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- align_virtual_atoms_in_carbohydrate_residue(...) method of builtins.PyCapsule instance
- align_virtual_atoms_in_carbohydrate_residue(*args, **kwargs)
Overloaded function.
1. align_virtual_atoms_in_carbohydrate_residue(conf : rosetta.core.conformation.Conformation, sequence_position : int) -> NoneType
Set coordinates of virtual atoms (used as angle reference points) within a saccharide residue of the given
conformation.
2. align_virtual_atoms_in_carbohydrate_residue(pose : rosetta.core.pose.Pose, sequence_position : int) -> NoneType
Set coordinates of virtual atoms (used as angle reference points) within a saccharide residue of the given
pose.
- delete_carbohydrate_branch(...) method of builtins.PyCapsule instance
- delete_carbohydrate_branch(pose : rosetta.core.pose.Pose, delete_to : int) -> NoneType
Delete the glycan from this residue onward toward the end of the branch. Like chopping off a tree trunk at position resnum (not including the resnum). Also known as defoliating.
If resnum is the protein branch point, will change variant.
- delete_leaf(...) method of builtins.PyCapsule instance
- delete_leaf(*args, **kwargs)
Overloaded function.
1. delete_leaf(pose : rosetta.core.pose.Pose, leaf : rosetta.utility.vector1_unsigned_long) -> NoneType
Delete a leaf of glycan residues. Use the ReferencePose to associate residue numbers.
Uses delete_residue_slow as the debug_assert in delete_polymer_residue causes a crash.
This is a bug in the FoldTree where chemical edges are being treated as Jumps.
This is being addressed in a branch and a FoldTree.
2. delete_leaf(pose : rosetta.core.pose.Pose, leaf : rosetta.utility.vector1_unsigned_long, ref_pose_name : str) -> NoneType
Delete a leaf of glycan residues. Use the ReferencePose to associate residue numbers.
Uses delete_residue_slow as the debug_assert in delete_polymer_residue causes a crash.
This is a bug in the FoldTree where chemical edges are being treated as Jumps.
This is being addressed in a branch and a FoldTree.
- fill_upstream_children_res_and_tips(...) method of builtins.PyCapsule instance
- fill_upstream_children_res_and_tips(pose : rosetta.core.pose.Pose, res : int, parent_residue : int, children_residues : rosetta.utility.vector1_unsigned_long, list_of_residues : rosetta.utility.vector1_unsigned_long, tips : rosetta.utility.vector1_unsigned_long) -> NoneType
Find all children residues, list of residues, and any found tips from a given residue not including parent
Children Residues: Filled in list of children residues found if not tips.
List Of Residues: All the residue nums found.
Tips: All 'ends' of of children found.
See Also: get_carbohydrate_residues_upstream
trim_carbohydrate_branch_from_X
- find_seqpos_of_saccharides_parent_residue(...) method of builtins.PyCapsule instance
- find_seqpos_of_saccharides_parent_residue(residue : rosetta.core.conformation.Residue) -> int
Use a saccharide residue's connections to find the residue from which it follows or branches.
- get_branching_residues(...) method of builtins.PyCapsule instance
- get_branching_residues(pose : rosetta.core.pose.Pose, parent_residue : int, children_residues : rosetta.utility.vector1_unsigned_long, list_of_residues : rosetta.utility.vector1_unsigned_long, tips : rosetta.utility.vector1_unsigned_long) -> NoneType
Recursive function to get branches of a set of residues, etc.
list_of_residues and tips are arrays are non-const references and modified by this function.
Children Residues: Residue nums of parent residue connected that we are interested in finding connected branchs.
List Of Residues: All the residue nums of the branching from children residues
Tips: All 'ends' of all the branches found using this function.
See Also: get_carbohydrate_residues_upstream
trim_carbohydrate_branch_from_X
- get_carbohydrate_residues_upstream(...) method of builtins.PyCapsule instance
- get_carbohydrate_residues_upstream(pose : rosetta.core.pose.Pose, starting_position : int) -> (rosetta.utility.vector1_unsigned_long, rosetta.utility.vector1_unsigned_long)
Get residues further down the branch from this residue. starting_position ->
May require a better name.
Returns pair of all_upstream_residues, tips.
Tips are the ends of linear glycan branches.
- get_glycosidic_bond_residues(...) method of builtins.PyCapsule instance
- get_glycosidic_bond_residues(pose : rosetta.core.pose.Pose, sequence_position : int) -> (rosetta.core.conformation.Residue, rosetta.core.conformation.Residue)
Return pointers to the two residues of the glycosidic bond.
- get_glycosidic_torsion(...) method of builtins.PyCapsule instance
- get_glycosidic_torsion(torsion_id : int, pose : rosetta.core.pose.Pose, sequence_position : int) -> float
Return the requested torsion angle between a saccharide residue of the given pose and the previous residue.
- get_linkage_position_of_saccharide_residue(...) method of builtins.PyCapsule instance
- get_linkage_position_of_saccharide_residue(*args, **kwargs)
Overloaded function.
1. get_linkage_position_of_saccharide_residue(pose : rosetta.core.pose.Pose, seqpos : int) -> int
Use a saccharide residue's connections to find its linkage number on the previous residue.
2. get_linkage_position_of_saccharide_residue(rsd : rosetta.core.conformation.Residue, parent_rsd : rosetta.core.conformation.Residue) -> int
- get_linkage_type_for_residue_for_CHI(...) method of builtins.PyCapsule instance
- get_linkage_type_for_residue_for_CHI(torsion_id : int, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose) -> rosetta.core.chemical.carbohydrates.LinkageType
Get the linkage type for a particular residue.
Be warned: If NO STATISTICS for that residue exist for SugarBB/CHI (such as not a pyranose, will return LINKAGE_NA )
- get_n_glycosidic_torsions_in_res(...) method of builtins.PyCapsule instance
- get_n_glycosidic_torsions_in_res(pose : rosetta.core.pose.Pose, sequence_position : int) -> int
Get the number of glycosidic torsions for this residue. Up to 4 (omega2).
- get_reference_atoms(...) method of builtins.PyCapsule instance
- get_reference_atoms(torsion_id : int, pose : rosetta.core.pose.Pose, sequence_position : int) -> rosetta.utility.vector1_core_id_AtomID
Return the AtomIDs of the four reference atoms for the requested torsion.
- get_reference_atoms_for_1st_omega(...) method of builtins.PyCapsule instance
- get_reference_atoms_for_1st_omega(pose : rosetta.core.pose.Pose, sequence_position : int) -> rosetta.utility.vector1_core_id_AtomID
Return the AtomIDs of the four omega torsion reference atoms.
- get_reference_atoms_for_2nd_omega(...) method of builtins.PyCapsule instance
- get_reference_atoms_for_2nd_omega(pose : rosetta.core.pose.Pose, sequence_position : int) -> rosetta.utility.vector1_core_id_AtomID
Return the AtomIDs of the four omega2 torsion reference atoms.
- get_reference_atoms_for_phi(...) method of builtins.PyCapsule instance
- get_reference_atoms_for_phi(pose : rosetta.core.pose.Pose, sequence_position : int) -> rosetta.utility.vector1_core_id_AtomID
Return the AtomIDs of the four phi torsion reference atoms.
- get_reference_atoms_for_psi(...) method of builtins.PyCapsule instance
- get_reference_atoms_for_psi(pose : rosetta.core.pose.Pose, sequence_position : int) -> rosetta.utility.vector1_core_id_AtomID
Return the AtomIDs of the four psi torsion reference atoms.
- get_resnums_in_leaf(...) method of builtins.PyCapsule instance
- get_resnums_in_leaf(pose : rosetta.core.pose.Pose, tip_residue : int, stop_at_residue : int) -> rosetta.utility.vector1_unsigned_long
Get all residue numbers in order from the tip to (and not including) stop_at_residue or a branch point.
All residue numbers are the tip or a linear polymer of glycans.
Useful for glycan stripping.
- glycosylate_pose(...) method of builtins.PyCapsule instance
- glycosylate_pose(*args, **kwargs)
Overloaded function.
1. glycosylate_pose(pose : rosetta.core.pose.Pose, sequence_position : int, atom_name : str, iupac_sequence : str) -> NoneType
Glycosylate the Pose at the given sequence position and atom using an IUPAC sequence.
2. glycosylate_pose(pose : rosetta.core.pose.Pose, sequence_position : int, atom_name : str, iupac_sequence : str, idealize_linkages : bool) -> NoneType
Glycosylate the Pose at the given sequence position and atom using an IUPAC sequence.
3. glycosylate_pose(pose : rosetta.core.pose.Pose, sequence_position : int, iupac_sequence : str) -> NoneType
Glycosylate the Pose at the given sequence position using an IUPAC sequence.
4. glycosylate_pose(pose : rosetta.core.pose.Pose, sequence_position : int, iupac_sequence : str, idealize_linkages : bool) -> NoneType
Glycosylate the Pose at the given sequence position using an IUPAC sequence.
- glycosylate_pose_by_file(...) method of builtins.PyCapsule instance
- glycosylate_pose_by_file(*args, **kwargs)
Overloaded function.
1. glycosylate_pose_by_file(pose : rosetta.core.pose.Pose, sequence_position : int, atom_name : str, filename : str) -> NoneType
Glycosylate the Pose at the given sequence position and atom using a .GWS or IUPAC sequence file.
2. glycosylate_pose_by_file(pose : rosetta.core.pose.Pose, sequence_position : int, atom_name : str, filename : str, idealize_linkages : bool) -> NoneType
Glycosylate the Pose at the given sequence position and atom using a .GWS or IUPAC sequence file.
3. glycosylate_pose_by_file(pose : rosetta.core.pose.Pose, sequence_position : int, filename : str) -> NoneType
Glycosylate the Pose at the given sequence position using a .GWS or IUPAC sequence file.
4. glycosylate_pose_by_file(pose : rosetta.core.pose.Pose, sequence_position : int, filename : str, idealize_linkages : bool) -> NoneType
Glycosylate the Pose at the given sequence position using a .GWS or IUPAC sequence file.
- has_exocyclic_glycosidic_linkage(...) method of builtins.PyCapsule instance
- has_exocyclic_glycosidic_linkage(*args, **kwargs)
Overloaded function.
1. has_exocyclic_glycosidic_linkage(pose : rosetta.core.pose.Pose, seqpos : int) -> bool
Get whether the glycosidic linkage between the residue and previous residue (parent residue) has an exocyclic carbon.
Does not currently work for aa->glycan. Returns false if previous residue is not carbohydrate.
2. has_exocyclic_glycosidic_linkage(rsd : rosetta.core.conformation.Residue, parent_rsd : rosetta.core.conformation.Residue) -> bool
Get whether the glycosidic linkage between the residue and previous residue (parent residue) has an exocyclic carbon.
Does not currently work for aa->glycan. Returns false if previous residue is not carbohydrate.
- idealize_last_n_glycans_in_pose(...) method of builtins.PyCapsule instance
- idealize_last_n_glycans_in_pose(pose : rosetta.core.pose.Pose, n_glycans_added : int) -> NoneType
Idealize the glycosidic torsion angles for the last n glycan residues added or built.
- is_glycosidic_omega_torsion(...) method of builtins.PyCapsule instance
- is_glycosidic_omega_torsion(pose : rosetta.core.pose.Pose, torsion_id : rosetta.core.id.TorsionID) -> bool
Is this is an omega torsion angle of a glycosidic linkage?
- is_glycosidic_phi_torsion(...) method of builtins.PyCapsule instance
- is_glycosidic_phi_torsion(pose : rosetta.core.pose.Pose, torsion_id : rosetta.core.id.TorsionID) -> bool
Is this is the phi torsion angle of a glycosidic linkage?
- is_glycosidic_psi_torsion(...) method of builtins.PyCapsule instance
- is_glycosidic_psi_torsion(pose : rosetta.core.pose.Pose, torsion_id : rosetta.core.id.TorsionID) -> bool
Is this is the psi torsion angle of a glycosidic linkage?
- remove_carbohydrate_branch_point_variants(...) method of builtins.PyCapsule instance
- remove_carbohydrate_branch_point_variants(pose : rosetta.core.pose.Pose, seqpos : int) -> NoneType
Remove ALL/Any branch points from a carbohydrate or aa residue.
- set_dihedrals_from_linkage_conformer_data(...) method of builtins.PyCapsule instance
- set_dihedrals_from_linkage_conformer_data(*args, **kwargs)
Overloaded function.
1. set_dihedrals_from_linkage_conformer_data(pose : rosetta.core.pose.Pose, upper_residue : int, conformer : rosetta.core.chemical.carbohydrates.LinkageConformerData) -> NoneType
Set the dihedral angles involved in a glycosidic linkage based on statistical data.
2. set_dihedrals_from_linkage_conformer_data(pose : rosetta.core.pose.Pose, upper_residue : int, conformer : rosetta.core.chemical.carbohydrates.LinkageConformerData, idealize : bool) -> NoneType
Set the dihedral angles involved in a glycosidic linkage based on statistical data.
3. set_dihedrals_from_linkage_conformer_data(pose : rosetta.core.pose.Pose, upper_residue : int, conformer : rosetta.core.chemical.carbohydrates.LinkageConformerData, idealize : bool, use_prob_for_sd : bool) -> NoneType
Set the dihedral angles involved in a glycosidic linkage based on statistical data.
- set_glycosidic_torsion(...) method of builtins.PyCapsule instance
- set_glycosidic_torsion(torsion_id : int, pose : rosetta.core.pose.Pose, sequence_position : int, setting : float) -> NoneType
Set the requested torsion angle between a saccharide residue of the given pose and the previous residue.
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