utils

Bindings for protocols::fold_from_loops::utils namespace

pyrosetta.rosetta.protocols.fold_from_loops.utils.append_pose_to_pose_keep_fold_tree(scaffold: pyrosetta.rosetta.core.pose.Pose, insert: pyrosetta.rosetta.core.pose.Pose, new_chain: bool) → None

Basically works as ‘core::pose::append_pose_to_pose’ but the FoldTree is build by joining by jump the

root of ‘insert’ FoldTree to that of ‘scaffold’ FoldTree. PDBInfo is lost.

C++: protocols::fold_from_loops::utils::append_pose_to_pose_keep_fold_tree(class core::pose::Pose &, const class core::pose::Pose &, bool) –> void

pyrosetta.rosetta.protocols.fold_from_loops.utils.attach_n_and_c_unfolded_poses_to_pose(n_insert: pyrosetta.rosetta.core.pose.Pose, scaffold: pyrosetta.rosetta.core.pose.Pose, c_insert: pyrosetta.rosetta.core.pose.Pose) → None

To a given scaffold it attaches a unfolded version of a pose to the N-terminal and another to the C-terminal

Generates a FoldTree that goes from the middle of ‘scaffold’ towards both directions

C++: protocols::fold_from_loops::utils::attach_n_and_c_unfolded_poses_to_pose(const class core::pose::Pose &, class core::pose::Pose &, const class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.fold_from_loops.utils.attach_unfolded_pose_to_pose_c_term(insert: pyrosetta.rosetta.core.pose.Pose, scaffold: pyrosetta.rosetta.core.pose.Pose, rsd_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → None

adds the ‘insert’ unfolded pose to the C-terminal of the provided pose

C++: protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_c_term(const class core::pose::Pose &, class core::pose::Pose &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>) –> void

pyrosetta.rosetta.protocols.fold_from_loops.utils.attach_unfolded_pose_to_pose_n_term(insert: pyrosetta.rosetta.core.pose.Pose, scaffold: pyrosetta.rosetta.core.pose.Pose, rsd_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → None

adds the ‘insert’ unfolded pose to the N-terminal of the provided pose

C++: protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_n_term(const class core::pose::Pose &, class core::pose::Pose &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>) –> void

pyrosetta.rosetta.protocols.fold_from_loops.utils.find_cutpoint_from_secondary_structure(structure: str) → int

Given a Secondary Structure definition as a string, it finds what

it considers the optimal cutpoint. This means that, if there is no loop ‘L’ segment it will return the middle point as a residue; otherwise it will try to split the larger loop ‘L’ region.

C++: protocols::fold_from_loops::utils::find_cutpoint_from_secondary_structure(class std::basic_string<char>) –> unsigned long

pyrosetta.rosetta.protocols.fold_from_loops.utils.map_by_residue_subsets(p1: pyrosetta.rosetta.core.pose.Pose, r1: pyrosetta.rosetta.utility.vector1_bool, p2: pyrosetta.rosetta.core.pose.Pose, r2: pyrosetta.rosetta.utility.vector1_bool) → pyrosetta.rosetta.core.id.SequenceMapping

Creates a sequence mapping betwee two proteins assuming that the False selections on a ResidueSubset

marks the residues that are the same for both of them. Assumes the same number of non-selected patches for each pose.

C++: protocols::fold_from_loops::utils::map_by_residue_subsets(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) –> class core::id::SequenceMapping

pyrosetta.rosetta.protocols.fold_from_loops.utils.report_unfolded(pose: pyrosetta.rosetta.core.pose.Pose, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None

@ brief reports the conditions of the pose

C++: protocols::fold_from_loops::utils::report_unfolded(const class core::pose::Pose &, class std::shared_ptr<class core::kinematics::MoveMap>) –> void

pyrosetta.rosetta.protocols.fold_from_loops.utils.split_mid_ranges(structure: str, ranges: pyrosetta.rosetta.core.select.residue_selector.ResidueRanges) → pyrosetta.rosetta.core.select.residue_selector.ResidueRanges

It will take each range that is not the first or the last one

and split it into two, following the logic of `find_cutpoint_from_secondary_structure` Input Ranges are not modified, a new ResidueRanges is returned. WARNING1: When splitting a range of 1 residue, it splits into 1 range of 1 and another from 0 to 0, so that it is easy to filter afterwards ( for the purpose of NubInitio, this means adding and empty pose to the vector, for example ). WARNING2: If the first ResidueRange does not start with 1, an empty_range (0,0) is set at the begining too.

C++: protocols::fold_from_loops::utils::split_mid_ranges(class std::basic_string<char>, const class core::select::residue_selector::ResidueRanges &) –> class core::select::residue_selector::ResidueRanges