pose_manipulation

Bindings for protocols::toolbox::pose_manipulation namespace

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.add_chainbreaks_according_to_jumps(pose: pyrosetta.rosetta.core.pose.Pose) → None

Florian Richter( floric.washington.edu), nov 11

adds chainbreak residue types depending on fold tree jumps

C++: protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.construct_poly_XXX_pose(*args, **kwargs)

Overloaded function.

1. construct_poly_XXX_pose(aa: str, pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long, keep_pro: bool, keep_gly: bool, keep_disulfide_cys: bool) -> None

Nobuyasu Koga ( nobuyasu.edu ), Oct 09

puts in XXX residues at the positions specified in the ‘positions’ input array

C++: protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(const class std::basic_string<char> &, class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool, bool, bool) –> void

2. construct_poly_XXX_pose(aa: str, pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long, restype_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, keep_pro: bool, keep_gly: bool, keep_disulfide_cys: bool) -> None

Nobuyasu Koga ( nobuyasu.edu ), Oct 09; Tom Linsky (tlinsky.edu), Nov 2014

puts in XXX residues at the positions from the given residue typeset specified in the ‘positions’ input array

C++: protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(const class std::basic_string<char> &, class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>, bool, bool, bool) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.construct_poly_ala_pose(pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long, keep_pro: bool, keep_gly: bool, keep_disulfide_cys: bool) → None

Florian Richter( floric.washington.edu) , june 08

puts in ala residues at the positions specified in the ‘positions’ input array

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

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.construct_poly_beta_ala_pose(pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long, keep_pro: bool, keep_gly: bool, keep_disulfide_cys: bool) → None

Vikram K. Mulligan (vmullig.edu)

puts in beta-3-ala residues at the positions specified in the ‘positions’ input array.

C++: protocols::toolbox::pose_manipulation::construct_poly_beta_ala_pose(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool, const bool, const bool) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.construct_poly_d_ala_pose(pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long, keep_pro: bool, keep_gly: bool, keep_disulfide_cys: bool) → None

Vikram K. Mulligan (vmullig.edu)

puts in D-ala residues at the positions specified in the ‘positions’ input array

C++: protocols::toolbox::pose_manipulation::construct_poly_d_ala_pose(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool, const bool, const bool) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.construct_poly_d_beta_ala_pose(pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long, keep_pro: bool, keep_gly: bool, keep_disulfide_cys: bool) → None

Vikram K. Mulligan (vmullig.edu)

puts in D-beta-3-ala residues at the positions specified in the ‘positions’ input array

C++: protocols::toolbox::pose_manipulation::construct_poly_d_beta_ala_pose(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool, const bool, const bool) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.construct_poly_uniq_restype_pose(pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long, restype: pyrosetta.rosetta.core.chemical.ResidueType, keep_pro: bool, keep_gly: bool, keep_disulfide_cys: bool) → None

Possu Huang ( possu.edu)

allows construction of a polymer of any residue type

C++: protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::chemical::ResidueType &, const bool, const bool, const bool) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.remove_chainbreaks_according_to_jumps(pose: pyrosetta.rosetta.core.pose.Pose) → None

Florian Richter( floric.washington.edu), nov 11

removes chainbreak residue types depending on fold tree jumps

C++: protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.remove_non_protein_residues(pose: pyrosetta.rosetta.core.pose.Pose) → None

Florian Richter( floric.washington.edu) , aug 08

deletes all nonprotein residues from a pose

C++: protocols::toolbox::pose_manipulation::remove_non_protein_residues(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.superimpose_pose_on_subset_CA(*args, **kwargs)

Overloaded function.

1. superimpose_pose_on_subset_CA(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long) -> float
2. superimpose_pose_on_subset_CA(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long, offset: int) -> float

Florian Richter( floric.washington.edu) , sep 08

superimposes one pose onto the other at the positions specified and

with the offset specified

C++: protocols::toolbox::pose_manipulation::superimpose_pose_on_subset_CA(class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const int) –> double