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- builtins.object
-
- AbstractRotamerTrie
- Atom
- Conformation
- ConformationKinWriter
- PointGraphEdgeData
-
- AtomGraphEdgeData
- PointGraphVertexData
-
- AtomGraphVertexData
- PseudoBond
- PseudoBondCollection
- Residue
- ResidueFactory
- ResidueKinWriter
- ResidueMatcher
-
- ExactResidueMatcher
- WatsonCrickResidueMatcher
- RotamerSetBase
- Strategy
- UltraLightResidue
- ppo_torsion_bin
- rosetta.core.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t(builtins.object)
-
- PointGraphPy
- rosetta.std.unary_function_numeric_xyzTriple_unsigned_long_unsigned_long_t(builtins.object)
-
- DefaultCubeHash
class Atom(builtins.object) |
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This atom class differs from the chameical::Atom, AtomType, and AtomTypeSet classes in that it only
contains the information about the xyz coordinates. In the future, it might contain information about such things
as B-factor. This information is generally initialized and set by conformation::Residue.
chemical::Atoms are stored in chemical::ResidueType (within its ResidueGraph);
conformation::Atoms are stored in conformation::Residue
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.conformation.Atom) -> NoneType
2. __init__(self : rosetta.core.conformation.Atom, type_in : int, mm_type_in : int) -> NoneType
3. __init__(self : rosetta.core.conformation.Atom, xyz_in : rosetta.numeric.xyzVector_double_t, type_in : int, mm_type_in : int) -> NoneType
4. __init__(self : rosetta.core.conformation.Atom, : rosetta.core.conformation.Atom) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.conformation.Atom) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.conformation.Atom, : rosetta.core.conformation.Atom) -> rosetta.core.conformation.Atom
- mm_type(...) from builtins.PyCapsule
- mm_type(*args, **kwargs)
Overloaded function.
1. mm_type(self : rosetta.core.conformation.Atom, mm_type_in : int) -> NoneType
set the mm atom type number
2. mm_type(rosetta.core.conformation.Atom) -> int
get the mm atom type number
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(self : rosetta.core.conformation.Atom, type_in : int) -> NoneType
set the atom type number
2. type(rosetta.core.conformation.Atom) -> int
Returns the AtomType number
- xyz(...) from builtins.PyCapsule
- xyz(*args, **kwargs)
Overloaded function.
1. xyz(rosetta.core.conformation.Atom) -> rosetta.numeric.xyzVector_double_t
Returns the atom coordinates as an xyzVector
2. xyz(self : rosetta.core.conformation.Atom, xyz_in : rosetta.numeric.xyzVector_double_t) -> NoneType
Sets the atom coordinates using an xyzVector
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class AtomGraphVertexData(PointGraphVertexData) |
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- Method resolution order:
- AtomGraphVertexData
- PointGraphVertexData
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.conformation.AtomGraphVertexData) -> NoneType
2. __init__(self : rosetta.core.conformation.AtomGraphVertexData, coors : rosetta.numeric.xyzVector_double_t, atom_name : str, residue_id : int) -> NoneType
3. __init__(self : rosetta.core.conformation.AtomGraphVertexData, : rosetta.core.conformation.AtomGraphVertexData) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.conformation.AtomGraphVertexData, : rosetta.core.conformation.AtomGraphVertexData) -> rosetta.core.conformation.AtomGraphVertexData
- atom_name(...) from builtins.PyCapsule
- atom_name(*args, **kwargs)
Overloaded function.
1. atom_name(rosetta.core.conformation.AtomGraphVertexData) -> str
2. atom_name(rosetta.core.conformation.AtomGraphVertexData) -> str
- atom_radius_squared(...) from builtins.PyCapsule
- atom_radius_squared(*args, **kwargs)
Overloaded function.
1. atom_radius_squared(rosetta.core.conformation.AtomGraphVertexData) -> float
2. atom_radius_squared(rosetta.core.conformation.AtomGraphVertexData) -> float
- residue_id(...) from builtins.PyCapsule
- residue_id(*args, **kwargs)
Overloaded function.
1. residue_id(rosetta.core.conformation.AtomGraphVertexData) -> int
2. residue_id(rosetta.core.conformation.AtomGraphVertexData) -> int
Methods inherited from PointGraphVertexData:
- xyz(...) from builtins.PyCapsule
- xyz(*args, **kwargs)
Overloaded function.
1. xyz(rosetta.core.conformation.PointGraphVertexData) -> rosetta.numeric.xyzVector_double_t
Get a non-const reference to xyz data in order to set the data by reference.
2. xyz(rosetta.core.conformation.PointGraphVertexData) -> rosetta.numeric.xyzVector_double_t
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class Conformation(builtins.object) |
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A container of Residues and the kinematics to manage them
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.conformation.Conformation) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.conformation.Conformation) -> str
- aa(...) from builtins.PyCapsule
- aa(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.chemical.AA
Returns the AA enum for position <seqpos>
- add_parameters_set(...) from builtins.PyCapsule
- add_parameters_set(self : rosetta.core.conformation.Conformation, newset : rosetta.core.conformation.parametric.ParametersSet) -> NoneType
Add a (predefined) ParametersSet object (via its owning pointer)
to the current Conformation object.
Vikram K. Mulligan (vmullig.edu)
- annotated_sequence(...) from builtins.PyCapsule
- annotated_sequence(self : rosetta.core.conformation.Conformation, show_all_variants : bool) -> str
Returns the variant-tagged string representing the
residue types that make up a conformation; e.g.
M[MET:N-Terminus-Variant]CDH[HIS_D]LLR[ARG:C-Terminus-Variant]
- append_polymer_residue_after_seqpos(...) from builtins.PyCapsule
- append_polymer_residue_after_seqpos(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, seqpos : int, build_ideal_geometry : bool) -> NoneType
glues to seqpos and perhaps also seqpos+1
- append_residue_by_bond(...) from builtins.PyCapsule
- append_residue_by_bond(*args, **kwargs)
Overloaded function.
1. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue) -> NoneType
Append a new residue by a bond.
2. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool) -> NoneType
Append a new residue by a bond.
3. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int) -> NoneType
Append a new residue by a bond.
4. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int, anchor_residue : int) -> NoneType
Append a new residue by a bond.
5. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int, anchor_residue : int, anchor_connection_index : int) -> NoneType
Append a new residue by a bond.
6. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int, anchor_residue : int, anchor_connection_index : int, start_new_chain : bool) -> NoneType
Append a new residue by a bond.
7. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int, anchor_residue : int, anchor_connection_index : int, start_new_chain : bool, lookup_bond_length : bool) -> NoneType
Append a new residue by a bond.
- append_residue_by_jump(...) from builtins.PyCapsule
- append_residue_by_jump(*args, **kwargs)
Overloaded function.
1. append_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, anchor_residue : int) -> NoneType
Append a new residue by a jump.
2. append_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, anchor_residue : int, anchor_atom : str) -> NoneType
Append a new residue by a jump.
3. append_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, anchor_residue : int, anchor_atom : str, root_atom : str) -> NoneType
Append a new residue by a jump.
4. append_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, anchor_residue : int, anchor_atom : str, root_atom : str, start_new_chain : bool) -> NoneType
Append a new residue by a jump.
- apply_transform_Rx_plus_v(...) from builtins.PyCapsule
- apply_transform_Rx_plus_v(self : rosetta.core.conformation.Conformation, R : rosetta.numeric.xyzMatrix_double_t, v : rosetta.numeric.xyzVector_double_t) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.conformation.Conformation, src : rosetta.core.conformation.Conformation) -> rosetta.core.conformation.Conformation
equals operator
- atom_is_backbone_norefold(...) from builtins.PyCapsule
- atom_is_backbone_norefold(self : rosetta.core.conformation.Conformation, pos : int, atomno : int) -> bool
returns true if atom is part of backbone.
- atom_tree(...) from builtins.PyCapsule
- atom_tree(rosetta.core.conformation.Conformation) -> core::kinematics::AtomTree
Returns the conformation's AtomTree
- batch_get_xyz(...) from builtins.PyCapsule
- batch_get_xyz(self : rosetta.core.conformation.Conformation, id : rosetta.utility.vector1_core_id_AtomID, position : rosetta.utility.vector1_numeric_xyzVector_double_t) -> NoneType
- batch_set_xyz(...) from builtins.PyCapsule
- batch_set_xyz(self : rosetta.core.conformation.Conformation, id : rosetta.utility.vector1_core_id_AtomID, position : rosetta.utility.vector1_numeric_xyzVector_double_t) -> NoneType
- block_signals(...) from builtins.PyCapsule
- block_signals(rosetta.core.conformation.Conformation) -> NoneType
block signals from being sent
- blocking_signals(...) from builtins.PyCapsule
- blocking_signals(rosetta.core.conformation.Conformation) -> bool
are signals being blocked?
- bond_angle(...) from builtins.PyCapsule
- bond_angle(self : rosetta.core.conformation.Conformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID) -> float
Returns the bond angle defined by <atom[1-3]> through the AtomTree
- bond_length(...) from builtins.PyCapsule
- bond_length(self : rosetta.core.conformation.Conformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID) -> float
Returns the bond length between <atom1> and <atom2> through the AtomTree
- bonded_neighbor_all_res(...) from builtins.PyCapsule
- bonded_neighbor_all_res(*args, **kwargs)
Overloaded function.
1. bonded_neighbor_all_res(self : rosetta.core.conformation.Conformation, atomid : rosetta.core.id.AtomID) -> rosetta.utility.vector1_core_id_AtomID
get all atoms bonded to another
2. bonded_neighbor_all_res(self : rosetta.core.conformation.Conformation, atomid : rosetta.core.id.AtomID, virt : bool) -> rosetta.utility.vector1_core_id_AtomID
get all atoms bonded to another
- buffer_signals(...) from builtins.PyCapsule
- buffer_signals(rosetta.core.conformation.Conformation) -> NoneType
block signals from being sent and buffer them to be sent after unblocking
- buffering_signals(...) from builtins.PyCapsule
- buffering_signals(rosetta.core.conformation.Conformation) -> bool
are signals being blocked and buffered?
- chain_begin(...) from builtins.PyCapsule
- chain_begin(self : rosetta.core.conformation.Conformation, chain : int) -> int
Returns the position number of the first residue in <chain>
- chain_end(...) from builtins.PyCapsule
- chain_end(self : rosetta.core.conformation.Conformation, chain : int) -> int
Returns the position number of the last residue in <chain>
- chain_endings(...) from builtins.PyCapsule
- chain_endings(*args, **kwargs)
Overloaded function.
1. chain_endings(rosetta.core.conformation.Conformation) -> rosetta.utility.vector1_unsigned_long
Returns the list of chain endings
2. chain_endings(self : rosetta.core.conformation.Conformation, endings : rosetta.utility.vector1_unsigned_long) -> NoneType
Sets the list of chain endings
- chains_from_termini(...) from builtins.PyCapsule
- chains_from_termini(rosetta.core.conformation.Conformation) -> NoneType
Rederive the chains from the termini/polymer status
- check_valid_membrane(...) from builtins.PyCapsule
- check_valid_membrane(rosetta.core.conformation.Conformation) -> NoneType
Check that a new membrane position is valid
Given a new membrane normal/center pair, check that the newly constructed stub represents
an orthogonal coordinate frame
- clear(...) from builtins.PyCapsule
- clear(rosetta.core.conformation.Conformation) -> NoneType
clear data
- clear_observers(...) from builtins.PyCapsule
- clear_observers(rosetta.core.conformation.Conformation) -> NoneType
clear all observers
- clear_parameters_set_list(...) from builtins.PyCapsule
- clear_parameters_set_list(rosetta.core.conformation.Conformation) -> NoneType
Delete the list of ParametersSetOP objects.
Vikram K. Mulligan (vmullig.edu)
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.conformation.Conformation) -> rosetta.core.conformation.Conformation
clone the conformation
- const_residues(...) from builtins.PyCapsule
- const_residues(rosetta.core.conformation.Conformation) -> rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t
Inefficient -- constructs copy of residues_
- contains_carbohydrate_residues(...) from builtins.PyCapsule
- contains_carbohydrate_residues(*args, **kwargs)
Overloaded function.
1. contains_carbohydrate_residues(rosetta.core.conformation.Conformation) -> bool
Return true if this conformation contains any carbohydrate residues.
2. contains_carbohydrate_residues(self : rosetta.core.conformation.Conformation, setting : bool) -> NoneType
Set whether this conformation contains any carbohydrate residues.
- copy_segment(...) from builtins.PyCapsule
- copy_segment(self : rosetta.core.conformation.Conformation, size : int, src : rosetta.core.conformation.Conformation, begin : int, src_begin : int) -> NoneType
copy a stretch of coordinates/torsions from another Conformation
- create_new_parameters_set(...) from builtins.PyCapsule
- create_new_parameters_set(rosetta.core.conformation.Conformation) -> NoneType
Create a new (empty) ParametersSet object and add its owning pointer
to the current Conformation object.
Vikram K. Mulligan (vmullig.edu)
- debug_pause(...) from builtins.PyCapsule
- debug_pause(*args, **kwargs)
Overloaded function.
1. debug_pause(self : rosetta.core.conformation.Conformation, flag : bool) -> NoneType
wait for stdin after sending a GeneralEvent signal
2. debug_pause(rosetta.core.conformation.Conformation) -> bool
waiting for stdin after sending a GeneralEvent signal?
- debug_residue_torsions(...) from builtins.PyCapsule
- debug_residue_torsions(*args, **kwargs)
Overloaded function.
1. debug_residue_torsions(rosetta.core.conformation.Conformation) -> NoneType
debugging
2. debug_residue_torsions(self : rosetta.core.conformation.Conformation, verbose : bool) -> NoneType
debugging
- declare_chemical_bond(...) from builtins.PyCapsule
- declare_chemical_bond(self : rosetta.core.conformation.Conformation, seqpos1 : int, atom_name1 : str, seqpos2 : int, atom_name2 : str) -> NoneType
Declare that a chemical bond exists between two residues
- delete_chain_ending(...) from builtins.PyCapsule
- delete_chain_ending(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType
Deletes <seqpos> from the list of chain endings
- delete_polymer_residue(...) from builtins.PyCapsule
- delete_polymer_residue(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType
Delete polymer residue at the given sequence position
- delete_residue_range_slow(...) from builtins.PyCapsule
- delete_residue_range_slow(self : rosetta.core.conformation.Conformation, range_begin : int, range_end : int) -> NoneType
Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue
- delete_residue_slow(...) from builtins.PyCapsule
- delete_residue_slow(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType
Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue
- detached_copy(...) from builtins.PyCapsule
- detached_copy(self : rosetta.core.conformation.Conformation, src : rosetta.core.conformation.Conformation) -> NoneType
copy the other conformation into this, but make sure that the two
share no possibly-non-bitwise-const data nor do they refer to each other
(as the AtomTree does with its topological observer system).
- detect_bonds(...) from builtins.PyCapsule
- detect_bonds(rosetta.core.conformation.Conformation) -> NoneType
- detect_disulfides(...) from builtins.PyCapsule
- detect_disulfides(*args, **kwargs)
Overloaded function.
1. detect_disulfides(rosetta.core.conformation.Conformation) -> NoneType
2. detect_disulfides(self : rosetta.core.conformation.Conformation, disulf_one : rosetta.utility.vector1_unsigned_long) -> NoneType
3. detect_disulfides(self : rosetta.core.conformation.Conformation, disulf_one : rosetta.utility.vector1_unsigned_long, disulf_two : rosetta.utility.vector1_unsigned_long) -> NoneType
- detect_pseudobonds(...) from builtins.PyCapsule
- detect_pseudobonds(rosetta.core.conformation.Conformation) -> NoneType
- dof(...) from builtins.PyCapsule
- dof(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.DOF_ID) -> float
Returns the AtomTree degree of freedom (DOF) <id>
- dof_id_from_torsion_id(...) from builtins.PyCapsule
- dof_id_from_torsion_id(self : rosetta.core.conformation.Conformation, id : core::id::TorsionID) -> rosetta.core.id.DOF_ID
- downstream_jump_stub(...) from builtins.PyCapsule
- downstream_jump_stub(self : rosetta.core.conformation.Conformation, jump_number : int) -> rosetta.core.kinematics.Stub
The upstream and downstream Stubs are the coordinate frames between which this jump is transforming
- empty(...) from builtins.PyCapsule
- empty(rosetta.core.conformation.Conformation) -> bool
Returns true if this conformation does not have any residues
- fill_missing_atoms(...) from builtins.PyCapsule
- fill_missing_atoms(self : rosetta.core.conformation.Conformation, missing : rosetta.core.id.AtomID_Map_bool_t) -> NoneType
- fix_disulfides(...) from builtins.PyCapsule
- fix_disulfides(self : rosetta.core.conformation.Conformation, disulf_bonds : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> NoneType
Assigns disulfide bonds based on a pre-determined list
- fold_tree(...) from builtins.PyCapsule
- fold_tree(*args, **kwargs)
Overloaded function.
1. fold_tree(rosetta.core.conformation.Conformation) -> core::kinematics::FoldTree
Returns the conformation's FoldTree
2. fold_tree(self : rosetta.core.conformation.Conformation, fold_tree_in : core::kinematics::FoldTree) -> NoneType
Sets the FoldTree to <fold_tree_in>
- get_jump_atom_ids(...) from builtins.PyCapsule
- get_jump_atom_ids(self : rosetta.core.conformation.Conformation, jump_number : int, upstream_id : rosetta.core.id.AtomID, downstream_id : rosetta.core.id.AtomID) -> bool
get two atoms connect by jump
- get_residue_mask(...) from builtins.PyCapsule
- get_residue_mask(rosetta.core.conformation.Conformation) -> rosetta.utility.vector1_bool
returns a mask of residues to be used in scoring
- get_residue_weight(...) from builtins.PyCapsule
- get_residue_weight(self : rosetta.core.conformation.Conformation, : int, : int) -> float
returns a residue-pair weight
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.core.conformation.Conformation) -> rosetta.core.conformation.Conformation
self pointers
2. get_self_ptr(rosetta.core.conformation.Conformation) -> rosetta.core.conformation.Conformation
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.core.conformation.Conformation) -> rosetta.std.weak_ptr_const_core_conformation_Conformation_t
2. get_self_weak_ptr(rosetta.core.conformation.Conformation) -> rosetta.std.weak_ptr_core_conformation_Conformation_t
- get_stub_transform(...) from builtins.PyCapsule
- get_stub_transform(self : rosetta.core.conformation.Conformation, stub_id1 : rosetta.core.id.StubID, stub_id2 : rosetta.core.id.StubID) -> rosetta.core.kinematics.RT
get the transform between two stubs
- get_torsion_angle_atom_ids(...) from builtins.PyCapsule
- get_torsion_angle_atom_ids(self : rosetta.core.conformation.Conformation, tor_id : core::id::TorsionID, id1 : rosetta.core.id.AtomID, id2 : rosetta.core.id.AtomID, id3 : rosetta.core.id.AtomID, id4 : rosetta.core.id.AtomID) -> bool
get four atoms which defined this torsion
- has_passport(...) from builtins.PyCapsule
- has_passport(rosetta.core.conformation.Conformation) -> bool
- insert_chain_ending(...) from builtins.PyCapsule
- insert_chain_ending(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType
Marks <seqpos> as the end of a new chain
- insert_conformation_by_jump(...) from builtins.PyCapsule
- insert_conformation_by_jump(*args, **kwargs)
Overloaded function.
1. insert_conformation_by_jump(self : rosetta.core.conformation.Conformation, conf : rosetta.core.conformation.Conformation, insert_seqpos : int, insert_jumppos : int, anchor_pos : int) -> NoneType
Insert one conformation into another. See FoldTree::insert_fold_tree_by_jump
2. insert_conformation_by_jump(self : rosetta.core.conformation.Conformation, conf : rosetta.core.conformation.Conformation, insert_seqpos : int, insert_jumppos : int, anchor_pos : int, anchor_jump_number : int) -> NoneType
Insert one conformation into another. See FoldTree::insert_fold_tree_by_jump
3. insert_conformation_by_jump(self : rosetta.core.conformation.Conformation, conf : rosetta.core.conformation.Conformation, insert_seqpos : int, insert_jumppos : int, anchor_pos : int, anchor_jump_number : int, anchor_atom : str) -> NoneType
Insert one conformation into another. See FoldTree::insert_fold_tree_by_jump
4. insert_conformation_by_jump(self : rosetta.core.conformation.Conformation, conf : rosetta.core.conformation.Conformation, insert_seqpos : int, insert_jumppos : int, anchor_pos : int, anchor_jump_number : int, anchor_atom : str, root_atom : str) -> NoneType
Insert one conformation into another. See FoldTree::insert_fold_tree_by_jump
- insert_ideal_geometry_at_polymer_bond(...) from builtins.PyCapsule
- insert_ideal_geometry_at_polymer_bond(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType
- insert_ideal_geometry_at_residue_connection(...) from builtins.PyCapsule
- insert_ideal_geometry_at_residue_connection(self : rosetta.core.conformation.Conformation, pos1 : int, connid1 : int) -> NoneType
- insert_residue_by_bond(...) from builtins.PyCapsule
- insert_residue_by_bond(*args, **kwargs)
Overloaded function.
1. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
2. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
3. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
4. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str, root_atom : str) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
5. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str, root_atom : str, new_chain : bool) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
6. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str, root_atom : str, new_chain : bool, lookup_bond_length : bool) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
- insert_residue_by_jump(...) from builtins.PyCapsule
- insert_residue_by_jump(*args, **kwargs)
Overloaded function.
1. insert_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
2. insert_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, anchor_atom : str) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
3. insert_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, anchor_atom : str, root_atom : str) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
4. insert_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, anchor_atom : str, root_atom : str, new_chain : bool) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
- inter_residue_connection_partner(...) from builtins.PyCapsule
- inter_residue_connection_partner(self : rosetta.core.conformation.Conformation, seqpos : int, connection_index : int) -> rosetta.core.id.AtomID
This returns the AtomID of the atom in the other residue to which the "connection_index"-th
connection of residue seqpos is connected to.
- is_centroid(...) from builtins.PyCapsule
- is_centroid(rosetta.core.conformation.Conformation) -> bool
convenience test for residue_type_set ( based on two middle residue -- to avoid hitting on ligands or pseudos )
- is_fullatom(...) from builtins.PyCapsule
- is_fullatom(rosetta.core.conformation.Conformation) -> bool
convenience test for residue_type_set ( based on two middle residue -- to avoid hitting on ligands or pseudos )
- is_membrane(...) from builtins.PyCapsule
- is_membrane(rosetta.core.conformation.Conformation) -> bool
convenience test for if the conformation contains information for a membrane protein
- is_protected(...) from builtins.PyCapsule
- is_protected(rosetta.core.conformation.Conformation) -> bool
- is_residue_typeset(...) from builtins.PyCapsule
- is_residue_typeset(self : rosetta.core.conformation.Conformation, tag : str) -> bool
convenience test for residue_type_set ( based on two middle residue -- to avoid hitting on ligands or pseudos )
- jump(...) from builtins.PyCapsule
- jump(*args, **kwargs)
Overloaded function.
1. jump(self : rosetta.core.conformation.Conformation, jump_number : int) -> rosetta.core.kinematics.Jump
Returns the Jump with jump number <jump_number>
2. jump(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.AtomID) -> rosetta.core.kinematics.Jump
access a jump
- jump_atom_id(...) from builtins.PyCapsule
- jump_atom_id(self : rosetta.core.conformation.Conformation, jump_number : int) -> rosetta.core.id.AtomID
- membrane_info(...) from builtins.PyCapsule
- membrane_info(rosetta.core.conformation.Conformation) -> core::conformation::membrane::MembraneInfo
Returns the const MembraneInfo object in conformation
Membrane Info contains information describing location of the
membrane virtual residue in the pose sequence, membrane spanning region definitions
and lipid exposure/burial data
- n_parameters_sets(...) from builtins.PyCapsule
- n_parameters_sets(rosetta.core.conformation.Conformation) -> int
Get the number of parameters sets defined for this Conformation.
Vikram K. Mulligan (vmullig.edu)
- num_chains(...) from builtins.PyCapsule
- num_chains(rosetta.core.conformation.Conformation) -> int
Returns the number of chains
- parameters_set(...) from builtins.PyCapsule
- parameters_set(*args, **kwargs)
Overloaded function.
1. parameters_set(self : rosetta.core.conformation.Conformation, index : int) -> rosetta.core.conformation.parametric.ParametersSet
Access one of the ParametersSets objects linked to this Conformation.
Vikram K. Mulligan (vmullig.edu)
2. parameters_set(self : rosetta.core.conformation.Conformation, index : int) -> rosetta.core.conformation.parametric.ParametersSet
Const access to one of the ParametersSets objects linked to this Conformation.
Vikram K. Mulligan (vmullig.edu)
- pop_passport(...) from builtins.PyCapsule
- pop_passport(rosetta.core.conformation.Conformation) -> core::environment::DofPassport
- prepend_polymer_residue_before_seqpos(...) from builtins.PyCapsule
- prepend_polymer_residue_before_seqpos(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, seqpos : int, build_ideal_geometry : bool) -> NoneType
glues to seqpos and perhaps also seqpos-1
- push_passport(...) from builtins.PyCapsule
- push_passport(self : rosetta.core.conformation.Conformation, : core::environment::DofPassport) -> NoneType
- rebuild_polymer_bond_dependent_atoms(...) from builtins.PyCapsule
- rebuild_polymer_bond_dependent_atoms(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType
Rebuild the atoms ( like HN(seqpos), OC(seqpos+1) ) that are dependent on the polymer bond between seqpos and seqpos+1
- rebuild_polymer_bond_dependent_atoms_this_residue_only(...) from builtins.PyCapsule
- rebuild_polymer_bond_dependent_atoms_this_residue_only(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType
Rebuilds the atoms that are depenent on polymer bonds for the specified residue only.
Vikram K. Mulligan (vmullig.edu)
- rebuild_residue_connection_dependent_atoms(...) from builtins.PyCapsule
- rebuild_residue_connection_dependent_atoms(self : rosetta.core.conformation.Conformation, seqpos : int, connid : int) -> NoneType
- receive_observers_from(...) from builtins.PyCapsule
- receive_observers_from(self : rosetta.core.conformation.Conformation, src : rosetta.core.conformation.Conformation) -> NoneType
fire a ConnectionEvent::TRANSFER to transfer observers from some source Conformation
- replace_residue(...) from builtins.PyCapsule
- replace_residue(*args, **kwargs)
Overloaded function.
1. replace_residue(self : rosetta.core.conformation.Conformation, seqpos : int, new_rsd : rosetta.core.conformation.Residue, orient_backbone : bool) -> NoneType
replace residue
2. replace_residue(self : rosetta.core.conformation.Conformation, seqpos : int, new_rsd : rosetta.core.conformation.Residue, atom_pairs : rosetta.utility.vector1_std_pair_std_string_std_string_t) -> NoneType
function to replace a residue based on superposition on the specified input atom pairs
- reset_chain_endings(...) from builtins.PyCapsule
- reset_chain_endings(rosetta.core.conformation.Conformation) -> NoneType
Resets chain data so that the Conformation is marked as a single chain
- reset_move_data(...) from builtins.PyCapsule
- reset_move_data(rosetta.core.conformation.Conformation) -> NoneType
forget all the structure modifications
- reset_structure_moved(...) from builtins.PyCapsule
- reset_structure_moved(rosetta.core.conformation.Conformation) -> NoneType
reset the structure_moved_ bool
- residue(...) from builtins.PyCapsule
- residue(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.conformation.Residue
access one of the residues
this access is inlined, since otherwise it
shows up in the profiler. This will call non-inlined refold methods if necessary.
update coordinates and torsions for this and all other residues before
allowing read access
- residue_cop(...) from builtins.PyCapsule
- residue_cop(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.conformation.Residue
access one of the residues, using COP
- residue_op(...) from builtins.PyCapsule
- residue_op(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.conformation.Residue
Access one of the residues, using OP
Non-const access.
- residue_type(...) from builtins.PyCapsule
- residue_type(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.chemical.ResidueType
access one of the residue's types -- avoids coord/torsion update
- safely_append_polymer_residue_after_seqpos(...) from builtins.PyCapsule
- safely_append_polymer_residue_after_seqpos(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, seqpos : int, build_ideal_geometry : bool) -> NoneType
glues to seqpos and perhaps also seqpos+1, removes termini variants if necessary
- safely_prepend_polymer_residue_before_seqpos(...) from builtins.PyCapsule
- safely_prepend_polymer_residue_before_seqpos(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, seqpos : int, build_ideal_geometry : bool) -> NoneType
glues to seqpos and perhaps also seqpos-1, removes termini variants if necessary
- same_type_as_me(...) from builtins.PyCapsule
- same_type_as_me(*args, **kwargs)
Overloaded function.
1. same_type_as_me(self : rosetta.core.conformation.Conformation, other : rosetta.core.conformation.Conformation) -> bool
determine the type of the ConformationOP
2. same_type_as_me(self : rosetta.core.conformation.Conformation, other : rosetta.core.conformation.Conformation, recurse : bool) -> bool
determine the type of the ConformationOP
- secstruct(...) from builtins.PyCapsule
- secstruct(self : rosetta.core.conformation.Conformation, seqpos : int) -> str
Returns the secondary structure the position <seqpos>
character representing secondary structure; returns 'L' if the
requested sequence position is larger than the length in the
secondary structure array
- sequence_matches(...) from builtins.PyCapsule
- sequence_matches(self : rosetta.core.conformation.Conformation, other : rosetta.core.conformation.Conformation) -> bool
do the names of all residues in this and src match?
- set_bond_angle(...) from builtins.PyCapsule
- set_bond_angle(self : rosetta.core.conformation.Conformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID, setting : float) -> NoneType
Sets the bond angle defined by <atom[1-3]> to <setting>
- set_bond_length(...) from builtins.PyCapsule
- set_bond_length(self : rosetta.core.conformation.Conformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, setting : float) -> NoneType
Sets the cond length between <atom1> and <atom2> to <setting>
- set_dof(...) from builtins.PyCapsule
- set_dof(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.DOF_ID, setting : float) -> NoneType
Sets the AtomTree degree of freedom (DOF) <id> to <setting>
- set_jump(...) from builtins.PyCapsule
- set_jump(*args, **kwargs)
Overloaded function.
1. set_jump(self : rosetta.core.conformation.Conformation, jump_number : int, new_jump : rosetta.core.kinematics.Jump) -> NoneType
Sets the jump <jump_number> to <new_jump>
2. set_jump(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.AtomID, new_jump : rosetta.core.kinematics.Jump) -> NoneType
set a jump
- set_jump_atom_stub_id(...) from builtins.PyCapsule
- set_jump_atom_stub_id(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.StubID) -> NoneType
- set_membrane_info(...) from builtins.PyCapsule
- set_membrane_info(self : rosetta.core.conformation.Conformation, mem_info : core::conformation::membrane::MembraneInfo) -> NoneType
Setup a Membrane Info object in Conformation - pos & topology
Add a MembraneInfo object - describes the position of the
membrane virtual residue, information on membrane spanning regions,
lipid exposure/burial of residues in the pose, and fullatom steepness
and thickness parameters. At construction, specify membrane position
and list of spanning topology objects by chain.
- set_noncanonical_connection(...) from builtins.PyCapsule
- set_noncanonical_connection(self : rosetta.core.conformation.Conformation, res_id_lower : int, lr_conn_id : int, res_id_upper : int, ur_conn_id : int) -> NoneType
Create an arbitrary covalent connection between two residues.
- set_polymeric_connection(...) from builtins.PyCapsule
- set_polymeric_connection(self : rosetta.core.conformation.Conformation, res_id_lower : int, res_id_upper : int) -> NoneType
identify polymeric connections
- set_secstruct(...) from builtins.PyCapsule
- set_secstruct(self : rosetta.core.conformation.Conformation, seqpos : int, setting : str) -> NoneType
Sets the secondary structure of the position <seqpos> to <setting>
Sets secondary structure character of a sequence position.
Will resize the secondary structure array if the requested sequence
position is larger than the length of the array.
- set_stub_transform(...) from builtins.PyCapsule
- set_stub_transform(self : rosetta.core.conformation.Conformation, stub_id1 : rosetta.core.id.StubID, stub_id2 : rosetta.core.id.StubID, target_rt : rosetta.core.kinematics.RT) -> NoneType
Set the transform between two stubs -- only works if there's a jump between the two sets of stubatoms
- set_torsion(...) from builtins.PyCapsule
- set_torsion(self : rosetta.core.conformation.Conformation, id : core::id::TorsionID, setting : float) -> NoneType
Sets the AtomTree DOF and the torsion OR rigid-body offset in the corresponding Residue or Jump
- set_torsion_angle(...) from builtins.PyCapsule
- set_torsion_angle(*args, **kwargs)
Overloaded function.
1. set_torsion_angle(self : rosetta.core.conformation.Conformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID, atom4 : rosetta.core.id.AtomID, setting : float) -> NoneType
Sets the torsion angle defined by <atom[1-4]> to <setting>
2. set_torsion_angle(self : rosetta.core.conformation.Conformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID, atom4 : rosetta.core.id.AtomID, setting : float, quiet : bool) -> NoneType
Sets the torsion angle defined by <atom[1-4]> to <setting>
- set_xyz(...) from builtins.PyCapsule
- set_xyz(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.AtomID, position : rosetta.numeric.xyzVector_double_t) -> NoneType
- show_residue_connections(...) from builtins.PyCapsule
- show_residue_connections(rosetta.core.conformation.Conformation) -> NoneType
Show residue connections for debugging purposes.
- size(...) from builtins.PyCapsule
- size(rosetta.core.conformation.Conformation) -> int
Returns the number of residues in the Conformation
- structure_moved(...) from builtins.PyCapsule
- structure_moved(rosetta.core.conformation.Conformation) -> bool
has the structure moved since the last call to reset_move_data or reset_structure_moved
- stub_from_id(...) from builtins.PyCapsule
- stub_from_id(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.StubID) -> rosetta.core.kinematics.Stub
- torsion(...) from builtins.PyCapsule
- torsion(self : rosetta.core.conformation.Conformation, id : core::id::TorsionID) -> float
Return the torsion angle OR rigid-body offset for <id>
- torsion_angle(...) from builtins.PyCapsule
- torsion_angle(self : rosetta.core.conformation.Conformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID, atom4 : rosetta.core.id.AtomID) -> float
Returns the torsion angle defined by <atom[1-4]>
- unblock_signals(...) from builtins.PyCapsule
- unblock_signals(rosetta.core.conformation.Conformation) -> NoneType
allow signals to be sent
- update_actcoord(...) from builtins.PyCapsule
- update_actcoord(self : rosetta.core.conformation.Conformation, resid : int) -> NoneType
- update_actcoords(...) from builtins.PyCapsule
- update_actcoords(rosetta.core.conformation.Conformation) -> NoneType
- update_domain_map(...) from builtins.PyCapsule
- update_domain_map(self : rosetta.core.conformation.Conformation, domain_map : ObjexxFCL::FArray1D<int>) -> NoneType
Generate a domain_map from the current dof/xyz moved data
- update_membrane_position(...) from builtins.PyCapsule
- update_membrane_position(self : rosetta.core.conformation.Conformation, center : rosetta.numeric.xyzVector_double_t, normal : rosetta.numeric.xyzVector_double_t) -> NoneType
Update Normal, Center in the Membrane
Sets the center and normal coordinates to the appropriate
parameters and checks for a valid stub prior to returning.
- update_noncanonical_connection(...) from builtins.PyCapsule
- update_noncanonical_connection(self : rosetta.core.conformation.Conformation, lower_seqpos : int, lr_conn_id : int, upper_seqpos : int, ur_conn_id : int) -> NoneType
Update the connection status between the lower_seqpos residue's lr_conn_id connection ID and
the upper_seqpos residue's ur_conn_id connection ID.
- update_orbital_coords(...) from builtins.PyCapsule
- update_orbital_coords(*args, **kwargs)
Overloaded function.
1. update_orbital_coords(self : rosetta.core.conformation.Conformation, rsd : rosetta.core.conformation.Residue) -> NoneType
2. update_orbital_coords(self : rosetta.core.conformation.Conformation, resid : int) -> NoneType
- update_polymeric_connection(...) from builtins.PyCapsule
- update_polymeric_connection(*args, **kwargs)
Overloaded function.
1. update_polymeric_connection(self : rosetta.core.conformation.Conformation, lower_seqpos : int) -> NoneType
Update the polymer connection status between lower_seqpos and lower_seqpos+1
based on chainID's and termini. If update_connection_dep_atoms is true, positions of
atoms dependent on the polymer connection are updated.
2. update_polymeric_connection(self : rosetta.core.conformation.Conformation, lower_seqpos : int, update_connection_dep_atoms : bool) -> NoneType
Update the polymer connection status between lower_seqpos and lower_seqpos+1
based on chainID's and termini. If update_connection_dep_atoms is true, positions of
atoms dependent on the polymer connection are updated.
- upstream_jump_stub(...) from builtins.PyCapsule
- upstream_jump_stub(self : rosetta.core.conformation.Conformation, jump_number : int) -> rosetta.core.kinematics.Stub
The upstream and downstream Stubs are the coordinate frames between which this jump is transforming
- xyz(...) from builtins.PyCapsule
- xyz(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.AtomID) -> rosetta.numeric.xyzVector_double_t
access xyz coordinates of an atom
|
class PointGraphPy(rosetta.core.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) |
| | |
- Method resolution order:
- PointGraphPy
- rosetta.core.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.core.conformation.PointGraphPy) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.conformation.PointGraphPy, : rosetta.core.conformation.PointGraphPy) -> rosetta.core.conformation.PointGraphPy
Methods inherited from rosetta.core.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t:
- add_edge(...) from builtins.PyCapsule
- add_edge(*args, **kwargs)
Overloaded function.
1. add_edge(self : rosetta.core.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, lower_vertex : int, upper_vertex : int) -> NoneType
2. add_edge(self : rosetta.core.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, lower_vertex : int, upper_vertex : int, edge_data : core::conformation::PointGraphEdgeData) -> NoneType
- drop_all_edges(...) from builtins.PyCapsule
- drop_all_edges(rosetta.core.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) -> NoneType
- edge_exists(...) from builtins.PyCapsule
- edge_exists(self : rosetta.core.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, lower_vertex : int, upper_vertex : int) -> bool
- get_edge(...) from builtins.PyCapsule
- get_edge(self : rosetta.core.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, lower_vertex : int, upper_vertex : int) -> rosetta.core.graph.UEEdge_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t
- get_vertex(...) from builtins.PyCapsule
- get_vertex(*args, **kwargs)
Overloaded function.
1. get_vertex(self : rosetta.core.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, index : int) -> rosetta.core.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t
2. get_vertex(self : rosetta.core.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, index : int) -> rosetta.core.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t
- num_edges(...) from builtins.PyCapsule
- num_edges(rosetta.core.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) -> int
- num_vertices(...) from builtins.PyCapsule
- num_vertices(rosetta.core.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) -> int
- set_num_vertices(...) from builtins.PyCapsule
- set_num_vertices(self : rosetta.core.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, num_vertices : int) -> NoneType
|
class PseudoBond(builtins.object) |
| | |
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.core.conformation.PseudoBond, rhs : rosetta.core.conformation.PseudoBond) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.conformation.PseudoBond) -> NoneType
2. __init__(self : rosetta.core.conformation.PseudoBond, : rosetta.core.conformation.PseudoBond) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.conformation.PseudoBond, rhs : rosetta.core.conformation.PseudoBond) -> rosetta.core.conformation.PseudoBond
- lr(...) from builtins.PyCapsule
- lr(*args, **kwargs)
Overloaded function.
1. lr(rosetta.core.conformation.PseudoBond) -> int
2. lr(self : rosetta.core.conformation.PseudoBond, : int) -> NoneType
- lr_conn_id(...) from builtins.PyCapsule
- lr_conn_id(*args, **kwargs)
Overloaded function.
1. lr_conn_id(rosetta.core.conformation.PseudoBond) -> int
2. lr_conn_id(self : rosetta.core.conformation.PseudoBond, : int) -> NoneType
- lr_resconnid(...) from builtins.PyCapsule
- lr_resconnid(*args, **kwargs)
Overloaded function.
1. lr_resconnid(rosetta.core.conformation.PseudoBond) -> rosetta.core.chemical.ResConnID
2. lr_resconnid(self : rosetta.core.conformation.PseudoBond, : rosetta.core.chemical.ResConnID) -> NoneType
- nbonds(...) from builtins.PyCapsule
- nbonds(*args, **kwargs)
Overloaded function.
1. nbonds(rosetta.core.conformation.PseudoBond) -> int
2. nbonds(self : rosetta.core.conformation.PseudoBond, : int) -> NoneType
- ur(...) from builtins.PyCapsule
- ur(*args, **kwargs)
Overloaded function.
1. ur(rosetta.core.conformation.PseudoBond) -> int
2. ur(self : rosetta.core.conformation.PseudoBond, : int) -> NoneType
- ur_conn_id(...) from builtins.PyCapsule
- ur_conn_id(*args, **kwargs)
Overloaded function.
1. ur_conn_id(rosetta.core.conformation.PseudoBond) -> int
2. ur_conn_id(self : rosetta.core.conformation.PseudoBond, : int) -> NoneType
- ur_resconnid(...) from builtins.PyCapsule
- ur_resconnid(*args, **kwargs)
Overloaded function.
1. ur_resconnid(rosetta.core.conformation.PseudoBond) -> rosetta.core.chemical.ResConnID
2. ur_resconnid(self : rosetta.core.conformation.PseudoBond, : rosetta.core.chemical.ResConnID) -> NoneType
|
class Residue(builtins.object) |
| |
Instance Residue class, used for placed residues and rotamers
This class is designed to be lightweight. It holds a const-reference ("rsd_type_")
to a ResidueType object for access to information common to all instances
of a single type, e.g., Alanine or Thymine. Residue stores any data unique
to a placed residue or rotamer, currently:
- a vector1 of Atoms, which holds the positions (and also the atom-types for
fast access during scoring);
- the sequence position and chain, both integers
- the backbone, side-chain, and internal ring (if applicable) torsion angles (of course backbone torsions are
not unique to a rotamer, and the chi angles are derivable from the coordinates,
but storing them in the residue is convenient for scoring purposes).
- the coordinates of an interaction center or centroid, used e.g., in the
knowledge-based full-atom pair term ("actcoord_"). Maybe this will also
hold the centroid position for centroid-mode scoring??
|
| |
Methods defined here:
- Haro_index(...) from builtins.PyCapsule
- Haro_index(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_unsigned_long
Returns the AtomIndices of this residue's aromatic hydrogens
: AtomIndices == vector1< Size >
example(s):
residue.Haro_index()
See also:
Residue
Residue.atoms
Residue.Hpol_index
Pose
- Hpol_index(...) from builtins.PyCapsule
- Hpol_index(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_unsigned_long
Returns the AtomIndices of this residue's polar hydrogens
: AtomIndices == vector1< Size >
example(s):
residue.Hpol_index()
See also:
Residue
Residue.atoms
Residue.Hpol_index
Residue.Hpos_apolar
Residue.Hpos_polar
Pose
- Hpos_apolar(...) from builtins.PyCapsule
- Hpos_apolar(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_unsigned_long
Returns the AtomIndices of this residue's apolar hydrogens
: AtomIndices == vector1< Size >
example(s):
residue.Hpos_apolar()
See also:
Residue
Residue.atoms
Residue.Hpol_index()
Residue.Hpos_polar
Pose
- Hpos_polar(...) from builtins.PyCapsule
- Hpos_polar(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_unsigned_long
Returns the AtomIndices of this residue's polar hydrogens
: AtomIndices == vector1< Size >
example(s):
residue.Hpos_polar()
See also:
Residue
Residue.atoms
Residue.Hpol_index
Residue.Hpos_apolar
Pose
- Hpos_polar_sc(...) from builtins.PyCapsule
- Hpos_polar_sc(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_unsigned_long
Returns the AtomIndices of this residue's polar sidechain hydrogens
: AtomIndices == vector1< Size >
example(s):
residue.Hpos_polar_sc()
See also:
Residue
Residue.atoms
Residue.Hpol_index
Residue.Hpos_polar
Pose
- RNA_type(...) from builtins.PyCapsule
- RNA_type(rosetta.core.conformation.Residue) -> rosetta.core.chemical.rna.RNA_ResidueType
Return the RNA_residueType object. This is RNA specific.
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.core.conformation.Residue, rsd_type_in : rosetta.core.chemical.ResidueType, dummy_arg : bool) -> NoneType
2. __init__(self : rosetta.core.conformation.Residue, rsd_type_in : rosetta.core.chemical.ResidueType, dummy_arg : bool) -> NoneType
3. __init__(rosetta.core.conformation.Residue, rosetta.core.chemical.ResidueType, rosetta.core.conformation.Residue, core::conformation::Conformation) -> NoneType
doc
4. __init__(self : rosetta.core.conformation.Residue, rsd_type_in : rosetta.core.chemical.ResidueType, current_rsd : rosetta.core.conformation.Residue, conformation : core::conformation::Conformation, preserve_c_beta : bool) -> NoneType
5. __init__(self : rosetta.core.conformation.Residue, src : rosetta.core.conformation.Residue) -> NoneType
6. __init__(self : rosetta.core.conformation.Residue, src : rosetta.core.conformation.Residue, flip_chirality : bool) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.conformation.Residue) -> str
- aa(...) from builtins.PyCapsule
- aa(rosetta.core.conformation.Residue) -> rosetta.core.chemical.AA
Returns this residue's AA type, if any
Used for knowledge-based scores, dunbrack, etc. could be "aa_unk"
AA is enumeration
- abase2(...) from builtins.PyCapsule
- abase2(self : rosetta.core.conformation.Residue, atomno : int) -> int
Returns the atom index of the <atomno> atom's second base atom
note: abase2 is this atom's first bonded neighbor other than
this atom's base atom (unless it has only one neighbor)
- accpt_pos(...) from builtins.PyCapsule
- accpt_pos(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_unsigned_long
Returns the AtomIndices of this residue's h-bond acceptor atoms
: AtomIndices == vector1< Size >
example(s):
residue.accpt_pos()
See also:
Residue
Residue.accpt_pos_sc
Residue.atoms
Pose
- accpt_pos_sc(...) from builtins.PyCapsule
- accpt_pos_sc(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_unsigned_long
Returns the AtomIndices of this residue's sidechain h-bond acceptor atoms
: AtomIndices == vector1< Size >
example(s):
residue.accpt_pos_sc()
See also:
Residue
Residue.accpt_pos
Residue.atoms
Pose
- actcoord(...) from builtins.PyCapsule
- actcoord(*args, **kwargs)
Overloaded function.
1. actcoord(rosetta.core.conformation.Residue) -> rosetta.numeric.xyzVector_double_t
Returns the coordinates used for pairE calculations (amino acids only)
2. actcoord(rosetta.core.conformation.Residue) -> rosetta.numeric.xyzVector_double_t
Returns the coordinates used for pairE calculations (amino acids only)
- actcoord_atoms(...) from builtins.PyCapsule
- actcoord_atoms(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_unsigned_long
Returns the AtomIndices of atoms that will be used to define this residue's actcoord.
- actual_residue_connection(...) from builtins.PyCapsule
- actual_residue_connection(self : rosetta.core.conformation.Residue, resconnid : int) -> rosetta.core.chemical.ResConnID
Get the residue connection.
How is this different than residue_connection?
- all_bb_atoms(...) from builtins.PyCapsule
- all_bb_atoms(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_unsigned_long
Returns the AtomIndices of this residue's backbone atoms
: heavyatoms and hydrogens, AtomIndices == vector1< Size >
example(s):
residue.all_bb_atoms()
See also:
Residue
Residue.atoms
Pose
- apply_transform_Rx_plus_v(...) from builtins.PyCapsule
- apply_transform_Rx_plus_v(self : rosetta.core.conformation.Residue, R : rosetta.numeric.xyzMatrix_double_t, v : rosetta.numeric.xyzVector_double_t) -> NoneType
Applies a transform of the form Rx + v, where R is a rotation
matrix, V is a vector, and x is the original position in xyz space
- atom(...) from builtins.PyCapsule
- atom(*args, **kwargs)
Overloaded function.
1. atom(self : rosetta.core.conformation.Residue, atm_index : int) -> rosetta.core.conformation.Atom
Returns this residue's Atom with index number <atm_index> (const)
: Atom object is xyz and atom_type
example(s):
residue.atom(3)
See also:
Residue
Residue.atoms
Pose
2. atom(self : rosetta.core.conformation.Residue, atm_index : int) -> rosetta.core.conformation.Atom
Returns this residue's Atom with index number <atm_index> (non-const)
: Atom object is xyz and atom_type
example(s):
residue.atom(3)
See also:
Residue
Residue.atoms
Pose
3. atom(self : rosetta.core.conformation.Residue, atm_name : str) -> rosetta.core.conformation.Atom
Returns this residue's Atom with name <atm_name> (const)
: Atom object is xyz and atom_type, slower but safer than hard-coding an integer index in code where you
need a specific atom
example(s):
residue.atom(3)
See also:
Residue
Residue.atoms
Pose
4. atom(self : rosetta.core.conformation.Residue, atm_name : str) -> rosetta.core.conformation.Atom
Returns this residue's Atom with name <atm_name> (non-const)
: Atom object is xyz and atom_type, slower but safer than hard-coding an integer index in code where you
need a specific atom
example(s):
residue.atom(3)
See also:
Residue
Residue.atoms
Pose
- atom_base(...) from builtins.PyCapsule
- atom_base(self : rosetta.core.conformation.Residue, atomno : int) -> int
Returns the atom index of the <atomno> atom's base atom
- atom_begin(...) from builtins.PyCapsule
- atom_begin(*args, **kwargs)
Overloaded function.
1. atom_begin(rosetta.core.conformation.Residue) -> __gnu_cxx::__normal_iterator<core::conformation::Atom*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >
begin interator, to iterate over atoms
2. atom_begin(rosetta.core.conformation.Residue) -> __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >
- atom_end(...) from builtins.PyCapsule
- atom_end(*args, **kwargs)
Overloaded function.
1. atom_end(rosetta.core.conformation.Residue) -> __gnu_cxx::__normal_iterator<core::conformation::Atom*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >
end interator, to iterate over atoms
2. atom_end(rosetta.core.conformation.Residue) -> __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >
- atom_index(...) from builtins.PyCapsule
- atom_index(self : rosetta.core.conformation.Residue, atm : str) -> int
Returns the index number of the <atm> in this residue
example: residue.atom_index("CA") returns 2 for a normal amino acid
example(s):
residue.atom_index("CA")
See also:
Residue
AtomType
Pose
- atom_is_backbone(...) from builtins.PyCapsule
- atom_is_backbone(self : rosetta.core.conformation.Residue, atomno : int) -> bool
Returns true if this residue's atom with index number <atomno> is a backbone atom
example(s):
residue.atom_is_backbone(3)
See also:
Residue
Residue.all_bb_atoms
Residue.atom
Residue.atoms
Pose
- atom_is_hydrogen(...) from builtins.PyCapsule
- atom_is_hydrogen(self : rosetta.core.conformation.Residue, atomno : int) -> bool
Returns true if this residue's atom with index number <atomno> is a hydrogen
example(s):
residue.atom_is_backbone(3)
See also:
Residue
Residue.all_bb_atoms
Residue.atom
Residue.atoms
Pose
- atom_is_polar_hydrogen(...) from builtins.PyCapsule
- atom_is_polar_hydrogen(self : rosetta.core.conformation.Residue, ind : int) -> bool
Is a particular atom a polar hydrogen?
- atom_name(...) from builtins.PyCapsule
- atom_name(self : rosetta.core.conformation.Residue, atm : int) -> str
//////////////////////////
Returns the name of this residue's atom with index number <atm>
- atom_type(...) from builtins.PyCapsule
- atom_type(self : rosetta.core.conformation.Residue, atomno : int) -> rosetta.core.chemical.AtomType
Returns the AtomType of this residue's atom with index number <atomno>
example(s):
residue.atom_type(3)
See also:
Residue
Residue.atom_index
AtomType
Pose
- atom_type_index(...) from builtins.PyCapsule
- atom_type_index(self : rosetta.core.conformation.Residue, atomno : int) -> int
Returns the atom_type_index of this residue's atom with index number <atomno>
atom_type_index is used to query this atom's AtomType from an AtomTypeSet,
example: AtomTypeSet[atom_type_index] = AtomType
example(s):
residue.atom_type_index(3)
See also:
Residue
Residue.atom_index
AtomType
Pose
- atom_type_set(...) from builtins.PyCapsule
- atom_type_set(rosetta.core.conformation.Residue) -> rosetta.core.chemical.AtomTypeSet
Returns the AtomTypeSet of this residue
example(s):
residue.atom_type_set()
See also:
Residue
Residue.atom_type_index
AtomType
Pose
- atomic_charge(...) from builtins.PyCapsule
- atomic_charge(self : rosetta.core.conformation.Residue, atomno : int) -> float
Returns the atom charge of this residue's atom with index number <atomno>
example(s):
residue.atomic_charge(3)
See also:
Residue
Residue.atom_index
Pose
- atoms(...) from builtins.PyCapsule
- atoms(*args, **kwargs)
Overloaded function.
1. atoms(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_core_conformation_Atom
Returns this residue's Atoms (const), a vector1 of Atom objects
example(s):
residue.atoms()
See also:
Residue
Pose
2. atoms(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_core_conformation_Atom
Returns this residue's Atoms (non-const), a vector1 of Atom objects
example(s):
residue.atoms()
See also:
Residue
Pose
- atoms_with_orb_index(...) from builtins.PyCapsule
- atoms_with_orb_index(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_unsigned_long
- attached_H_begin(...) from builtins.PyCapsule
- attached_H_begin(*args, **kwargs)
Overloaded function.
1. attached_H_begin(self : rosetta.core.conformation.Residue, atom : int) -> int
Returns the index number of the first hydrogen attached to the atom
with index number <atom>
example(s):
residue.attached_H_begin()
See also:
Residue
Residue.atom
Residue.atoms
Residue.attached_H_end
Pose
2. attached_H_begin(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_unsigned_long
Returns the AtomIndices of the first hydrogen attached to each heavyatom
example(s):
residue.attached_H_begin()
See also:
Residue
Residue.atom
Residue.atoms
Residue.attached_H_end
Residue.nheavyatoms
Pose
- attached_H_end(...) from builtins.PyCapsule
- attached_H_end(*args, **kwargs)
Overloaded function.
1. attached_H_end(self : rosetta.core.conformation.Residue, atom : int) -> int
Returns the index number of the last hydrogen attached to the atom
with index number <atom>
example(s):
residue.attached_H_end()
See also:
Residue
Residue.atom
Residue.atoms
Residue.attached_H_begin
Pose
2. attached_H_end(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_unsigned_long
Returns the AtomIndices of the last hydrogen attached to each heavyatom
example(s):
residue.attached_H_end()
See also:
Residue
Residue.atom
Residue.atoms
Residue.attached_H_begin
Residue.nheavyatoms
Pose
- backbone_aa(...) from builtins.PyCapsule
- backbone_aa(rosetta.core.conformation.Residue) -> rosetta.core.chemical.AA
Returns this residue's backbone_aa type, if any.
This is used for noncanonical alpha-amino acids that are templated on canonicals.
For example, 4,5-dihydroxyisoleucine uses the ramachandran and p_aa_pp scoring of isoleucine.
- bonded_neighbor(...) from builtins.PyCapsule
- bonded_neighbor(self : rosetta.core.conformation.Residue, atm : int) -> rosetta.utility.vector1_unsigned_long
Returns the AtomIndices for all bonded neighbor atoms of <atm>
- bonded_orbitals(...) from builtins.PyCapsule
- bonded_orbitals(self : rosetta.core.conformation.Residue, atm : int) -> rosetta.utility.vector1_unsigned_long
- build_atom_ideal(...) from builtins.PyCapsule
- build_atom_ideal(self : rosetta.core.conformation.Residue, atomno : int, conformation : core::conformation::Conformation) -> rosetta.numeric.xyzVector_double_t
Return coordinates for building an atom from ideal internal coordinates,
used for building missing atoms
- build_orbital_xyz(...) from builtins.PyCapsule
- build_orbital_xyz(self : rosetta.core.conformation.Residue, orbital_index : int) -> rosetta.numeric.xyzVector_double_t
- carbohydrate_info(...) from builtins.PyCapsule
- carbohydrate_info(rosetta.core.conformation.Residue) -> rosetta.core.chemical.carbohydrates.CarbohydrateInfo
Return the CarbohydrateInfo object containing sugar-specific properties for this residue.
- chain(...) from builtins.PyCapsule
- chain(*args, **kwargs)
Overloaded function.
1. chain(rosetta.core.conformation.Residue) -> int
Returns this residue's chain id
2. chain(self : rosetta.core.conformation.Residue, setting : int) -> NoneType
Sets this residue's chain id
- chi(...) from builtins.PyCapsule
- chi(*args, **kwargs)
Overloaded function.
1. chi(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_double
Returns the chi torsion angles of this residue (const)
example(s):
residue.chi()
See also:
Residue
Residue.nchi
Pose
Pose.chi
2. chi(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_double
Returns the chi torsion angles of this residue (non-const)
3. chi(self : rosetta.core.conformation.Residue, chis : rosetta.utility.vector1_double) -> NoneType
Sets the chi torsion angles of this residue
CAUTION: This function does not cause updating to any internal coordinate data.
See Residue::set_chi() and Residue::set_all_chi() functions for
versions which handle coordinate updates.
example(s):
See also:
Residue
Pose
Pose.set_chi
4. chi(self : rosetta.core.conformation.Residue, chino : int) -> float
get a specific chi torsion angle
example(s):
residue.chi(1)
See also:
Residue
Pose
Pose.chi
- chi_atoms(...) from builtins.PyCapsule
- chi_atoms(*args, **kwargs)
Overloaded function.
1. chi_atoms(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t
Returns the AtomIndices of each set of four atoms defining each chi angle
2. chi_atoms(self : rosetta.core.conformation.Residue, chino : int) -> rosetta.utility.vector1_unsigned_long
Returns the AtomIndices of the four atoms defining this residue's <chino> chi angle
- chi_rotamers(...) from builtins.PyCapsule
- chi_rotamers(self : rosetta.core.conformation.Residue, chino : int) -> rosetta.utility.vector1_std_pair_double_double_t
Returns the chi rotamers available for this residue's chi angle <chino>
- clear_residue_connections(...) from builtins.PyCapsule
- clear_residue_connections(rosetta.core.conformation.Residue) -> NoneType
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.conformation.Residue) -> rosetta.core.conformation.Residue
Copy this residue( allocate actual memory for it )
- clone_flipping_chirality(...) from builtins.PyCapsule
- clone_flipping_chirality(rosetta.core.conformation.Residue) -> rosetta.core.conformation.Residue
Copy this residue( allocate actual memory for it ), keeping everything the same EXCEPT the type.
Switches the ResidueType to the mirror type (D->L or L->D). Preserves it for achiral residues.
This function is the best way to convert a D-residue to its L-counterpart, or an L-residue to its D-counterpart.
It assumes that you've already mirrored all of the coordinates, and just allows you to generate a replacement residue
of the mirror type that preserves all other Residue information (connections, seqpos, xyz coordinates of all atoms,
variant types, etc.).
Vikram K. Mulligan (vmullig.edu)
- connect_atom(...) from builtins.PyCapsule
- connect_atom(self : rosetta.core.conformation.Residue, other : rosetta.core.conformation.Residue) -> int
Returns the index number of this residue's atom connected to the <other> Residue
example(s):
See also:
Residue
Residue.atom
Residue.atoms
Residue.lower_connect_atom
Residue.upper_connect_atom
Pose
- connect_map(...) from builtins.PyCapsule
- connect_map(self : rosetta.core.conformation.Residue, resconn_index : int) -> rosetta.core.chemical.ResConnID
- connect_map_size(...) from builtins.PyCapsule
- connect_map_size(rosetta.core.conformation.Residue) -> int
Returns the size (number of elements) in the connect_map_ object.
- connected_residue_at_resconn(...) from builtins.PyCapsule
- connected_residue_at_resconn(self : rosetta.core.conformation.Residue, resconn_index : int) -> int
Returns the residue number of a residue connected to this residue
at this residue's connection resconn_index.
For example, in a normally-connected pose made of alpha-amino
acids, calling residue_connection_partner(1) on residue 6 should return
5, since residue 6 is connected to residue 5 at the first connection of
residue 6.
Exactly the same as residue_connection_partner
- connection_distance(...) from builtins.PyCapsule
- connection_distance(self : rosetta.core.conformation.Residue, conf : core::conformation::Conformation, resconn_index : int, matchpoint : rosetta.numeric.xyzVector_double_t) -> float
Distance between a potential residue connection match and the position of the expected atom
- connection_incomplete(...) from builtins.PyCapsule
- connection_incomplete(self : rosetta.core.conformation.Residue, resconnid : int) -> bool
- connections_match(...) from builtins.PyCapsule
- connections_match(self : rosetta.core.conformation.Residue, other : rosetta.core.conformation.Residue) -> bool
Returns true if ???
- connections_to_residue(...) from builtins.PyCapsule
- connections_to_residue(*args, **kwargs)
Overloaded function.
1. connections_to_residue(self : rosetta.core.conformation.Residue, other : rosetta.core.conformation.Residue) -> rosetta.utility.vector1_unsigned_long
Returns the vector1 of resconn ids that connect this residue to other
2. connections_to_residue(self : rosetta.core.conformation.Residue, other_resid : int) -> rosetta.utility.vector1_unsigned_long
Returns the vector1 of resconn ids that connect this residue to other
- copy_residue_connections(...) from builtins.PyCapsule
- copy_residue_connections(self : rosetta.core.conformation.Residue, src_rsd : rosetta.core.conformation.Residue) -> NoneType
attempt to take residue connection info from src_rsd
- copy_residue_connections_from(...) from builtins.PyCapsule
- copy_residue_connections_from(self : rosetta.core.conformation.Residue, src : rosetta.core.conformation.Residue) -> NoneType
- create_residue(...) from builtins.PyCapsule
- create_residue(rosetta.core.conformation.Residue) -> rosetta.core.conformation.Residue
Returns a ResidueOP for creating a copy of residue, same as clone()
Temporary hack until Residue hierarchy is worked out
- create_rotamer(...) from builtins.PyCapsule
- create_rotamer(rosetta.core.conformation.Residue) -> rosetta.core.conformation.Residue
Returns a ResidueOP for creating a rotamer of this residue
Temporary hack until Residue hierarchy is worked out
- cut_bond_neighbor(...) from builtins.PyCapsule
- cut_bond_neighbor(self : rosetta.core.conformation.Residue, atm : int) -> rosetta.utility.vector1_unsigned_long
atom indices for bonded neighbors to which atom-tree connections are disallowed.
- data_ptr(...) from builtins.PyCapsule
- data_ptr(rosetta.core.conformation.Residue) -> rosetta.basic.datacache.BasicDataCache
BasicDataCache indexed by enum in residue_datacache.hh
- fill_missing_atoms(...) from builtins.PyCapsule
- fill_missing_atoms(self : rosetta.core.conformation.Residue, missing : rosetta.utility.vector1_bool, conformation : core::conformation::Conformation) -> NoneType
Builds coordinates for atoms missing from this residue
assuming ideal internal coordinates
- first_adjacent_heavy_atom(...) from builtins.PyCapsule
- first_adjacent_heavy_atom(self : rosetta.core.conformation.Residue, atom_index : int) -> int
Scan through the list of atoms connected to a given atom and return the 1st heavy atom found.
- first_sidechain_atom(...) from builtins.PyCapsule
- first_sidechain_atom(rosetta.core.conformation.Residue) -> int
Returns the index number of the first sidechain heavyatom
example(s):
residue.first_sidechain_atom()
See also:
Residue
Residue.atom
Residue.atoms
Residue.last_backbone_atom
Pose
- first_sidechain_hydrogen(...) from builtins.PyCapsule
- first_sidechain_hydrogen(rosetta.core.conformation.Residue) -> int
Returns the index number of the first sidechain hydrogen
example(s):
residue.first_sidechain_hydrogen()
See also:
Residue
Residue.atom
Residue.atoms
Residue.first_sidechain_atom
Pose
- get_adjacent_heavy_atoms(...) from builtins.PyCapsule
- get_adjacent_heavy_atoms(self : rosetta.core.conformation.Residue, atom_index : int) -> rosetta.utility.vector1_unsigned_long
Get a list of heavy atoms connected to a given atom.
- get_metal_binding_atoms(...) from builtins.PyCapsule
- get_metal_binding_atoms(self : rosetta.core.conformation.Residue, metal_binding_indices : rosetta.utility.vector1_unsigned_long) -> NoneType
Gets the AtomIndices of the atoms in this residue that can bind to metals
: AtomIndices == vector1< Size >
: Vikram K. Mulligan (vmullig.edu)
- get_pseudobonds_to_residue(...) from builtins.PyCapsule
- get_pseudobonds_to_residue(self : rosetta.core.conformation.Residue, resid : int) -> core::conformation::PseudoBondCollection
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.core.conformation.Residue) -> rosetta.core.conformation.Residue
self pointers
2. get_self_ptr(rosetta.core.conformation.Residue) -> rosetta.core.conformation.Residue
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.core.conformation.Residue) -> rosetta.std.weak_ptr_const_core_conformation_Residue_t
2. get_self_weak_ptr(rosetta.core.conformation.Residue) -> rosetta.std.weak_ptr_core_conformation_Residue_t
- has(...) from builtins.PyCapsule
- has(self : rosetta.core.conformation.Residue, atm : str) -> bool
Returns true if this residue has an atom named <atm>
- has_incomplete_connection(...) from builtins.PyCapsule
- has_incomplete_connection(*args, **kwargs)
Overloaded function.
1. has_incomplete_connection(rosetta.core.conformation.Residue) -> bool
2. has_incomplete_connection(self : rosetta.core.conformation.Residue, atomno : int) -> bool
Returns true is <atomno> has complete connectivity?
- has_lower_connect(...) from builtins.PyCapsule
- has_lower_connect(rosetta.core.conformation.Residue) -> bool
Returns true if residue has a valid lower connection.
example(s):
residue.has_lower_connect()
- has_property(...) from builtins.PyCapsule
- has_property(self : rosetta.core.conformation.Residue, property : str) -> bool
Return true if the residue has <property>.
- has_sc_orbitals(...) from builtins.PyCapsule
- has_sc_orbitals(rosetta.core.conformation.Residue) -> bool
Returns true if the residue has side chain orbitals
- has_shadow_atoms(...) from builtins.PyCapsule
- has_shadow_atoms(rosetta.core.conformation.Residue) -> bool
Return true if and only if this residue's type has shadow atoms.
- has_upper_connect(...) from builtins.PyCapsule
- has_upper_connect(rosetta.core.conformation.Residue) -> bool
Returns true if residue has a valid upper connection.
example(s):
residue.has_upper_connect()
- has_variant_type(...) from builtins.PyCapsule
- has_variant_type(self : rosetta.core.conformation.Residue, variant_type : rosetta.core.chemical.VariantType) -> bool
Generic variant access
- heavyAtoms_end(...) from builtins.PyCapsule
- heavyAtoms_end(rosetta.core.conformation.Residue) -> __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >
- heavyatom_has_polar_hydrogens(...) from builtins.PyCapsule
- heavyatom_has_polar_hydrogens(self : rosetta.core.conformation.Residue, ind : int) -> bool
Is a particular atom a heavy atom with chemically bound polar hydrogens? (i.e. a donor heavy atom)
- heavyatom_is_an_acceptor(...) from builtins.PyCapsule
- heavyatom_is_an_acceptor(self : rosetta.core.conformation.Residue, ind : int) -> bool
Is a particular atom a heavy atom acceptor?
- icoor(...) from builtins.PyCapsule
- icoor(self : rosetta.core.conformation.Residue, atm : int) -> rosetta.core.chemical.AtomICoor
Returns the internal coordinates of this residue's atom with index number <atm>
- is_DNA(...) from builtins.PyCapsule
- is_DNA(rosetta.core.conformation.Residue) -> bool
Returns true if this residue is a DNA residue
- is_NA(...) from builtins.PyCapsule
- is_NA(rosetta.core.conformation.Residue) -> bool
Returns true if this residue is a nucleic acid
- is_RNA(...) from builtins.PyCapsule
- is_RNA(rosetta.core.conformation.Residue) -> bool
Returns true if this residue is a RNA residue
- is_apolar(...) from builtins.PyCapsule
- is_apolar(rosetta.core.conformation.Residue) -> bool
true if the residue is apolar
: apolar is classified as NOT polar, aromatic, or charged
- is_aromatic(...) from builtins.PyCapsule
- is_aromatic(rosetta.core.conformation.Residue) -> bool
Returns true if the residue is aromatic
- is_bonded(...) from builtins.PyCapsule
- is_bonded(*args, **kwargs)
Overloaded function.
1. is_bonded(self : rosetta.core.conformation.Residue, other : rosetta.core.conformation.Residue) -> bool
Am I bonded to other?
Meaningful for arbitrary topologies (e.g. circular peptides, disulfides)
2. is_bonded(self : rosetta.core.conformation.Residue, other_index : int) -> bool
Am I bonded to other?
Looks at all residue connections as opposed to doing arithmetic
- is_branch_lower_terminus(...) from builtins.PyCapsule
- is_branch_lower_terminus(rosetta.core.conformation.Residue) -> bool
Return true if the residue is a branch lower terminus variant.
- is_branch_point(...) from builtins.PyCapsule
- is_branch_point(rosetta.core.conformation.Residue) -> bool
Return true if the residue is a branch point variant.
- is_carbohydrate(...) from builtins.PyCapsule
- is_carbohydrate(rosetta.core.conformation.Residue) -> bool
Returns true if this residue is a carbohydrate
- is_charged(...) from builtins.PyCapsule
- is_charged(rosetta.core.conformation.Residue) -> bool
Returns true if the residue is charged
- is_coarse(...) from builtins.PyCapsule
- is_coarse(rosetta.core.conformation.Residue) -> bool
residue is coarse (used for RNA right now)
- is_ligand(...) from builtins.PyCapsule
- is_ligand(rosetta.core.conformation.Residue) -> bool
Returns true if this residue is a ligand
- is_lower_terminus(...) from builtins.PyCapsule
- is_lower_terminus(rosetta.core.conformation.Residue) -> bool
Returns true if the residue has a lower terminus variant
- is_metal(...) from builtins.PyCapsule
- is_metal(rosetta.core.conformation.Residue) -> bool
Returns true if this residue is a metal ion, false otherwise. The METAL property is specified in the params file under PROPERTIES.
Vikram K. Mulligan (vmullig.edu)
- is_metalbinding(...) from builtins.PyCapsule
- is_metalbinding(rosetta.core.conformation.Residue) -> bool
Returns true if this residue is a type capable of binding to a metal ion (e.g. His, Cys, etc.), false otherwise. The METALBINDING property is specified in the params file under PROPERTIES.
Vikram K. Mulligan (vmullig.edu)
- is_peptoid(...) from builtins.PyCapsule
- is_peptoid(rosetta.core.conformation.Residue) -> bool
Returns if this residue is a peptoid
- is_polar(...) from builtins.PyCapsule
- is_polar(rosetta.core.conformation.Residue) -> bool
Returns true if the residue is polar
- is_polymer(...) from builtins.PyCapsule
- is_polymer(rosetta.core.conformation.Residue) -> bool
Returns true if this residue is a polymer
- is_polymer_bonded(...) from builtins.PyCapsule
- is_polymer_bonded(*args, **kwargs)
Overloaded function.
1. is_polymer_bonded(self : rosetta.core.conformation.Residue, other : rosetta.core.conformation.Residue) -> bool
Am I polymer bonded to other?
2. is_polymer_bonded(self : rosetta.core.conformation.Residue, other_index : int) -> bool
Am I polymer-bonded to other? checks lower and upper connections
- is_protein(...) from builtins.PyCapsule
- is_protein(rosetta.core.conformation.Residue) -> bool
Returns true if this residue is an amino acid
- is_pseudo_bonded(...) from builtins.PyCapsule
- is_pseudo_bonded(*args, **kwargs)
Overloaded function.
1. is_pseudo_bonded(self : rosetta.core.conformation.Residue, other : rosetta.core.conformation.Residue) -> bool
Do I have any pseudobonds to other?
2. is_pseudo_bonded(self : rosetta.core.conformation.Residue, other_index : int) -> bool
Do I have any pseudobonds to other?
- is_repulsive(...) from builtins.PyCapsule
- is_repulsive(self : rosetta.core.conformation.Residue, atomno : int) -> bool
Check if atom is repulsive.
- is_similar_aa(...) from builtins.PyCapsule
- is_similar_aa(self : rosetta.core.conformation.Residue, other : rosetta.core.conformation.Residue) -> bool
Returns true if the aa residue types are the same
- is_similar_rotamer(...) from builtins.PyCapsule
- is_similar_rotamer(self : rosetta.core.conformation.Residue, other : rosetta.core.conformation.Residue) -> bool
Returns true if the chi angles of another residue all fall within 5 deg
- is_sri(...) from builtins.PyCapsule
- is_sri(rosetta.core.conformation.Residue) -> bool
Is this one of SRI's special heteropolymer building blocks?
- is_surface(...) from builtins.PyCapsule
- is_surface(rosetta.core.conformation.Residue) -> bool
Returns true if this residue is a surface residue
- is_terminus(...) from builtins.PyCapsule
- is_terminus(rosetta.core.conformation.Residue) -> bool
Returns true if the residue has a terminus variant
- is_triazolemer(...) from builtins.PyCapsule
- is_triazolemer(rosetta.core.conformation.Residue) -> bool
Returns true if and only if this residue is a triazolemer
- is_upper_terminus(...) from builtins.PyCapsule
- is_upper_terminus(rosetta.core.conformation.Residue) -> bool
Return true if the residue has an upper terminus variant
- is_virtual(...) from builtins.PyCapsule
- is_virtual(self : rosetta.core.conformation.Residue, atomno : int) -> bool
Check if atom is virtual.
- is_virtual_residue(...) from builtins.PyCapsule
- is_virtual_residue(rosetta.core.conformation.Residue) -> bool
Check if residue is virtual.
- last_backbone_atom(...) from builtins.PyCapsule
- last_backbone_atom(rosetta.core.conformation.Residue) -> int
Returns the index number of the last backbone heavyatom
The heavyatoms come first in atom ordering,
first backbone then sidechain, hydrogens follow the order
of their attached heavyatom.
example(s):
residue.last_backbone_atom()
See also:
Residue
Residue.atom
Residue.atoms
Residue.first_sidechain_atom
Pose
- lower_connect(...) from builtins.PyCapsule
- lower_connect(rosetta.core.conformation.Residue) -> rosetta.core.chemical.ResidueConnection
Returns this residue's lower_connection
a ResidueConnection has internal coords info
on how to build the atom in the previous residue which
connects to this residue
- lower_connect_atom(...) from builtins.PyCapsule
- lower_connect_atom(rosetta.core.conformation.Residue) -> int
Returns the index number of this residue's atom which connects to
the residue before it in sequence
: polymers only, example: for an amino acid, residue.lower_connect_atom() = atom_index("N")
example(s):
residue.lower_connect_atom()
See also:
Residue
Residue.atom
Residue.atoms
Residue.upper_connect_atom
Pose
- mainchain_atom(...) from builtins.PyCapsule
- mainchain_atom(self : rosetta.core.conformation.Residue, i : int) -> int
Returns the atom index of the residue's ith mainchain atom
- mainchain_atoms(...) from builtins.PyCapsule
- mainchain_atoms(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_unsigned_long
Returns the AtomIndices of this residue's mainchain atoms
- mainchain_torsion(...) from builtins.PyCapsule
- mainchain_torsion(self : rosetta.core.conformation.Residue, torsion : int) -> float
Returns a specific mainchain torsion angle for this residue
example: mainchain_torsion(2) will be the psi angle for an amino acid
example(s):
residue.mainchain_torsion(2)
See also:
Residue
Pose
Pose.omega
Pose.phi
Pose.psi
- mainchain_torsions(...) from builtins.PyCapsule
- mainchain_torsions(*args, **kwargs)
Overloaded function.
1. mainchain_torsions(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_double
Returns the mainchain torsion angles of this residue (const)
example(s):
residue.mainchain_torsions()
See also:
Residue
Pose
Pose.omega
Pose.phi
Pose.psi
2. mainchain_torsions(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_double
Returns the mainchain torsion angles of this residue (non-const)
3. mainchain_torsions(self : rosetta.core.conformation.Residue, torsions : rosetta.utility.vector1_double) -> NoneType
Sets the mainchain torsion angles of this residue to <torsions>
example(s):
residue.mainchain_torsions()
See also:
Residue
Pose
Pose.set_omega
Pose.set_phi
Pose.set_psi
- mm_atom_name(...) from builtins.PyCapsule
- mm_atom_name(self : rosetta.core.conformation.Residue, atom : int) -> str
Returns the mm_atom_name of this residue's atom with index number <atom>
- n_bonded_neighbor_all_res(...) from builtins.PyCapsule
- n_bonded_neighbor_all_res(*args, **kwargs)
Overloaded function.
1. n_bonded_neighbor_all_res(self : rosetta.core.conformation.Residue, atomno : int) -> int
Returns the number of atoms bonded to <atomno> in all residues?
2. n_bonded_neighbor_all_res(self : rosetta.core.conformation.Residue, atomno : int, virt : bool) -> int
Returns the number of atoms bonded to <atomno> in all residues?
- n_current_residue_connections(...) from builtins.PyCapsule
- n_current_residue_connections(rosetta.core.conformation.Residue) -> int
Returns the number of ResidueConnections on this residue
including polymeric residue connections.
This is the total number of actual connections to other residues.
The index here does not nessessarily match with the connection index as n_possible_residue_connections does!!!!
- n_hbond_acceptors(...) from builtins.PyCapsule
- n_hbond_acceptors(rosetta.core.conformation.Residue) -> int
number of hbond_donors
- n_hbond_donors(...) from builtins.PyCapsule
- n_hbond_donors(rosetta.core.conformation.Residue) -> int
number of hbond_donors
- n_mainchain_atoms(...) from builtins.PyCapsule
- n_mainchain_atoms(rosetta.core.conformation.Residue) -> int
Returns the number of the residue's mainchain atoms
- n_non_polymeric_residue_connections(...) from builtins.PyCapsule
- n_non_polymeric_residue_connections(rosetta.core.conformation.Residue) -> int
Returns the number of non-polymeric ResidueConnections on this residue
- n_nus(...) from builtins.PyCapsule
- n_nus(rosetta.core.conformation.Residue) -> int
Return the number of nu (internal ring) angles this residue has.
Example: residue.n_nus()
See also:
Residue
Residue.nu
Residue.nus
Pose.set_ring_conformation
Pose
Pose.nu
- n_orbitals(...) from builtins.PyCapsule
- n_orbitals(rosetta.core.conformation.Residue) -> int
Returns the number of orbitals in this residue
- n_polymeric_residue_connections(...) from builtins.PyCapsule
- n_polymeric_residue_connections(rosetta.core.conformation.Residue) -> int
Returns the number of polymeric ResidueConnections on this residue
- n_possible_residue_connections(...) from builtins.PyCapsule
- n_possible_residue_connections(rosetta.core.conformation.Residue) -> int
Returns the number of ResidueConnections on this residue
including polymeric residue connections.
This is the total number of possible connections from the ResidueType
- n_virtual_atoms(...) from builtins.PyCapsule
- n_virtual_atoms(rosetta.core.conformation.Residue) -> int
Returns the number of virtual atoms in this residue.
This calls the function with the same name in ResidueType, which counts virts on the fly (memory-efficient, performance-poor).
This being the case, don't call this function repeatedly! Call it once, and store the return value!
Vikram K. Mulligan (vmullig.edu)
- name(...) from builtins.PyCapsule
- name(rosetta.core.conformation.Residue) -> str
Returns this residue's ResidueType name
: for proteins, this will be the amino acid type and variant type
- name1(...) from builtins.PyCapsule
- name1(rosetta.core.conformation.Residue) -> str
Returns this residue's 1-letter representation
: for proteins, this will be the 1-letter amino acid code
- name3(...) from builtins.PyCapsule
- name3(rosetta.core.conformation.Residue) -> str
Returns this residue's 3-letter representation
: for proteins, this will be the 3-letter amino acid code
- natoms(...) from builtins.PyCapsule
- natoms(rosetta.core.conformation.Residue) -> int
Returns the number of atoms in this residue
example(s):
residue.natoms()
See also:
Residue
Pose
- nbr_atom(...) from builtins.PyCapsule
- nbr_atom(rosetta.core.conformation.Residue) -> int
Returns the index number of this residue's atom used as a center for neighbor definition
example: C-beta atom for some amino acids
- nbr_atom_xyz(...) from builtins.PyCapsule
- nbr_atom_xyz(rosetta.core.conformation.Residue) -> rosetta.numeric.xyzVector_double_t
- nbr_radius(...) from builtins.PyCapsule
- nbr_radius(rosetta.core.conformation.Residue) -> float
Returns the distance cutoff value used as a radius for neighbor definition
- nbrs(...) from builtins.PyCapsule
- nbrs(self : rosetta.core.conformation.Residue, atm : int) -> rosetta.utility.vector1_unsigned_long
Convenience synonym for bonded_neighbor
- nchi(...) from builtins.PyCapsule
- nchi(rosetta.core.conformation.Residue) -> int
Returns the number of chi angles this residue has
example(s):
residue.nchi()
See also:
Residue
Pose
Pose.chi
Pose.set_chi
- nheavyatoms(...) from builtins.PyCapsule
- nheavyatoms(rosetta.core.conformation.Residue) -> int
Returns the number of heavyatoms in this residue
example(s):
residue.nheavyatoms()
See also:
Residue
Pose
- nonconst_data_ptr(...) from builtins.PyCapsule
- nonconst_data_ptr(rosetta.core.conformation.Residue) -> rosetta.basic.datacache.BasicDataCache
BasicDataCache indexed by enum in residue_datacache.hh
- nu(...) from builtins.PyCapsule
- nu(self : rosetta.core.conformation.Residue, index : int) -> float
Get a specific nu (internal ring) torsion angle by index.
Example: residue.nu(1)
See also:
Residue
Residue.nus
Residue.n_nus
Pose.set_ring_conformation
Pose
Pose.nu
It is intentional that there is no set_nu() function; nu angles should only be modified together.
Use Pose.set_ring_conformation() instead.
- nu_atoms(...) from builtins.PyCapsule
- nu_atoms(*args, **kwargs)
Overloaded function.
1. nu_atoms(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t
Return the AtomIndices of each set of four atoms defining each nu angle.
2. nu_atoms(self : rosetta.core.conformation.Residue, index : int) -> rosetta.utility.vector1_unsigned_long
Return the AtomIndices of the four atoms defining the specified nu angle.
- nus(...) from builtins.PyCapsule
- nus(*args, **kwargs)
Overloaded function.
1. nus(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_double
Return the nu (internal ring) torsion angles of this residue.
Example: residue.nus()
See also:
Residue
Residue.nu
Residue.n_nus
Pose.set_ring_conformation
Pose
Pose.nu
2. nus(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_double
Return the nu (internal ring) torsion angles of this residue. (non-const)
- orbital_name(...) from builtins.PyCapsule
- orbital_name(self : rosetta.core.conformation.Residue, orbital_index : int) -> str
- orbital_type(...) from builtins.PyCapsule
- orbital_type(self : rosetta.core.conformation.Residue, orbital_index : int) -> rosetta.core.chemical.orbitals.OrbitalType
- orbital_type_index(...) from builtins.PyCapsule
- orbital_type_index(self : rosetta.core.conformation.Residue, orbital_index : int) -> int
- orbital_xyz(...) from builtins.PyCapsule
- orbital_xyz(self : rosetta.core.conformation.Residue, orbital_index : int) -> rosetta.numeric.xyzVector_double_t
- orient_onto_residue(...) from builtins.PyCapsule
- orient_onto_residue(*args, **kwargs)
Overloaded function.
1. orient_onto_residue(self : rosetta.core.conformation.Residue, src : rosetta.core.conformation.Residue) -> NoneType
Orient our coords onto those of <src>, using the atoms from select_orient_atoms
2. orient_onto_residue(self : rosetta.core.conformation.Residue, src : rosetta.core.conformation.Residue, atom_pairs : rosetta.utility.vector1_std_pair_std_string_std_string_t) -> NoneType
- orient_onto_residue_peptoid(...) from builtins.PyCapsule
- orient_onto_residue_peptoid(self : rosetta.core.conformation.Residue, src : rosetta.core.conformation.Residue, conformation : core::conformation::Conformation) -> NoneType
Orient our coords onto those of src, uses hard coded atom names (yuck) and will work for peptoid on to peptoid/peptide
- path_distance(...) from builtins.PyCapsule
- path_distance(*args, **kwargs)
Overloaded function.
1. path_distance(self : rosetta.core.conformation.Residue, atom : int) -> rosetta.utility.vector1_int
Returns the shortest path distance from <atom> to any other atom in this residue
example(s):
See also:
Residue
Residue.atom
Residue.atoms
Pose
2. path_distance(self : rosetta.core.conformation.Residue, at1 : int, at2 : int) -> int
Returns the number of bonds separating atom <at1> from <at2>
example(s):
See also:
Residue
Residue.atom
Residue.atoms
Residue.path_distance
Pose
- path_distances(...) from builtins.PyCapsule
- path_distances(rosetta.core.conformation.Residue) -> rosetta.utility.vector1_utility_vector1_int_std_allocator_int_t
Returns the shortest path distance for any atom pair in this residue
example: path_distances()[atom1][atom2]
example(s):
See also:
Residue
Residue.atom
Residue.atoms
Residue.path_distance
Pose
- place(...) from builtins.PyCapsule
- place(*args, **kwargs)
Overloaded function.
1. place(self : rosetta.core.conformation.Residue, src : rosetta.core.conformation.Residue, conformation : core::conformation::Conformation) -> NoneType
Place this rotamer at the sequence position occupied by <src>
by reorienting the ideal side chain coordinates to match
2. place(self : rosetta.core.conformation.Residue, src : rosetta.core.conformation.Residue, conformation : core::conformation::Conformation, preserve_c_beta : bool) -> NoneType
Place this rotamer at the sequence position occupied by <src>
by reorienting the ideal side chain coordinates to match
- polymeric_oriented_sequence_distance(...) from builtins.PyCapsule
- polymeric_oriented_sequence_distance(self : rosetta.core.conformation.Residue, other : rosetta.core.conformation.Residue) -> int
Returns the sequence separation distance between this residue and <other>
positive if the other residue is downstream in sequence
- polymeric_sequence_distance(...) from builtins.PyCapsule
- polymeric_sequence_distance(self : rosetta.core.conformation.Residue, other : rosetta.core.conformation.Residue) -> int
Returns the sequence separation distance between this residue and <other>
: magnitude of distance only
- pseudobonds(...) from builtins.PyCapsule
- pseudobonds(rosetta.core.conformation.Residue) -> rosetta.std.map_unsigned_long_std_shared_ptr_const_core_conformation_PseudoBondCollection_t
- requires_actcoord(...) from builtins.PyCapsule
- requires_actcoord(rosetta.core.conformation.Residue) -> bool
does this residue require an actcoord?
- residue_connect_atom_index(...) from builtins.PyCapsule
- residue_connect_atom_index(self : rosetta.core.conformation.Residue, resconn_id : int) -> int
- residue_connection(...) from builtins.PyCapsule
- residue_connection(self : rosetta.core.conformation.Residue, resconn_index : int) -> rosetta.core.chemical.ResidueConnection
Returns this residue's ResidueConnection
a ResidueConnection has internal coords info
on how to build the atom in a different residue which
connects to this residue
- residue_connection_conn_id(...) from builtins.PyCapsule
- residue_connection_conn_id(self : rosetta.core.conformation.Residue, resconn_index : int) -> int
Returns the connection id on the OTHER residue connected to this residue at this residue's
connection resconn_index.
For example, if this were a normally-connected alpha amino acid, residue_connection_conn_id(1)
would return 2, since the first connection in this residue is attached to the second connection in the
previous residue.
- residue_connection_partner(...) from builtins.PyCapsule
- residue_connection_partner(*args, **kwargs)
Overloaded function.
1. residue_connection_partner(self : rosetta.core.conformation.Residue, resconn_index : int) -> int
Returns the residue number of a residue connected to this residue
at this residue's connection resconn_index.
For example, in a normally-connected pose made of alpha-amino
acids, calling residue_connection_partner(1) on residue 6 should return
5, since residue 6 is connected to residue 5 at the first connection of
residue 6.
2. residue_connection_partner(self : rosetta.core.conformation.Residue, resconn_index : int, otherres : int, other_connid : int) -> NoneType
set a connection to this residue by adding its partner's residue number
- residue_type_set(...) from builtins.PyCapsule
- residue_type_set(rosetta.core.conformation.Residue) -> rosetta.core.chemical.ResidueTypeSet
Returns this residue's ResidueTypeSet
- ring_conformer(...) from builtins.PyCapsule
- ring_conformer(self : rosetta.core.conformation.Residue, ring_num : int) -> rosetta.core.chemical.rings.RingConformer
Return the current RingConformer of this residue's nth ring.
- select_orient_atoms(...) from builtins.PyCapsule
- select_orient_atoms(self : rosetta.core.conformation.Residue, center : int, nbr1 : int, nbr2 : int) -> NoneType
Selects three atoms for orienting this residue
- seqpos(...) from builtins.PyCapsule
- seqpos(*args, **kwargs)
Overloaded function.
1. seqpos(rosetta.core.conformation.Residue) -> int
Returns the sequence position of this residue
2. seqpos(self : rosetta.core.conformation.Residue, setting : int) -> NoneType
Sets this residue's sequence position to <setting>
- set_all_chi(...) from builtins.PyCapsule
- set_all_chi(self : rosetta.core.conformation.Residue, chis : rosetta.utility.vector1_double) -> NoneType
Sets all of this residue's chi angles using the set_chi function
(wrapper function)
- set_all_nu(...) from builtins.PyCapsule
- set_all_nu(self : rosetta.core.conformation.Residue, nus : rosetta.utility.vector1_double, taus : rosetta.utility.vector1_double) -> NoneType
- set_all_ring_nu(...) from builtins.PyCapsule
- set_all_ring_nu(self : rosetta.core.conformation.Residue, start : int, end : int, nus : rosetta.utility.vector1_double, taus : rosetta.utility.vector1_double) -> NoneType
- set_chi(...) from builtins.PyCapsule
- set_chi(self : rosetta.core.conformation.Residue, chino : int, setting : float) -> NoneType
Sets this residue's chi angle <chino> to <setting>
assuming that changes propagate according to the atom_base tree
- set_d(...) from builtins.PyCapsule
- set_d(self : rosetta.core.conformation.Residue, chino : int, setting : float) -> NoneType
bondlength analog to set_chi
like set_chi, assumes changes propagate to atomtree
keyed off of chi#, so we only allow distances corresponding to chi angles to refine
distance corresponds to the distance between atoms 3 and 4 defining the chi
chino==0 ==> CA-CB distance, which allows us to refine ALA CB position for example
fpd
- set_orbital_xyz(...) from builtins.PyCapsule
- set_orbital_xyz(self : rosetta.core.conformation.Residue, orbital_index : int, xyz_in : rosetta.numeric.xyzVector_double_t) -> NoneType
- set_pseudobonds_to_residue(...) from builtins.PyCapsule
- set_pseudobonds_to_residue(self : rosetta.core.conformation.Residue, resid : int, pbs : core::conformation::PseudoBondCollection) -> NoneType
- set_tau(...) from builtins.PyCapsule
- set_tau(self : rosetta.core.conformation.Residue, nuno : int, setting : float) -> NoneType
set_theta for nus
- set_theta(...) from builtins.PyCapsule
- set_theta(self : rosetta.core.conformation.Residue, chino : int, setting : float) -> NoneType
bondangle analog to set_chi
same idea as set_d
fpd
- set_xyz(...) from builtins.PyCapsule
- set_xyz(*args, **kwargs)
Overloaded function.
1. set_xyz(self : rosetta.core.conformation.Residue, atm_index : int, xyz_in : rosetta.numeric.xyzVector_double_t) -> NoneType
Sets the position of this residue's atom with index number <atm_index>
example(s):
See also:
Residue
Residue.atom
Residue.atoms
Residue.xyz
Pose
2. set_xyz(self : rosetta.core.conformation.Residue, atm_name : str, xyz_in : rosetta.numeric.xyzVector_double_t) -> NoneType
Sets the position of this residue's atom with name <atm_name>
example(s):
See also:
Residue
Residue.atom
Residue.atoms
Residue.xyz
Pose
- sidechainAtoms_begin(...) from builtins.PyCapsule
- sidechainAtoms_begin(rosetta.core.conformation.Residue) -> __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >
should be safe, given the atom ordering rules?
- type(...) from builtins.PyCapsule
- type(rosetta.core.conformation.Residue) -> rosetta.core.chemical.ResidueType
Returns this residue's ResidueType
example(s):
residue.type()
See also:
Residue
Residue.atom_type
- update_actcoord(...) from builtins.PyCapsule
- update_actcoord(rosetta.core.conformation.Residue) -> NoneType
Updates actcoord for this residue
- update_connections_to_other_residue(...) from builtins.PyCapsule
- update_connections_to_other_residue(self : rosetta.core.conformation.Residue, other_rsd : rosetta.core.conformation.Residue) -> NoneType
Search through the other residue for connections to this residue, and
ensure that this residue's connect_map is up to date with that residue's
connection indices (and residue number).
Vikram K. Mulligan (vmullig.edu)
- update_nus(...) from builtins.PyCapsule
- update_nus(rosetta.core.conformation.Residue) -> NoneType
Calculate the set of nu dihedrals from the xyz coordinates and store them.
- update_orbital_coords(...) from builtins.PyCapsule
- update_orbital_coords(rosetta.core.conformation.Residue) -> NoneType
- update_sequence_numbering(...) from builtins.PyCapsule
- update_sequence_numbering(self : rosetta.core.conformation.Residue, old2new : rosetta.utility.vector1_unsigned_long) -> NoneType
Updates the sequence numbers for this residue and the numbers
stored about its non-polymer connections
called by our owning conformation when the sequence numbers are remapped
- upper_connect(...) from builtins.PyCapsule
- upper_connect(rosetta.core.conformation.Residue) -> rosetta.core.chemical.ResidueConnection
Returns this residue's upper_connection
a ResidueConnection has internal coords info
on how to build the atom in the next residue which
connects to this residue
- upper_connect_atom(...) from builtins.PyCapsule
- upper_connect_atom(rosetta.core.conformation.Residue) -> int
Returns the index number of this residue's atom which connects to
the residue after it in sequence
: polymers only, example: for an amino acid, residue.upper_connect_atom() = atom_index("C")
example(s):
residue.upper_connect_atom()
See also:
Residue
Residue.atom
Residue.atoms
Residue.lower_connect_atom
Pose
- xyz(...) from builtins.PyCapsule
- xyz(*args, **kwargs)
Overloaded function.
1. xyz(self : rosetta.core.conformation.Residue, atm_index : int) -> rosetta.numeric.xyzVector_double_t
Returns the position of this residue's atom with index number <atm_index>
: position is a Vector
example(s):
residue.xyz(3)
See also:
Residue
Residue.atom
Residue.atoms
Residue.set_xyz
Pose
2. xyz(self : rosetta.core.conformation.Residue, atm_name : str) -> rosetta.numeric.xyzVector_double_t
Returns the position of this residue's atom with name <atm_name>
: position is a Vector
example(s):
residue.xyz("CA")
See also:
Residue
Residue.atom
Residue.atoms
Residue.set_xyz
Pose
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class ResidueFactory(builtins.object) |
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a collection of functions making a single residue
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.core.conformation.ResidueFactory) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- create_residue(...) from builtins.PyCapsule
- create_residue(*args, **kwargs)
Overloaded function.
1. create_residue(rsd_type : rosetta.core.chemical.ResidueType) -> rosetta.core.conformation.Residue
creates residue of desired type, coords are ideal values in some default spatial orientation
2. create_residue(rsd_type : rosetta.core.chemical.ResidueType, current_rsd : rosetta.core.conformation.Residue, conformation : rosetta.core.conformation.Conformation) -> rosetta.core.conformation.Residue
rotamer-style creation, uses backbone of existing residue (current_rsd)
3. create_residue(rsd_type : rosetta.core.chemical.ResidueType, current_rsd : rosetta.core.conformation.Residue, conformation : rosetta.core.conformation.Conformation, preserve_c_beta : bool) -> rosetta.core.conformation.Residue
rotamer-style creation, uses backbone of existing residue (current_rsd)
|
class ResidueKinWriter(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.conformation.ResidueKinWriter) -> NoneType
2. __init__(self : rosetta.core.conformation.ResidueKinWriter, : rosetta.core.conformation.ResidueKinWriter) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- animate(...) from builtins.PyCapsule
- animate(self : rosetta.core.conformation.ResidueKinWriter, setting : bool) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.conformation.ResidueKinWriter, : rosetta.core.conformation.ResidueKinWriter) -> rosetta.core.conformation.ResidueKinWriter
- dominant(...) from builtins.PyCapsule
- dominant(self : rosetta.core.conformation.ResidueKinWriter, setting : bool) -> NoneType
- group(...) from builtins.PyCapsule
- group(self : rosetta.core.conformation.ResidueKinWriter, setting : bool) -> NoneType
- master(...) from builtins.PyCapsule
- master(self : rosetta.core.conformation.ResidueKinWriter, setting : str) -> NoneType
- write_apolar_hydrogens(...) from builtins.PyCapsule
- write_apolar_hydrogens(self : rosetta.core.conformation.ResidueKinWriter, setting : bool) -> NoneType
- write_backbone_hydrogens(...) from builtins.PyCapsule
- write_backbone_hydrogens(self : rosetta.core.conformation.ResidueKinWriter, setting : bool) -> NoneType
- write_hydrogens(...) from builtins.PyCapsule
- write_hydrogens(self : rosetta.core.conformation.ResidueKinWriter, setting : bool) -> NoneType
Calling this function with the setting "true", turns on polar, apolar, and backbone hydrogen writing.
Calling this function with the setting "false", turns off polar, apolar, and backbone hydrogen writing.
- write_polar_hydrogens(...) from builtins.PyCapsule
- write_polar_hydrogens(self : rosetta.core.conformation.ResidueKinWriter, setting : bool) -> NoneType
- write_virtual_atoms(...) from builtins.PyCapsule
- write_virtual_atoms(self : rosetta.core.conformation.ResidueKinWriter, setting : bool) -> NoneType
|
class RotamerSetBase(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.core.conformation.RotamerSetBase) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.conformation.RotamerSetBase, : rosetta.core.conformation.RotamerSetBase) -> rosetta.core.conformation.RotamerSetBase
- data(...) from builtins.PyCapsule
- data(*args, **kwargs)
Overloaded function.
1. data(rosetta.core.conformation.RotamerSetBase) -> rosetta.basic.datacache.BasicDataCache
BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh
2. data(rosetta.core.conformation.RotamerSetBase) -> rosetta.basic.datacache.BasicDataCache
BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh
- get_n_residue_types(...) from builtins.PyCapsule
- get_n_residue_types(rosetta.core.conformation.RotamerSetBase) -> int
- get_n_rotamers_for_residue_type(...) from builtins.PyCapsule
- get_n_rotamers_for_residue_type(self : rosetta.core.conformation.RotamerSetBase, which_restype : int) -> int
- get_residue_type_begin(...) from builtins.PyCapsule
- get_residue_type_begin(self : rosetta.core.conformation.RotamerSetBase, which_restype : int) -> int
- get_residue_type_index_for_rotamer(...) from builtins.PyCapsule
- get_residue_type_index_for_rotamer(self : rosetta.core.conformation.RotamerSetBase, which_rotamer : int) -> int
Rotamers i to i+j of all the same residue type are grouped together.
This function returns the index of the residue type in a contiguous block
of rotamers. E.g. rotamers 100 to 120 might all be lysine rotamers, and might
be the 8th residue type, with the first 7 residue types spanning rotamers 1 to 99.
If new lysine rotamers are appended to the end of the rotamer set, they are
considered to be in a separate residue type block. Lysine rotamers 200 to 210 might
be block 15 while lysine rotamers 100 to 120 are still block 7.
- get_trie(...) from builtins.PyCapsule
- get_trie(self : rosetta.core.conformation.RotamerSetBase, method_enum_id : int) -> rosetta.core.conformation.AbstractRotamerTrie
- nonconst_rotamer(...) from builtins.PyCapsule
- nonconst_rotamer(self : rosetta.core.conformation.RotamerSetBase, rot_id : int) -> rosetta.core.conformation.Residue
mutatable access to a single rotamer in the set.
- num_rotamers(...) from builtins.PyCapsule
- num_rotamers(rosetta.core.conformation.RotamerSetBase) -> int
- resid(...) from builtins.PyCapsule
- resid(rosetta.core.conformation.RotamerSetBase) -> int
- rotamer(...) from builtins.PyCapsule
- rotamer(self : rosetta.core.conformation.RotamerSetBase, rot_id : int) -> rosetta.core.conformation.Residue
- rotamer_ref(...) from builtins.PyCapsule
- rotamer_ref(self : rosetta.core.conformation.RotamerSetBase, rot_id : int) -> rosetta.core.conformation.Residue
- store_trie(...) from builtins.PyCapsule
- store_trie(self : rosetta.core.conformation.RotamerSetBase, method_enum_id : int, trie : rosetta.core.conformation.AbstractRotamerTrie) -> NoneType
|
class UltraLightResidue(builtins.object) |
| | |
Methods defined here:
- __getitem__(...) from builtins.PyCapsule
- __getitem__(*args, **kwargs)
Overloaded function.
1. __getitem__(self : rosetta.core.conformation.UltraLightResidue, index : int) -> rosetta.numeric.xyzVector_double_t
2. __getitem__(self : rosetta.core.conformation.UltraLightResidue, index : int) -> rosetta.numeric.xyzVector_double_t
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.core.conformation.UltraLightResidue, residue : rosetta.core.conformation.Residue) -> NoneType
2. __init__(self : rosetta.core.conformation.UltraLightResidue, src : rosetta.core.conformation.UltraLightResidue) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- align_to_residue(...) from builtins.PyCapsule
- align_to_residue(self : rosetta.core.conformation.UltraLightResidue, other_residue : rosetta.core.conformation.UltraLightResidue) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.conformation.UltraLightResidue, : rosetta.core.conformation.UltraLightResidue) -> rosetta.core.conformation.UltraLightResidue
- center(...) from builtins.PyCapsule
- center(rosetta.core.conformation.UltraLightResidue) -> rosetta.numeric.xyzVector_double_t
get centerpoint of residue
- coords_vector(...) from builtins.PyCapsule
- coords_vector(rosetta.core.conformation.UltraLightResidue) -> rosetta.utility.vector1_numeric_xyzVector_double_t
get const ref to residue coords
- natoms(...) from builtins.PyCapsule
- natoms(rosetta.core.conformation.UltraLightResidue) -> int
return number of atoms in ultralight residue
- residue(...) from builtins.PyCapsule
- residue(rosetta.core.conformation.UltraLightResidue) -> rosetta.core.conformation.Residue
return a constant pointer to the base residue
- slide(...) from builtins.PyCapsule
- slide(self : rosetta.core.conformation.UltraLightResidue, translation_vector : rosetta.numeric.xyzVector_double_t) -> NoneType
- transform(...) from builtins.PyCapsule
- transform(self : rosetta.core.conformation.UltraLightResidue, rotation_matrix : rosetta.numeric.xyzMatrix_double_t, translation_vector : rosetta.numeric.xyzVector_double_t) -> NoneType
- update_conformation(...) from builtins.PyCapsule
- update_conformation(self : rosetta.core.conformation.UltraLightResidue, conformation : rosetta.core.conformation.Conformation) -> NoneType
update conformation with current coords. Slow.
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class ppo_torsion_bin(builtins.object) |
| |
Enumeration representing the different phi/psi/omega torsion bins
|
| |
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(rosetta.core.conformation.ppo_torsion_bin, rosetta.core.conformation.ppo_torsion_bin) -> bool
- __hash__(...) from builtins.PyCapsule
- __hash__(rosetta.core.conformation.ppo_torsion_bin) -> int
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.conformation.ppo_torsion_bin, int) -> NoneType
2. __init__(rosetta.core.conformation.ppo_torsion_bin, int) -> NoneType
- __int__(...) from builtins.PyCapsule
- __int__(rosetta.core.conformation.ppo_torsion_bin) -> int
- __ne__(...) from builtins.PyCapsule
- __ne__(rosetta.core.conformation.ppo_torsion_bin, rosetta.core.conformation.ppo_torsion_bin) -> bool
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __repr__(...) from builtins.PyCapsule
- __repr__(rosetta.core.conformation.ppo_torsion_bin) -> str
Data and other attributes defined here:
- n_ppo_torsion_bins = ppo_torsion_bin.n_ppo_torsion_bins
- ppo_torbin_A = ppo_torsion_bin.ppo_torbin_A
- ppo_torbin_B = ppo_torsion_bin.ppo_torbin_B
- ppo_torbin_E = ppo_torsion_bin.ppo_torbin_E
- ppo_torbin_G = ppo_torsion_bin.ppo_torbin_G
- ppo_torbin_U = ppo_torsion_bin.n_ppo_torsion_bins
- ppo_torbin_X = ppo_torsion_bin.ppo_torbin_X
- ppo_torbin_a = ppo_torsion_bin.ppo_torbin_a
- ppo_torbin_b = ppo_torsion_bin.ppo_torbin_b
- ppo_torbin_e = ppo_torsion_bin.ppo_torbin_e
- ppo_torbin_g = ppo_torsion_bin.ppo_torbin_g
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