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- rosetta.core.conformation.parametric.Parameters(builtins.object)
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- BundleParameters
- rosetta.core.conformation.parametric.ParametersSet(builtins.object)
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- BundleParametersSet
class BundleParameters(rosetta.core.conformation.parametric.Parameters) |
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Parameters class, used to store sets of parameters for parametric backbone generation.
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- Method resolution order:
- BundleParameters
- rosetta.core.conformation.parametric.Parameters
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.helical_bundle.parameters.BundleParameters) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_delta_omega1_value(...) from builtins.PyCapsule
- add_delta_omega1_value(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, val : float) -> NoneType
Adds a value to the list of minor helix angular offsets around the minor helix axis, defined on a per-atom basis.
In radians.
- add_delta_z1_value(...) from builtins.PyCapsule
- add_delta_z1_value(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, val : float) -> NoneType
Adds a value to the list of minor helix offsets along the minor helix axis, defined on a per-atom basis.
In radians.
- add_r1_value(...) from builtins.PyCapsule
- add_r1_value(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, val : float) -> NoneType
Adds a value to the minor helix radius list.
In Angstroms
- allow_bondangles(...) from builtins.PyCapsule
- allow_bondangles(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> bool
Should the generator set mainchain bond angle values?
- allow_bondlengths(...) from builtins.PyCapsule
- allow_bondlengths(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> bool
Should the generator set mainchain bond length values?
- allow_dihedrals(...) from builtins.PyCapsule
- allow_dihedrals(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> bool
Should the generator set mainchain dihedral values?
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, : rosetta.protocols.helical_bundle.parameters.BundleParameters) -> rosetta.protocols.helical_bundle.parameters.BundleParameters
- atoms_per_residue(...) from builtins.PyCapsule
- atoms_per_residue(*args, **kwargs)
Overloaded function.
1. atoms_per_residue(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, index_in_repeating_unit : int) -> int
Return the number of atoms in one of the residues in the repeating unit of the minor helix.
2. atoms_per_residue(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> rosetta.utility.vector1_unsigned_long
Return the atoms_per_residue vector (const-access).
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> rosetta.core.conformation.parametric.Parameters
Copy this residue( allocate actual memory for it )
- delta_omega0(...) from builtins.PyCapsule
- delta_omega0(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> float
Returns the major helix angular offset about the major helix (bundle) axis.
In radians.
- delta_omega1(...) from builtins.PyCapsule
- delta_omega1(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, index : int) -> float
Returns the minor helix angular offset around the minor helix axis, defined on a per-atom basis, in radians, for the atom with the index value.
The index value is checked to see whether it is in range ONLY in debug-mode compiliation.
- delta_omega1_all(...) from builtins.PyCapsule
- delta_omega1_all(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> float
Returns the minor helix angular offset around the minor helix axis, defined for all atoms (to "roll" the minor helix).
In radians.
- delta_omega1_vect(...) from builtins.PyCapsule
- delta_omega1_vect(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> rosetta.utility.vector1_double
Const-access to the whole delta_omega1 vector.
- delta_t(...) from builtins.PyCapsule
- delta_t(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> float
Residue offset, to "slide" the helix along its path.
In residues (i.e. a value of 0.5 is a half-residue offset).
- delta_z1(...) from builtins.PyCapsule
- delta_z1(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, index : int) -> float
Returns the minor helix offset along the minor helix axis, defined on a per-atom basis, in Angstroms, for the atom with the index value.
The index value is checked to see whether it is in range ONLY in debug-mode compiliation.
- delta_z1_vect(...) from builtins.PyCapsule
- delta_z1_vect(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> rosetta.utility.vector1_double
Const-access to the whole delta_z1 vector.
- get_pdb_remark(...) from builtins.PyCapsule
- get_pdb_remark(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, remark : std::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >) -> NoneType
Get a summary of this ParametersSet object, for output to remark lines of a PDB file.
- invert_helix(...) from builtins.PyCapsule
- invert_helix(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> bool
Should the helix direction be reversed?
- omega0(...) from builtins.PyCapsule
- omega0(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> float
Returns the major helix twist per residue.
In radians.
- omega1(...) from builtins.PyCapsule
- omega1(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> float
Returns the minor helix turn per residue, defined for all atoms.
In radians.
- r0(...) from builtins.PyCapsule
- r0(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> float
Returns the major helix radius.
In Angstroms.
- r1(...) from builtins.PyCapsule
- r1(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, index : int) -> float
Returns the minor helix r1 value for the atom with the index value, in Angstroms.
The index value is checked to see whether it is in range ONLY in debug-mode compiliation.
- r1_vect(...) from builtins.PyCapsule
- r1_vect(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> rosetta.utility.vector1_double
Const-access to the whole r1 vector.
- repeating_unit_offset(...) from builtins.PyCapsule
- repeating_unit_offset(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> int
Returns the residue offset in the repeating unit in the minor helix.
An offset of 0 means that the first residue in the helix is the first
residue of the repeating unit. An offset of 1 means that the first residue in
the helix is the second residue in the repeating unit, etc.
- reset_delta_omega1(...) from builtins.PyCapsule
- reset_delta_omega1(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> NoneType
Resets the list of minor helix angular offsets around the minor helix axis, defined on a per-atom basis.
- reset_delta_z1(...) from builtins.PyCapsule
- reset_delta_z1(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> NoneType
Resets the list of minor helix offsets along the minor helix axis, defined on a per-atom basis.
- reset_r1(...) from builtins.PyCapsule
- reset_r1(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> NoneType
Resets the minor helix radius list.
- residues_per_repeat(...) from builtins.PyCapsule
- residues_per_repeat(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> int
Returns the number of residues per repeating unit in the minor helix.
- set_allow_bondangles(...) from builtins.PyCapsule
- set_allow_bondangles(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, val : bool) -> NoneType
Set whether the generator should be able to set mainchain bond angle values.
- set_allow_bondlengths(...) from builtins.PyCapsule
- set_allow_bondlengths(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, val : bool) -> NoneType
Set whether the generator should be able to set mainchain bond length values.
- set_allow_dihedrals(...) from builtins.PyCapsule
- set_allow_dihedrals(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, val : bool) -> NoneType
Set whether the generator should be able to set mainchain dihedral values.
- set_atoms_per_residue(...) from builtins.PyCapsule
- set_atoms_per_residue(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, atoms_per_residue_in : rosetta.utility.vector1_unsigned_long) -> NoneType
Set the number of residues in the repeating unit in the helix.
Note that there is no check that the size of the atoms_per_residue_ vector matches residues_per_repeat_.
- set_delta_omega0(...) from builtins.PyCapsule
- set_delta_omega0(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, val : float) -> NoneType
Sets the major helix angular offset about the major helix (bundle) axis.
In radians.
- set_delta_omega1(...) from builtins.PyCapsule
- set_delta_omega1(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, vals : rosetta.utility.vector1_double) -> NoneType
Sets the list of minor helix angular offsets around the minor helix axis, defined on a per-atom basis, to a pre-defined list.
Values in radians.
- set_delta_omega1_all(...) from builtins.PyCapsule
- set_delta_omega1_all(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, val : float) -> NoneType
Sets the minor helix angular offset around the minor helix axis, defined for all atoms (to "roll" the minor helix).
In radians.
- set_delta_t(...) from builtins.PyCapsule
- set_delta_t(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, val : float) -> NoneType
Set the residue offset, to "slide" the helix along its path.
In residues (i.e. a value of 0.5 is a half-residue offset).
- set_delta_z1(...) from builtins.PyCapsule
- set_delta_z1(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, vals : rosetta.utility.vector1_double) -> NoneType
Sets the list of minor helix offsets along the minor helix axis, defined on a per-atom basis, to a pre-defined list.
Values in Angstroms.
- set_invert_helix(...) from builtins.PyCapsule
- set_invert_helix(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, val : bool) -> NoneType
Set whether the helix direction be reversed.
- set_omega0(...) from builtins.PyCapsule
- set_omega0(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, val : float) -> NoneType
Sets the major helix twist per residue.
In radians.
- set_omega1(...) from builtins.PyCapsule
- set_omega1(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, val : float) -> NoneType
Sets the minor helix twist per residue.
In radians.
- set_r0(...) from builtins.PyCapsule
- set_r0(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, val : float) -> NoneType
Sets the major helix radius.
In Angstroms.
- set_r1(...) from builtins.PyCapsule
- set_r1(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, vals : rosetta.utility.vector1_double) -> NoneType
Sets the minor helix radius list to a pre-defined list.
Values in Angstroms.
- set_repeating_unit_offset(...) from builtins.PyCapsule
- set_repeating_unit_offset(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, val : int) -> NoneType
Sets the residue offset in the repeating unit in the minor helix.
An offset of 0 means that the first residue in the helix is the first
residue of the repeating unit. An offset of 1 means that the first residue in
the helix is the second residue in the repeating unit, etc.
- set_residues_per_repeat(...) from builtins.PyCapsule
- set_residues_per_repeat(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, val : int) -> NoneType
Sets the number of residues per repeating unit in the minor helix.
- set_z0_offset(...) from builtins.PyCapsule
- set_z0_offset(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, val : float) -> NoneType
Sets the minor helix offset along the major helix axis, defined on a per-helix basis, in Angstroms.
- set_z1(...) from builtins.PyCapsule
- set_z1(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, val : float) -> NoneType
Sets the minor helix rise per residue, defined for all atoms.
In Angstroms.
- set_z1_offset(...) from builtins.PyCapsule
- set_z1_offset(self : rosetta.protocols.helical_bundle.parameters.BundleParameters, val : float) -> NoneType
Sets the minor helix offset along the minor helix axis, defined on a per-helix basis, in Angstroms.
- z0_offset(...) from builtins.PyCapsule
- z0_offset(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> float
Returns the minor helix offset along the major helix axis, defined on a per-helix basis, in Angstroms.
- z1(...) from builtins.PyCapsule
- z1(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> float
Returns the minor helix rise per residue, defined for all atoms.
In Angstroms.
- z1_offset(...) from builtins.PyCapsule
- z1_offset(rosetta.protocols.helical_bundle.parameters.BundleParameters) -> float
Returns the minor helix offset along the minor helix axis, defined on a per-helix basis, in Angstroms.
Methods inherited from rosetta.core.conformation.parametric.Parameters:
- add_residue(...) from builtins.PyCapsule
- add_residue(self : rosetta.core.conformation.parametric.Parameters, residue : rosetta.core.conformation.Residue) -> NoneType
Add a residue to the list of residues that these parameters describe.
- first_residue(...) from builtins.PyCapsule
- first_residue(rosetta.core.conformation.parametric.Parameters) -> rosetta.core.conformation.Residue
Get a const owning pointer to the first residue in the list of residues that these parameters describe.
Note that this might not be the first residue in linear sequence, if the residues were put in in non-
sequential order or the residue numbering has changed.
- first_residue_index(...) from builtins.PyCapsule
- first_residue_index(rosetta.core.conformation.parametric.Parameters) -> int
Get the index of the first residue.
MUST BE REWRITTEN when the OP issue is resolved.
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.core.conformation.parametric.Parameters) -> rosetta.core.conformation.parametric.Parameters
self pointers
2. get_self_ptr(rosetta.core.conformation.parametric.Parameters) -> rosetta.core.conformation.parametric.Parameters
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.core.conformation.parametric.Parameters) -> rosetta.std.weak_ptr_const_core_conformation_parametric_Parameters_t
2. get_self_weak_ptr(rosetta.core.conformation.parametric.Parameters) -> rosetta.std.weak_ptr_core_conformation_parametric_Parameters_t
- last_residue(...) from builtins.PyCapsule
- last_residue(rosetta.core.conformation.parametric.Parameters) -> rosetta.core.conformation.Residue
Get a const owning pointer to the last residue in the list of residues that these parameters describe.
Note that this might not be the last residue in linear sequence, if the residues were put in in non-
sequential order or the residue numbering has changed.
- last_residue_index(...) from builtins.PyCapsule
- last_residue_index(rosetta.core.conformation.parametric.Parameters) -> int
Get the index of the last residue.
MUST BE REWRITTEN when the OP issue is resolved.
- n_residue(...) from builtins.PyCapsule
- n_residue(rosetta.core.conformation.parametric.Parameters) -> int
Returns the number (count) of residues that these parameters describe.
- reset_residue_list(...) from builtins.PyCapsule
- reset_residue_list(rosetta.core.conformation.parametric.Parameters) -> NoneType
Clears the list of residues that these parameters describe.
- residue(...) from builtins.PyCapsule
- residue(self : rosetta.core.conformation.parametric.Parameters, index : int) -> rosetta.core.conformation.Residue
Get an owning pointer to a residue in the list of residues that these parameters describe.
- residue_cop(...) from builtins.PyCapsule
- residue_cop(self : rosetta.core.conformation.parametric.Parameters, index : int) -> rosetta.core.conformation.Residue
Get a const owning pointer to a residue in the list of residues that these parameters describe.
- set_residue(...) from builtins.PyCapsule
- set_residue(self : rosetta.core.conformation.parametric.Parameters, index : int, existing_residue : rosetta.core.conformation.Residue) -> NoneType
Assign an element in the residue list to be an owning pointer to an existing residue.
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class BundleParametersSet(rosetta.core.conformation.parametric.ParametersSet) |
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BundleParametersSet class, used to store sets of parameters for parametric helical bundle generation.
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- Method resolution order:
- BundleParametersSet
- rosetta.core.conformation.parametric.ParametersSet
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.helical_bundle.parameters.BundleParametersSet) -> 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.protocols.helical_bundle.parameters.BundleParametersSet, : rosetta.protocols.helical_bundle.parameters.BundleParametersSet) -> rosetta.protocols.helical_bundle.parameters.BundleParametersSet
- bundle_symmetry(...) from builtins.PyCapsule
- bundle_symmetry(rosetta.protocols.helical_bundle.parameters.BundleParametersSet) -> int
Returns the symmetry of the bundle created.
A value of 0 or 1 indicates no symmetry. Larger values indicate n-fold radial symmetry
(for example, 3 means threefold radial symmetry about the bundle axis, and each helix defined will
be replicated a total of three times).
- bundle_symmetry_copies(...) from builtins.PyCapsule
- bundle_symmetry_copies(rosetta.protocols.helical_bundle.parameters.BundleParametersSet) -> int
Returns the number of symmetry copies to generate.
A value of 0 means to generate all copies. Higher values mean to generate only the first N
copies. For example, if the symmetry were 16 but bundle_symmetry_copies_ were set to 4, only the
first 4 symmetry repeats would be generated.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.helical_bundle.parameters.BundleParametersSet) -> rosetta.core.conformation.parametric.ParametersSet
Copy this residue( allocate actual memory for it )
- get_pdb_remark(...) from builtins.PyCapsule
- get_pdb_remark(self : rosetta.protocols.helical_bundle.parameters.BundleParametersSet, remark : std::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >) -> NoneType
Get a summary of this ParametersSet object, for output to remark lines of a PDB file.
Default function can be overridden by derived classes. This version actually outputs
Crick parameter information.
- n_helices(...) from builtins.PyCapsule
- n_helices(rosetta.protocols.helical_bundle.parameters.BundleParametersSet) -> int
Get the number of helices defined in each symmetry copy of this bundle.
- set_bundle_symmetry(...) from builtins.PyCapsule
- set_bundle_symmetry(self : rosetta.protocols.helical_bundle.parameters.BundleParametersSet, val : int) -> NoneType
Sets the symmetry of the bundle created.
A value of 0 or 1 indicates no symmetry. Larger values indicate n-fold radial symmetry
(for example, 3 means threefold radial symmetry about the bundle axis, and each helix defined will
be replicated a total of three times).
- set_bundle_symmetry_copies(...) from builtins.PyCapsule
- set_bundle_symmetry_copies(self : rosetta.protocols.helical_bundle.parameters.BundleParametersSet, val : int) -> NoneType
Sets the number of symmetry copies to generate.
A value of 0 means to generate all copies. Higher values mean to generate only the first N
copies. For example, if the symmetry were 16 but bundle_symmetry_copies_ were set to 4, only the
first 4 symmetry repeats would be generated.
- set_n_helices(...) from builtins.PyCapsule
- set_n_helices(self : rosetta.protocols.helical_bundle.parameters.BundleParametersSet, val : int) -> NoneType
Set the number of helices defined in each symmetry copy of this bundle.
Methods inherited from rosetta.core.conformation.parametric.ParametersSet:
- add_parameters(...) from builtins.PyCapsule
- add_parameters(self : rosetta.core.conformation.parametric.ParametersSet, new_parameters : rosetta.core.conformation.parametric.Parameters) -> NoneType
Add a Parameters object to the set included in this ParametersSet object.
- clear_parameters_list(...) from builtins.PyCapsule
- clear_parameters_list(rosetta.core.conformation.parametric.ParametersSet) -> NoneType
Delete all owning pointers in the parameters_ list and reset the list.
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.core.conformation.parametric.ParametersSet) -> rosetta.core.conformation.parametric.ParametersSet
self pointers
2. get_self_ptr(rosetta.core.conformation.parametric.ParametersSet) -> rosetta.core.conformation.parametric.ParametersSet
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.core.conformation.parametric.ParametersSet) -> rosetta.std.weak_ptr_const_core_conformation_parametric_ParametersSet_t
2. get_self_weak_ptr(rosetta.core.conformation.parametric.ParametersSet) -> rosetta.std.weak_ptr_core_conformation_parametric_ParametersSet_t
- n_parameters(...) from builtins.PyCapsule
- n_parameters(rosetta.core.conformation.parametric.ParametersSet) -> int
Get the number of Parameters objects associated with this ParametersSet.
- parameters(...) from builtins.PyCapsule
- parameters(*args, **kwargs)
Overloaded function.
1. parameters(self : rosetta.core.conformation.parametric.ParametersSet, index : int) -> rosetta.core.conformation.parametric.Parameters
Get a Parameters object by index.
2. parameters(self : rosetta.core.conformation.parametric.ParametersSet, index : int) -> rosetta.core.conformation.parametric.Parameters
Get a Parameters object by index (const-access).
- update_residue_links(...) from builtins.PyCapsule
- update_residue_links(self : rosetta.core.conformation.parametric.ParametersSet, new_conf : core::conformation::Conformation) -> NoneType
Only for copying Conformation objects, this ensures that the new ParametersSet object's
Parameters objects have lists of ResidueOPs that point to residues in the new Conformation object,
rather than to residues that only exist in the Parameters objects.
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