denovo_design

• architects
• components
• connection
• constraints
• filters
• movers
• residue_selectors
• task_operations

Bindings for protocols::denovo_design namespace

pyrosetta.rosetta.protocols.denovo_design.abego_str(abego: pyrosetta.rosetta.utility.vector1_std_string) → str

C++: protocols::denovo_design::abego_str(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> std::string

pyrosetta.rosetta.protocols.denovo_design.abego_vector(ab: str) → pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::denovo_design::abego_vector(const class std::basic_string<char> &) –> class utility::vector1<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.protocols.denovo_design.add_chain_from_pose(to_add: pyrosetta.rosetta.core.pose.Pose, combined: pyrosetta.rosetta.core.pose.Pose) → None

dumps a pose into another pose as a new chain

C++: protocols::denovo_design::add_chain_from_pose(class std::shared_ptr<const class core::pose::Pose>, class std::shared_ptr<class core::pose::Pose>) –> void

pyrosetta.rosetta.protocols.denovo_design.add_cutpoints(pose: pyrosetta.rosetta.core.pose.Pose, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) → None

C++: protocols::denovo_design::add_cutpoints(class core::pose::Pose &, const class protocols::denovo_design::components::StructureData &) –> void

pyrosetta.rosetta.protocols.denovo_design.add_remark(remarks: pyrosetta.rosetta.core.io.Remarks, num: int, str_val: str) → None

adds a remark to a Remarks object, splitting it into multiple remarks if it is too long

C++: protocols::denovo_design::add_remark(class core::io::Remarks &, const unsigned long, const class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.denovo_design.add_residues_to_pose(pose: pyrosetta.rosetta.core.pose.Pose, template_pose: pyrosetta.rosetta.core.pose.Pose, new_chain: bool) → None

adds residues from template_pose to pose. If new_chain == true, creates covalent bond

C++: protocols::denovo_design::add_residues_to_pose(class core::pose::Pose &, const class core::pose::Pose &, const bool) –> void

pyrosetta.rosetta.protocols.denovo_design.construct_dummy_pose(*args, **kwargs)

Overloaded function.

1. construct_dummy_pose(restype_name: str) -> pyrosetta.rosetta.core.pose.Pose

builds an extended-conformation poly-XXX pose

C++: protocols::denovo_design::construct_dummy_pose(const class std::basic_string<char> &) –> class std::shared_ptr<class core::pose::Pose>

2. construct_dummy_pose(restype_name: str, length: int) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::denovo_design::construct_dummy_pose(const class std::basic_string<char> &, const unsigned long) –> class std::shared_ptr<class core::pose::Pose>

3. construct_dummy_pose(restype: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::denovo_design::construct_dummy_pose(const class core::chemical::ResidueType &) –> class std::shared_ptr<class core::pose::Pose>

4. construct_dummy_pose(restype: pyrosetta.rosetta.core.chemical.ResidueType, length: int) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::denovo_design::construct_dummy_pose(const class core::chemical::ResidueType &, const unsigned long) –> class std::shared_ptr<class core::pose::Pose>

pyrosetta.rosetta.protocols.denovo_design.construct_poly_ala_pose(*args, **kwargs)

Overloaded function.

1. construct_poly_ala_pose(pose: pyrosetta.rosetta.core.pose.Pose, keep_disulf: bool, set1: pyrosetta.rosetta.utility.vector1_bool, set2: pyrosetta.rosetta.utility.vector1_bool) -> None
2. construct_poly_ala_pose(pose: pyrosetta.rosetta.core.pose.Pose, keep_disulf: bool, set1: pyrosetta.rosetta.utility.vector1_bool, set2: pyrosetta.rosetta.utility.vector1_bool, keep_chirality: bool) -> None

creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine

If keep_chirality is true, the D-amino acids are mutated to D-alanine.

C++: protocols::denovo_design::construct_poly_ala_pose(class core::pose::Pose &, const bool, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &, const bool) –> void

3. construct_poly_ala_pose(pose: pyrosetta.rosetta.core.pose.Pose, keep_disulf: bool, res_set: pyrosetta.rosetta.std.set_unsigned_long_t) -> None
4. construct_poly_ala_pose(pose: pyrosetta.rosetta.core.pose.Pose, keep_disulf: bool, res_set: pyrosetta.rosetta.std.set_unsigned_long_t, keep_chirality: bool) -> None

creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine

If keep_chirality is true, the D-amino acids are mutated to D-alanine.

C++: protocols::denovo_design::construct_poly_ala_pose(class core::pose::Pose &, const bool, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, const bool) –> void

pyrosetta.rosetta.protocols.denovo_design.count_bulges(perm: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment: str) → int

counts the beta-bulges in the given segment. This simply counts all abego A’s in the segment

C++: protocols::denovo_design::count_bulges(const class protocols::denovo_design::components::StructureData &, const class std::basic_string<char> &) –> unsigned long

pyrosetta.rosetta.protocols.denovo_design.extract_int(num: float, m: int, n: int) → int

given a number 0 <= x < 1, calculate an integer M <= x <= N

NOTE THAT THIS FUNCTION MODIFIES THE PARAMETER

C++: protocols::denovo_design::extract_int(double &, const unsigned long, const unsigned long) –> unsigned long

pyrosetta.rosetta.protocols.denovo_design.find_jump_rec(ft: pyrosetta.rosetta.core.kinematics.FoldTree, residue: int) → int

helper function that looks for the given residue in a fold tree and returns the jump that controls its 6D-DoFs

C++: protocols::denovo_design::find_jump_rec(const class core::kinematics::FoldTree &, const unsigned long) –> int

pyrosetta.rosetta.protocols.denovo_design.get_remark_line(it_rem: __gnu_cxx::__normal_iterator<core::io::RemarkInfo const*, std::vector<core::io::RemarkInfo, std::allocator<core::io::RemarkInfo> > >, end: __gnu_cxx::__normal_iterator<core::io::RemarkInfo const*, std::vector<core::io::RemarkInfo, std::allocator<core::io::RemarkInfo> > >) → str

C++: protocols::denovo_design::get_remark_line(class __gnu_cxx::__normal_iterator<const class core::io::RemarkInfo *, class std::vector<class core::io::RemarkInfo, class std::allocator<class core::io::RemarkInfo> > > &, const class __gnu_cxx::__normal_iterator<const class core::io::RemarkInfo *, class std::vector<class core::io::RemarkInfo, class std::allocator<class core::io::RemarkInfo> > > &) –> std::string

pyrosetta.rosetta.protocols.denovo_design.get_resid(sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, resid_str: str) → int

C++: protocols::denovo_design::get_resid(const class protocols::denovo_design::components::StructureData &, const class std::basic_string<char> &) –> unsigned long

pyrosetta.rosetta.protocols.denovo_design.get_residue_selector(data: pyrosetta.rosetta.basic.datacache.DataMap, name: str) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: protocols::denovo_design::get_residue_selector(const class basic::datacache::DataMap &, const class std::basic_string<char> &) –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

pyrosetta.rosetta.protocols.denovo_design.insert_peptide_edges(ft: pyrosetta.rosetta.core.kinematics.FoldTree, jedge: pyrosetta.rosetta.core.kinematics.Edge) → None

inserts the peptide edges to accomodate the new jump edge given

C++: protocols::denovo_design::insert_peptide_edges(class core::kinematics::FoldTree &, const class core::kinematics::Edge &) –> void

pyrosetta.rosetta.protocols.denovo_design.linear_chainbreak(pose: pyrosetta.rosetta.core.pose.Pose, pos: int) → float

evaluate linear chainbreak at a position

If necessary, will evaluate using a copy of the Pose with a cut

fold tree. If cutpoint variants are present at chainbreak, will use existing variants and not modify them. If cutpoint variants are not found will add them and then remove them once calculation is finished. Eventually this should be merged into protocols/forge/methods/linear_chainbreak.cc However, the changes I needed to make to that file break certain parts of remodel

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

pyrosetta.rosetta.protocols.denovo_design.loop_start_without_overlap(pose: pyrosetta.rosetta.core.pose.Pose, startres: int, overlap: int) → int

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

pyrosetta.rosetta.protocols.denovo_design.loop_stop_without_overlap(pose: pyrosetta.rosetta.core.pose.Pose, stopres: int, overlap: int) → int

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

pyrosetta.rosetta.protocols.denovo_design.parse_length_string(len_str: str) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::denovo_design::parse_length_string(const class std::basic_string<char> &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.denovo_design.parse_motif_string(motif_str: str, secstruct: str, abego: str) → None

Computes secondary structure string from the given motifs

Motif string to be parsed (e.g. “5EB-2LG-5EB”)

Secondary structure string to be cleared and filled

ABEGO string to be cleared and filled

C++: protocols::denovo_design::parse_motif_string(const class std::basic_string<char> &, class std::basic_string<char> &, class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.denovo_design.rebuild_missing_atoms(pose: pyrosetta.rosetta.core.pose.Pose, resi: int) → None

given a residue, rebuilds all missing atoms

C++: protocols::denovo_design::rebuild_missing_atoms(class core::pose::Pose &, const unsigned long) –> void

pyrosetta.rosetta.protocols.denovo_design.remove_all_jump_atoms(orig: pyrosetta.rosetta.core.kinematics.FoldTree) → pyrosetta.rosetta.core.kinematics.FoldTree

C++: protocols::denovo_design::remove_all_jump_atoms(const class core::kinematics::FoldTree &) –> class core::kinematics::FoldTree

pyrosetta.rosetta.protocols.denovo_design.remove_missing_jump_atoms(pose: pyrosetta.rosetta.core.pose.Pose, orig: pyrosetta.rosetta.core.kinematics.FoldTree) → pyrosetta.rosetta.core.kinematics.FoldTree

C++: protocols::denovo_design::remove_missing_jump_atoms(const class core::pose::Pose &, const class core::kinematics::FoldTree &) –> class core::kinematics::FoldTree

pyrosetta.rosetta.protocols.denovo_design.same_pose(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) → bool

Tells whether the two given poses are identical based on # resides and dihedrals

C++: protocols::denovo_design::same_pose(const class core::pose::Pose &, const class core::pose::Pose &) –> bool

pyrosetta.rosetta.protocols.denovo_design.slide_jump(ft_orig: pyrosetta.rosetta.core.kinematics.FoldTree, jump_idx: int, new_start: int, new_stop: int) → pyrosetta.rosetta.core.kinematics.FoldTree

C++: protocols::denovo_design::slide_jump(const class core::kinematics::FoldTree &, const unsigned long, const unsigned long, const unsigned long) –> class core::kinematics::FoldTree

pyrosetta.rosetta.protocols.denovo_design.symmetric_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose, asymm_ft: pyrosetta.rosetta.core.kinematics.FoldTree) → pyrosetta.rosetta.core.kinematics.FoldTree

Given a symmetric pose, and a fold tree for the asymmetric unit, constructs and

returns a symmetric fold tree while preserving the topology of the aysmmetric unit’s fold tree

C++: protocols::denovo_design::symmetric_fold_tree(const class core::pose::Pose &, const class core::kinematics::FoldTree &) –> class core::kinematics::FoldTree

pyrosetta.rosetta.protocols.denovo_design.symmetric_residue_subset(pose: pyrosetta.rosetta.core.pose.Pose, subset: pyrosetta.rosetta.utility.vector1_bool) → pyrosetta.rosetta.utility.vector1_bool

Given a symmetric pose and a ResidueSubset for the asymmetric unit, constructs

and returns a residue subset compatible with the symmetric pose based on the given asymmetric unit residue subset

C++: protocols::denovo_design::symmetric_residue_subset(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) –> class utility::vector1<bool, class std::allocator<bool> >

pyrosetta.rosetta.protocols.denovo_design.symmetric_secstruct(pose: pyrosetta.rosetta.core.pose.Pose, asymm_secstruct: str) → str

Given a symmetric pose and a secstruct for the asymmetric unit, constructs and

returns a secondary structure string compatible with the symmetric pose based on the secondary structure of the asymmetric unit

C++: protocols::denovo_design::symmetric_secstruct(const class core::pose::Pose &, const class std::basic_string<char> &) –> std::string