sample_cis_pro_ to “true” if freq_in is not 0.0, “false” if it is.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_sample_cis_pro_frequency(const double &) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, sfxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Sets the default scorefunction to use.

The scorefunction is cloned. The high-hbond version is constructed from this one. If necessary, the aa_composition score term will be turned on in that one; it needn’t be turned on in this one.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

set_sequence(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, seq: str) → None

Allows external code to provide a sequence, so that the SimpleCycpepPredictApplication doesn’t have to read

directly from disk.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_sequence(const std::string &) –> void

set_square_planar_metal_positions_from_string_vector(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, vect: pyrosetta.rosetta.utility.vector1_std_string) → None

Given an input vector of strings of the form “res1,res2,res3,res4,metal_name”, parse this and populate

the square_pyramidal_metal_positions_ vector.

Resets the square_pyramidal_metal_positions_ vector.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_square_planar_metal_positions_from_string_vector(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_square_pyramidal_metal_positions_from_string_vector(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, vect: pyrosetta.rosetta.utility.vector1_std_string) → None

Given an input vector of strings of the form “res1,res2,res3,res4,res5,metal_name”, parse this and populate

the square_pyramidal_metal_positions_ vector.

Resets the square_pyramidal_metal_positions_ vector.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_square_pyramidal_metal_positions_from_string_vector(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_suppress_checkpoints(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, suppress_checkpoints: bool) → None

Allows external code to suppress checkpointing, to prevent direct file I/O from disk.

Useful on Blue Gene.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_suppress_checkpoints(const bool) –> void

set_tetrahedral_metal_positions_from_string_vector(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, vect: pyrosetta.rosetta.utility.vector1_std_string) → None

Given an input vector of strings of the form “res1,res2,res3,res4,metal_name”, parse this and populate

the tetrahedral_metal_positions_ vector.

Resets the tetrahedral_metal_positions_ vector.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_tetrahedral_metal_positions_from_string_vector(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_total_energy_cutoff(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, value_in: float) → None

Set the total energy cutoff.

Also sets use_total_energy_cutoff_ to ‘true’.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_total_energy_cutoff(const double &) –> void

set_trigonal_planar_metal_positions_from_string_vector(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, vect: pyrosetta.rosetta.utility.vector1_std_string) → None

Given an input vector of strings of the form “res1,res2,res3,metal_name”, parse this and populate

the trigonal_planar_metal_positions_ vector.

Resets the trigonal_planar_metal_positions_ vector.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_trigonal_planar_metal_positions_from_string_vector(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_trigonal_pyramidal_metal_positions_from_string_vector(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, vect: pyrosetta.rosetta.utility.vector1_std_string) → None

Given an input vector of strings of the form “res1,res2,res3,metal_name”, parse this and populate

the trigonal_pyramidal_metal_positions_ vector.

Resets the trigonal_pyramidal_metal_positions_ vector.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_trigonal_pyramidal_metal_positions_from_string_vector(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_use_chainbreak_energy(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, setting: bool) → None

Set whether we should use the chainbreak energy (true) or constraints (false) to enforce

terminal amide bond geometry.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_use_chainbreak_energy(const bool) –> void

set_use_rama_prepro_for_sampling(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, setting: bool) → None

Set whether we’re using RamaPrePro tables for sampling.

Setting this to “false” lets us use classic rama tables. True by default.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_use_rama_prepro_for_sampling(const bool) –> void

pyrosetta.rosetta.protocols.cyclic_peptide_predict.is_canonical(resname: str) → bool

Given a residue name, return true if this is one of the 20

canonical amino acids, false otherwise.

C++: protocols::cyclic_peptide_predict::is_canonical(const std::string &) –> bool

pyrosetta.rosetta.protocols.cyclic_peptide_predict.read_file_into_string(output_string: str, filename: str, from_database: bool) → None

Given an ASCII file name, read the contents into a string. If from_database is true, the read is from the database.

The string that will be filled with the file contents. Overwritten by this operation.

The name of the file to read. If from_database is true, this is a relative database path.

If true, the file is assumed to be in the database. If false, the path is relative the execution directory, or is absolute.

C++: protocols::cyclic_peptide_predict::read_file_into_string(std::string &, const std::string &, const bool) –> void

pyrosetta.rosetta.protocols.cyclic_peptide_predict.read_peptide_design_file(filename: str, allowed_canonicals_by_position: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t, allowed_noncanonicals_by_position: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t) → None

Given a filename, read and parse the file, returning a list of canonical residues allowed at each position

and a list of noncanonicals allowed at each position.

This does the actual file read. It is NOT THREADSAFE. The file format is a series of lines with the pattern: residue_index residuetype_1_fullname residuetype_2_fullname residuetype_3_fullname … Anything after a pound sign should be ignored. A line with DEFAULT in place of the resiude index should be interpreted as providing default values, which should be stored as map key 0.

The file name from which we’ll read.

A map of [position->vector of strings of full names] listing the allowed canonical residue types at each position. Reset and populated by this function. Key 0 indicates default settings applied anywhere that lacks a map key.

A map of [position->vector of strings of full names] listing the allowed noncanonical residue types at each position. Reset and populated by this function. Key 0 indicates default settings applied anywhere that lacks a map key.

C++: protocols::cyclic_peptide_predict::read_peptide_design_file(const std::string &, class std::map<unsigned long, class utility::vector1<std::string, class std::allocator<std::string > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<std::string, class std::allocator<std::string > > > > > &, class std::map<unsigned long, class utility::vector1<std::string, class std::allocator<std::string > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<std::string, class std::allocator<std::string > > > > > &) –> void

pyrosetta.rosetta.protocols.cyclic_peptide_predict.register_with_citation_manager() → None

Registers the simple_cycpep_predict application with the CitationManager.

Cites Bhardwaj et al. 2016, Hosseinzadeh et al. 2017, Mulligan et al. 2021.

C++: protocols::cyclic_peptide_predict::register_with_citation_manager() –> void