| |
- builtins.object
-
- ResidueRange
- ResidueSelector
-
- AndResidueSelector
- BinSelector
- ChainSelector
- GlycanResidueSelector
- InterGroupInterfaceByVectorSelector
- JumpDownstreamSelector
- JumpUpstreamSelector
- LayerSelector
- NeighborhoodResidueSelector
- NotResidueSelector
- NumNeighborsSelector
- OrResidueSelector
- PhiSelector
- PrimarySequenceNeighborhoodSelector
- RandomResidueSelector
- ResidueIndexSelector
- ResidueNameSelector
- ResiduePDBInfoHasLabelSelector
- SecondaryStructureSelector
- TrueResidueSelector
- ResidueSelectorCreator
-
- AndResidueSelectorCreator
- BinSelectorCreator
- ChainSelectorCreator
- GlycanResidueSelectorCreator
- InterGroupInterfaceByVectorSelectorCreator
- JumpDownstreamSelectorCreator
- JumpUpstreamSelectorCreator
- LayerSelectorCreator
- NeighborhoodResidueSelectorCreator
- NotResidueSelectorCreator
- NumNeighborsSelectorCreator
- OrResidueSelectorCreator
- PhiSelectorCreator
- PrimarySequenceNeighborhoodSelectorCreator
- RandomResidueSelectorCreator
- ResidueIndexSelectorCreator
- ResidueNameSelectorCreator
- ResiduePDBInfoHasLabelSelectorCreator
- SecondaryStructureSelectorCreator
- TrueResidueSelectorCreator
- ResidueSelectorFactory
- rosetta.basic.datacache.CacheableData(builtins.object)
-
- CachedResidueSubset
- rosetta.utility.vector1_core_select_residue_selector_ResidueRange(builtins.object)
-
- ResidueRanges
- rosetta.utility.vector1_unsigned_long(builtins.object)
-
- ResidueVector
class AndResidueSelector(ResidueSelector) |
|
The AndResidueSelector combines the output of multiple ResidueSelectors using AND
logic, i.e., only residues selected by ALL contained ResidueSelectors will be selected.
ResidueSelecters can be pulled in from a DataMap, from subtags (for ResidueSelectors
known to the ResidueSelectorFactory) or programmatically through %add_residue_selector. |
|
- Method resolution order:
- AndResidueSelector
- ResidueSelector
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.select.residue_selector.AndResidueSelector) -> NoneType
3. __init__(self : handle, selector1 : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType
4. __init__(self : handle, selector1 : rosetta.core.select.residue_selector.ResidueSelector, selector2 : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_residue_selector(...) from builtins.PyCapsule
- add_residue_selector(self : rosetta.core.select.residue_selector.AndResidueSelector, selector : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType
adds a ResidueSelector
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.select.residue_selector.AndResidueSelector, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
- apply_and_to_subset(...) from builtins.PyCapsule
- apply_and_to_subset(self : rosetta.core.select.residue_selector.AndResidueSelector, newSubset : rosetta.utility.vector1_bool, existingSubset : rosetta.utility.vector1_bool) -> NoneType
applies newSubset to existingSubset and thereby modifies the latter
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.residue_selector.AndResidueSelector, : rosetta.core.select.residue_selector.AndResidueSelector) -> rosetta.core.select.residue_selector.AndResidueSelector
- class_name(...) from builtins.PyCapsule
- class_name() -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.AndResidueSelector) -> rosetta.core.select.residue_selector.ResidueSelector
Clone operator.
Copy this object and return an owning pointer to the new object.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.core.select.residue_selector.AndResidueSelector) -> str
- num_selectors(...) from builtins.PyCapsule
- num_selectors(rosetta.core.select.residue_selector.AndResidueSelector) -> int
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.select.residue_selector.AndResidueSelector, tag : rosetta.utility.tag.Tag, datamap : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
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class BinSelector(ResidueSelector) |
|
A ResidueSelector that selects residues based on their torsion bin (e.g. ABEGO bin). |
|
- Method resolution order:
- BinSelector
- ResidueSelector
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.select.residue_selector.BinSelector) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.select.residue_selector.BinSelector, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
"Apply" function.
Given the pose, generate a vector of bools with entries for every residue in the pose
indicating whether each residue is selected ("true") or not ("false").
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.residue_selector.BinSelector, : rosetta.core.select.residue_selector.BinSelector) -> rosetta.core.select.residue_selector.BinSelector
- bin_name(...) from builtins.PyCapsule
- bin_name(rosetta.core.select.residue_selector.BinSelector) -> str
Get the name of the bin that the residues that we will select must be in.
- bin_params_file_name(...) from builtins.PyCapsule
- bin_params_file_name(rosetta.core.select.residue_selector.BinSelector) -> str
Get the name of the bin params file that we'll be using.
- class_name(...) from builtins.PyCapsule
- class_name() -> str
Get the mover class name.
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.BinSelector) -> rosetta.core.select.residue_selector.ResidueSelector
Clone operator.
Copy the current object (creating the copy on the heap) and return an owning pointer
to the copy. All ResidueSelectors must implement this.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.core.select.residue_selector.BinSelector) -> str
Get the mover class name.
- initialize_and_check(...) from builtins.PyCapsule
- initialize_and_check(rosetta.core.select.residue_selector.BinSelector) -> NoneType
Load the bin params file and check that settings are consistent.
Must be called before apply() function.
- initialize_from_file_contents_and_check(...) from builtins.PyCapsule
- initialize_from_file_contents_and_check(self : rosetta.core.select.residue_selector.BinSelector, filecontents : str) -> NoneType
Load the bin params file baed on a file contents string (instead of loading directly
from disk) and check that settings are consistent.
Must be called as an alternative to initialize_and_check() before apply() function.
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.select.residue_selector.BinSelector, tag : rosetta.utility.tag.Tag, datamap : rosetta.basic.datacache.DataMap) -> NoneType
XML parse.
Parse RosettaScripts tags and set up this mover.
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
Provide XSD information, allowing automatic evaluation of bad XML.
- select_only_alpha_aas(...) from builtins.PyCapsule
- select_only_alpha_aas(rosetta.core.select.residue_selector.BinSelector) -> bool
Get whether we're selecting alpha-amino acids only.
- set_bin_name(...) from builtins.PyCapsule
- set_bin_name(self : rosetta.core.select.residue_selector.BinSelector, bin_name_in : str) -> NoneType
Set the name of the bin that the residues that we will select must be in.
- set_bin_params_file_name(...) from builtins.PyCapsule
- set_bin_params_file_name(self : rosetta.core.select.residue_selector.BinSelector, filename_in : str) -> NoneType
Set the name of the bin params file that we'll be using.
- set_select_only_alpha_aas(...) from builtins.PyCapsule
- set_select_only_alpha_aas(self : rosetta.core.select.residue_selector.BinSelector, setting : bool) -> NoneType
Set whether we're selecting alpha-amino acids only.
|
class CachedResidueSubset(rosetta.basic.datacache.CacheableData) |
| |
- Method resolution order:
- CachedResidueSubset
- rosetta.basic.datacache.CacheableData
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.select.residue_selector.CachedResidueSubset) -> 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.select.residue_selector.CachedResidueSubset, : rosetta.core.select.residue_selector.CachedResidueSubset) -> rosetta.core.select.residue_selector.CachedResidueSubset
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.CachedResidueSubset) -> rosetta.basic.datacache.CacheableData
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.core.select.residue_selector.CachedResidueSubset) -> rosetta.basic.datacache.CacheableData
- get_subset(...) from builtins.PyCapsule
- get_subset(self : rosetta.core.select.residue_selector.CachedResidueSubset, name : str) -> rosetta.utility.vector1_bool
- has_subset(...) from builtins.PyCapsule
- has_subset(self : rosetta.core.select.residue_selector.CachedResidueSubset, name : str) -> bool
- set_subset(...) from builtins.PyCapsule
- set_subset(self : rosetta.core.select.residue_selector.CachedResidueSubset, subset : rosetta.utility.vector1_bool, name : str) -> NoneType
Methods inherited from rosetta.basic.datacache.CacheableData:
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData
self pointers
2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t
2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t
|
class GlycanResidueSelector(ResidueSelector) |
|
A ResidueSelector for carbohydrates and individual carbohydrate trees.
Selects all Glycan residues if no option is given or the branch going out from the root residue.
Selecting from root residues allows you to choose the whole glycan branch or only tips, etc. |
|
- Method resolution order:
- GlycanResidueSelector
- ResidueSelector
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, root_residues : rosetta.utility.vector1_bool) -> NoneType
3. __init__(handle, rosetta.core.select.residue_selector.GlycanResidueSelector) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.select.residue_selector.GlycanResidueSelector, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
"Apply" function.
Given the pose, generate a vector of bools with entries for every residue in the pose
indicating whether each residue is selected ("true") or not ("false").
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.residue_selector.GlycanResidueSelector, : rosetta.core.select.residue_selector.GlycanResidueSelector) -> rosetta.core.select.residue_selector.GlycanResidueSelector
- class_name(...) from builtins.PyCapsule
- class_name() -> str
Get the mover class name.
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.GlycanResidueSelector) -> rosetta.core.select.residue_selector.ResidueSelector
Clone operator.
Copy the current object (creating the copy on the heap) and return an owning pointer
to the copy. All ResidueSelectors must implement this.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.core.select.residue_selector.GlycanResidueSelector) -> str
Get the mover class name.
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.select.residue_selector.GlycanResidueSelector, tag : rosetta.utility.tag.Tag, datamap : rosetta.basic.datacache.DataMap) -> NoneType
XML parse.
Parse RosettaScripts tags and set up this mover.
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
Provide XSD information, enabling mechanical validation of input XML.
- set_select_from_branch_residues(...) from builtins.PyCapsule
- set_select_from_branch_residues(self : rosetta.core.select.residue_selector.GlycanResidueSelector, root_residues : rosetta.utility.vector1_bool) -> NoneType
Set the residue(s) to select from. These can be the branch points of the glycans or
carbohydrate residues from which to select the downstream branch from.
Like the rest of a tree from a particular position. That position could be the trunk or individual branches, which keep branching out.
Note that the Subset will not include the Root residue, since many times it will be the ASN root.
|
class InterGroupInterfaceByVectorSelector(ResidueSelector) |
|
The %InterGroupInterfaceByVectorSelector identifies residues at the interface between
two groups of residues using two distance cutoffs: the first, shorter cutoff is based on
atom-atom distances, the second, longer cutoff is used if the c-alpha/c-beta vector of the
residues in the first group point toward the c-alphas of the other group. Each group may be
specified either explicitly through a std::set of residue indices, through a string of
comma-separated values giving either residue indices or PDB ids (e.g. 13B for residue
13 on chain B) or through a ResidueSelector. Clears the passed ReisueSubset. |
|
- Method resolution order:
- InterGroupInterfaceByVectorSelector
- ResidueSelector
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, : rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector
- cb_dist_cut(...) from builtins.PyCapsule
- cb_dist_cut(*args, **kwargs)
Overloaded function.
1. cb_dist_cut(rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> float
2. cb_dist_cut(self : rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting : float) -> NoneType
- class_name(...) from builtins.PyCapsule
- class_name() -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> rosetta.core.select.residue_selector.ResidueSelector
Clone operator.
Copy this object and return an owning pointer to the new object.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> str
- group1_resstring(...) from builtins.PyCapsule
- group1_resstring(*args, **kwargs)
Overloaded function.
1. group1_resstring(rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> str
2. group1_resstring(self : rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting : str) -> NoneType
- group1_selector(...) from builtins.PyCapsule
- group1_selector(*args, **kwargs)
Overloaded function.
1. group1_selector(rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> rosetta.core.select.residue_selector.ResidueSelector
2. group1_selector(self : rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType
- group1_set(...) from builtins.PyCapsule
- group1_set(*args, **kwargs)
Overloaded function.
1. group1_set(rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t
2. group1_set(self : rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType
- group2_resstring(...) from builtins.PyCapsule
- group2_resstring(*args, **kwargs)
Overloaded function.
1. group2_resstring(rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> str
2. group2_resstring(self : rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting : str) -> NoneType
- group2_selector(...) from builtins.PyCapsule
- group2_selector(*args, **kwargs)
Overloaded function.
1. group2_selector(rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> rosetta.core.select.residue_selector.ResidueSelector
2. group2_selector(self : rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType
- group2_set(...) from builtins.PyCapsule
- group2_set(*args, **kwargs)
Overloaded function.
1. group2_set(rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t
2. group2_set(self : rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType
- nearby_atom_cut(...) from builtins.PyCapsule
- nearby_atom_cut(*args, **kwargs)
Overloaded function.
1. nearby_atom_cut(rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> float
2. nearby_atom_cut(self : rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting : float) -> NoneType
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, tag : rosetta.utility.tag.Tag, datamap : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- vector_angle_cut(...) from builtins.PyCapsule
- vector_angle_cut(*args, **kwargs)
Overloaded function.
1. vector_angle_cut(rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> float
2. vector_angle_cut(self : rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting : float) -> NoneType
- vector_dist_cut(...) from builtins.PyCapsule
- vector_dist_cut(*args, **kwargs)
Overloaded function.
1. vector_dist_cut(rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> float
2. vector_dist_cut(self : rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting : float) -> NoneType
|
class JumpDownstreamSelector(ResidueSelector) |
|
The JumpDownstreamSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing
'true' for residue positions which lie downstream of a given jump in the FoldTree. The jump is
specified by an integer index. |
|
- Method resolution order:
- JumpDownstreamSelector
- ResidueSelector
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.select.residue_selector.JumpDownstreamSelector) -> NoneType
3. __init__(self : handle, jump : int) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.select.residue_selector.JumpDownstreamSelector, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.residue_selector.JumpDownstreamSelector, : rosetta.core.select.residue_selector.JumpDownstreamSelector) -> rosetta.core.select.residue_selector.JumpDownstreamSelector
- class_name(...) from builtins.PyCapsule
- class_name() -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.JumpDownstreamSelector) -> rosetta.core.select.residue_selector.ResidueSelector
Clone operator.
Copy this object and return an owning pointer to the new object.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.core.select.residue_selector.JumpDownstreamSelector) -> str
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.select.residue_selector.JumpDownstreamSelector, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_jump(...) from builtins.PyCapsule
- set_jump(self : rosetta.core.select.residue_selector.JumpDownstreamSelector, jump : int) -> NoneType
sets the string by which residues are selected
|
class JumpUpstreamSelector(ResidueSelector) |
|
The JumpUpstreamSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing
'true' for residue positions which lie upstream of a given jump in the FoldTree. The jump is
specified by its integer index. |
|
- Method resolution order:
- JumpUpstreamSelector
- ResidueSelector
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.select.residue_selector.JumpUpstreamSelector) -> NoneType
3. __init__(self : handle, jump : int) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.select.residue_selector.JumpUpstreamSelector, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.residue_selector.JumpUpstreamSelector, : rosetta.core.select.residue_selector.JumpUpstreamSelector) -> rosetta.core.select.residue_selector.JumpUpstreamSelector
- class_name(...) from builtins.PyCapsule
- class_name() -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.JumpUpstreamSelector) -> rosetta.core.select.residue_selector.ResidueSelector
Clone operator.
Copy this object and return an owning pointer to the new object.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.core.select.residue_selector.JumpUpstreamSelector) -> str
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.select.residue_selector.JumpUpstreamSelector, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_jump(...) from builtins.PyCapsule
- set_jump(self : rosetta.core.select.residue_selector.JumpUpstreamSelector, jump : int) -> NoneType
sets the string by which residues are selected
|
class LayerSelector(ResidueSelector) |
|
The LayerSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing
'true' for residue positions which match the given residue index. The index is read as comma-separated
list of either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). Detection
and mapping from PDB to Rosetta residue numbers is done internally. |
|
- Method resolution order:
- LayerSelector
- ResidueSelector
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.select.residue_selector.LayerSelector) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.select.residue_selector.LayerSelector, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
Apply function: generate a ResidueSubset given a Pose.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.residue_selector.LayerSelector, : rosetta.core.select.residue_selector.LayerSelector) -> rosetta.core.select.residue_selector.LayerSelector
- class_name(...) from builtins.PyCapsule
- class_name() -> str
Get the class name.
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.LayerSelector) -> rosetta.core.select.residue_selector.ResidueSelector
Clone operator.
Copy this object and return an owning pointer to the new object.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.core.select.residue_selector.LayerSelector) -> str
Get the class name.
Calls class_name().
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.select.residue_selector.LayerSelector, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
Parse xml tag setting up this selector.
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_angle_exponent(...) from builtins.PyCapsule
- set_angle_exponent(self : rosetta.core.select.residue_selector.LayerSelector, val : float) -> NoneType
Set the sidechain neighbor angle exponent.
See the core::select::util::SelectResiduesByLayer class for details of the math.
- set_angle_shift_factor(...) from builtins.PyCapsule
- set_angle_shift_factor(self : rosetta.core.select.residue_selector.LayerSelector, val : float) -> NoneType
Set the sidechain neighbor angle shift value.
See the core::select::util::SelectResiduesByLayer class for details of the math.
- set_ball_radius(...) from builtins.PyCapsule
- set_ball_radius(self : rosetta.core.select.residue_selector.LayerSelector, radius : float) -> NoneType
Set the radius for the rolling ball algorithm used to determine burial.
- set_cache_selection(...) from builtins.PyCapsule
- set_cache_selection(self : rosetta.core.select.residue_selector.LayerSelector, val : bool) -> NoneType
Set whether to cache versus recompute the layer selection whenever it is accessed.
- set_cutoffs(...) from builtins.PyCapsule
- set_cutoffs(self : rosetta.core.select.residue_selector.LayerSelector, core : float, surf : float) -> NoneType
Set the cutoffs for core and surface layers.
Boundary is defined implicitly. This can be a SASA cutoff or a neighbour count, depending
on the algorithm.
- set_dist_exponent(...) from builtins.PyCapsule
- set_dist_exponent(self : rosetta.core.select.residue_selector.LayerSelector, val : float) -> NoneType
Set the sidechain neighbor distance exponent.
See the core::select::util::SelectResiduesByLayer class for details of the math.
- set_layers(...) from builtins.PyCapsule
- set_layers(self : rosetta.core.select.residue_selector.LayerSelector, pick_core : bool, pick_boundary : bool, pick_surface : bool) -> NoneType
Set the layers that this selector will choose.
- set_sc_neighbor_denominator(...) from builtins.PyCapsule
- set_sc_neighbor_denominator(self : rosetta.core.select.residue_selector.LayerSelector, val : float) -> NoneType
Set the factor by which sidechain neighbor counts are divided if the sidechain
neighbors method is used to define layers.
- set_sc_neighbor_dist_midpoint(...) from builtins.PyCapsule
- set_sc_neighbor_dist_midpoint(self : rosetta.core.select.residue_selector.LayerSelector, val : float) -> NoneType
Set the midpoint of the distance falloff if the sidechain neighbors method is used
to define layers.
- set_use_sc_neighbors(...) from builtins.PyCapsule
- set_use_sc_neighbors(self : rosetta.core.select.residue_selector.LayerSelector, val : bool) -> NoneType
Set whether the sidechain neighbors algorithm is used to determine burial (as
opposed to the rolling ball algorithm).
- use_sc_neighbors(...) from builtins.PyCapsule
- use_sc_neighbors(rosetta.core.select.residue_selector.LayerSelector) -> bool
Get whether the sidechain neighbors algorithm is used to determine burial (as
opposed to the rolling ball algorithm).
|
class NeighborhoodResidueSelector(ResidueSelector) |
|
The NeighborhoodResidueSelector selects residues neighboring a defined set of residues
(the focus). The focus residue set can be obtained from another ResidueSelector, from a
set of positions. Focus is included in subset by default. Use include_focus_in_subset to change this!
Note: Uses the 10 A neighbor graph by default. If neighbor distance is great than this, we use slow-style double for loop. |
|
- Method resolution order:
- NeighborhoodResidueSelector
- ResidueSelector
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.select.residue_selector.NeighborhoodResidueSelector) -> NoneType
3. __init__(handle, rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, float) -> NoneType
doc
4. __init__(self : handle, focus : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, distance : float, include_focus_in_subset : bool) -> NoneType
5. __init__(handle, rosetta.utility.vector1_bool, float) -> NoneType
doc
6. __init__(self : handle, focus : rosetta.utility.vector1_bool, distance : float, include_focus_in_subset : bool) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.select.residue_selector.NeighborhoodResidueSelector, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.residue_selector.NeighborhoodResidueSelector, : rosetta.core.select.residue_selector.NeighborhoodResidueSelector) -> rosetta.core.select.residue_selector.NeighborhoodResidueSelector
- class_name(...) from builtins.PyCapsule
- class_name() -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.NeighborhoodResidueSelector) -> rosetta.core.select.residue_selector.ResidueSelector
Clone operator.
Copy this object and return an owning pointer to the new object.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.core.select.residue_selector.NeighborhoodResidueSelector) -> str
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.select.residue_selector.NeighborhoodResidueSelector, tag : rosetta.utility.tag.Tag, datamap : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_distance(...) from builtins.PyCapsule
- set_distance(self : rosetta.core.select.residue_selector.NeighborhoodResidueSelector, distance : float) -> NoneType
Set the distance we will be measuring to get neighbors
- set_focus(...) from builtins.PyCapsule
- set_focus(*args, **kwargs)
Overloaded function.
1. set_focus(self : rosetta.core.select.residue_selector.NeighborhoodResidueSelector, focus : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType
Set the focus, which is the residues for which we will be getting neighbors of.
2. set_focus(self : rosetta.core.select.residue_selector.NeighborhoodResidueSelector, focus_str : str) -> NoneType
Set the focus, which is the residues for which we will be getting neighbors of.
3. set_focus(self : rosetta.core.select.residue_selector.NeighborhoodResidueSelector, focus : rosetta.utility.vector1_bool) -> NoneType
Set the focus, which is the residues for which we will be getting neighbors of.
- set_focus_selector(...) from builtins.PyCapsule
- set_focus_selector(self : rosetta.core.select.residue_selector.NeighborhoodResidueSelector, rs : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType
Set a Residue Selector for the focus
- set_include_focus_in_subset(...) from builtins.PyCapsule
- set_include_focus_in_subset(self : rosetta.core.select.residue_selector.NeighborhoodResidueSelector, include_focus : bool) -> NoneType
Setting to include the fucus in the resulting subset or not. Default is TRUE
|
class NotResidueSelector(ResidueSelector) |
|
The NotResidueSelector negates the input of one loaded ResidueSelector, i.e., it is a logical NOT -
it selects all unselected residues and deselects the selected ones. True becomes false, false becomes true.
The ResidueSelector to be negated can be pulled in through RosettaScipt using the selector option, subtags for
ResidueSelectors known to the ResidueSelectorFactory or programmatically using set_residue_selector.
Note that since most ResidueSelectors clear the input ResidueSubset, NOT can be thought of as simply selecting
the opposite of the passed in selector. |
|
- Method resolution order:
- NotResidueSelector
- ResidueSelector
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.select.residue_selector.NotResidueSelector) -> NoneType
3. __init__(self : handle, selector : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.select.residue_selector.NotResidueSelector, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.residue_selector.NotResidueSelector, : rosetta.core.select.residue_selector.NotResidueSelector) -> rosetta.core.select.residue_selector.NotResidueSelector
- class_name(...) from builtins.PyCapsule
- class_name() -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.NotResidueSelector) -> rosetta.core.select.residue_selector.ResidueSelector
Clone operator.
Copy this object and return an owning pointer to the new object.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.core.select.residue_selector.NotResidueSelector) -> str
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.select.residue_selector.NotResidueSelector, tag : rosetta.utility.tag.Tag, datamap : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_residue_selector(...) from builtins.PyCapsule
- set_residue_selector(self : rosetta.core.select.residue_selector.NotResidueSelector, selector : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType
sets a ResidueSelector
|
class NumNeighborsSelector(ResidueSelector) |
| |
- Method resolution order:
- NumNeighborsSelector
- ResidueSelector
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.select.residue_selector.NumNeighborsSelector) -> NoneType
3. __init__(self : handle, threshold : int, distance_cutoff : float) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.select.residue_selector.NumNeighborsSelector, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.residue_selector.NumNeighborsSelector, : rosetta.core.select.residue_selector.NumNeighborsSelector) -> rosetta.core.select.residue_selector.NumNeighborsSelector
- class_name(...) from builtins.PyCapsule
- class_name() -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.NumNeighborsSelector) -> rosetta.core.select.residue_selector.ResidueSelector
Clone operator.
Copy this object and return an owning pointer to the new object.
- count_water(...) from builtins.PyCapsule
- count_water(*args, **kwargs)
Overloaded function.
1. count_water(rosetta.core.select.residue_selector.NumNeighborsSelector) -> bool
2. count_water(self : rosetta.core.select.residue_selector.NumNeighborsSelector, setting : bool) -> NoneType
- distance_cutoff(...) from builtins.PyCapsule
- distance_cutoff(*args, **kwargs)
Overloaded function.
1. distance_cutoff(rosetta.core.select.residue_selector.NumNeighborsSelector) -> float
2. distance_cutoff(self : rosetta.core.select.residue_selector.NumNeighborsSelector, setting : int) -> NoneType
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.core.select.residue_selector.NumNeighborsSelector) -> str
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.select.residue_selector.NumNeighborsSelector, tag : rosetta.utility.tag.Tag, datamap : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- threshold(...) from builtins.PyCapsule
- threshold(*args, **kwargs)
Overloaded function.
1. threshold(rosetta.core.select.residue_selector.NumNeighborsSelector) -> int
2. threshold(self : rosetta.core.select.residue_selector.NumNeighborsSelector, setting : int) -> NoneType
|
class OrResidueSelector(ResidueSelector) |
|
The OrResidueSelector combines the output of multiple ResidueSelectors using OR
logic, i.e., residues selected by ANY of the contained ResidueSelectors will be selected.
ResidueSelecters can be pulled in from a DataMap, from subtags (for ResidueSelectors
known to the ResidueSelectorFactory) or programmatically through %add_residue_selector. |
|
- Method resolution order:
- OrResidueSelector
- ResidueSelector
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.select.residue_selector.OrResidueSelector) -> NoneType
3. __init__(self : handle, selector1 : rosetta.core.select.residue_selector.ResidueSelector, selector2 : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_residue_selector(...) from builtins.PyCapsule
- add_residue_selector(self : rosetta.core.select.residue_selector.OrResidueSelector, selector : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType
adds a ResidueSelector
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.select.residue_selector.OrResidueSelector, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
- apply_or_to_subset(...) from builtins.PyCapsule
- apply_or_to_subset(self : rosetta.core.select.residue_selector.OrResidueSelector, newSubset : rosetta.utility.vector1_bool, existingSubset : rosetta.utility.vector1_bool) -> NoneType
applies newSubset to existingSubset and thereby modifies the latter
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.residue_selector.OrResidueSelector, : rosetta.core.select.residue_selector.OrResidueSelector) -> rosetta.core.select.residue_selector.OrResidueSelector
- class_name(...) from builtins.PyCapsule
- class_name() -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.OrResidueSelector) -> rosetta.core.select.residue_selector.ResidueSelector
Clone operator.
Copy this object and return an owning pointer to the new object.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.core.select.residue_selector.OrResidueSelector) -> str
- num_selectors(...) from builtins.PyCapsule
- num_selectors(rosetta.core.select.residue_selector.OrResidueSelector) -> int
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.select.residue_selector.OrResidueSelector, tag : rosetta.utility.tag.Tag, datamap : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
|
class PrimarySequenceNeighborhoodSelector(ResidueSelector) |
|
The PrimarySequenceNeighborhoodSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing
'true' for residue positions which are located near the given selected residues in primary sequence space |
|
- Method resolution order:
- PrimarySequenceNeighborhoodSelector
- ResidueSelector
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, lower_residues : int, upper_residues : int, selector : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, : rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector) -> rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector
- class_name(...) from builtins.PyCapsule
- class_name() -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector) -> rosetta.core.select.residue_selector.ResidueSelector
Clone operator.
Copy this object and return an owning pointer to the new object.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector) -> str
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_lower_residues(...) from builtins.PyCapsule
- set_lower_residues(self : rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, nres : int) -> NoneType
- set_selector(...) from builtins.PyCapsule
- set_selector(self : rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, selector : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType
- set_upper_residues(...) from builtins.PyCapsule
- set_upper_residues(self : rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, nres : int) -> NoneType
|
class RandomResidueSelector(ResidueSelector) |
|
The RandomResidueSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing
'true' for N randomly selected residue positions, where N is a user-specified integer. |
|
- Method resolution order:
- RandomResidueSelector
- ResidueSelector
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, selector : rosetta.core.select.residue_selector.ResidueSelector, num_residues : int) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.select.residue_selector.RandomResidueSelector, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.residue_selector.RandomResidueSelector, : rosetta.core.select.residue_selector.RandomResidueSelector) -> rosetta.core.select.residue_selector.RandomResidueSelector
- class_name(...) from builtins.PyCapsule
- class_name() -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.RandomResidueSelector) -> rosetta.core.select.residue_selector.ResidueSelector
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.core.select.residue_selector.RandomResidueSelector) -> str
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.select.residue_selector.RandomResidueSelector, tag : rosetta.utility.tag.Tag, data : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
|
class ResidueIndexSelector(ResidueSelector) |
|
The ResidueIndexSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing
'true' for residue positions which match the given residue index. The index is read as comma-separated
list of either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). Detection
and mapping from PDB to Rosetta residue numbers is done internally. |
|
- Method resolution order:
- ResidueIndexSelector
- ResidueSelector
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.select.residue_selector.ResidueIndexSelector) -> NoneType
3. __init__(self : handle, index_str : str) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.select.residue_selector.ResidueIndexSelector, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.residue_selector.ResidueIndexSelector, : rosetta.core.select.residue_selector.ResidueIndexSelector) -> rosetta.core.select.residue_selector.ResidueIndexSelector
- class_name(...) from builtins.PyCapsule
- class_name() -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.ResidueIndexSelector) -> rosetta.core.select.residue_selector.ResidueSelector
Clone operator.
Copy this object and return an owning pointer to the new object.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.core.select.residue_selector.ResidueIndexSelector) -> str
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.select.residue_selector.ResidueIndexSelector, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_index(...) from builtins.PyCapsule
- set_index(self : rosetta.core.select.residue_selector.ResidueIndexSelector, index_str : str) -> NoneType
sets the string by which residues are selected
|
class ResidueNameSelector(ResidueSelector) |
|
The ResidueNameSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing
'true' for residue positions which match the given residue index. The index is read as comma-separated
list of either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). Detection
and mapping from PDB to Rosetta residue numbers is done internally. |
|
- Method resolution order:
- ResidueNameSelector
- ResidueSelector
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, res_name_str : str) -> NoneType
3. __init__(handle, rosetta.core.select.residue_selector.ResidueNameSelector) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.select.residue_selector.ResidueNameSelector, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.residue_selector.ResidueNameSelector, : rosetta.core.select.residue_selector.ResidueNameSelector) -> rosetta.core.select.residue_selector.ResidueNameSelector
- class_name(...) from builtins.PyCapsule
- class_name() -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.ResidueNameSelector) -> rosetta.core.select.residue_selector.ResidueSelector
Clone operator.
Copy this object and return an owning pointer to the new object.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.core.select.residue_selector.ResidueNameSelector) -> str
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.select.residue_selector.ResidueNameSelector, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_residue_name3(...) from builtins.PyCapsule
- set_residue_name3(self : rosetta.core.select.residue_selector.ResidueNameSelector, res_name3_str : str) -> NoneType
sets the comma-separated string of 3-character residue names to be selected
- set_residue_names(...) from builtins.PyCapsule
- set_residue_names(self : rosetta.core.select.residue_selector.ResidueNameSelector, res_name_str : str) -> NoneType
sets the comma-separated string of residue names to be selected
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class ResiduePDBInfoHasLabelSelector(ResidueSelector) |
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The ResiduePDBInfoHasLabelSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing
'true' for residue positions with the given label in pose PDB info for that residue. |
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- Method resolution order:
- ResiduePDBInfoHasLabelSelector
- ResidueSelector
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, label_str : str) -> NoneType
3. __init__(handle, rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector, : rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector) -> rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector
- class_name(...) from builtins.PyCapsule
- class_name() -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector) -> rosetta.core.select.residue_selector.ResidueSelector
Clone operator.
Copy this object and return an owning pointer to the new object.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector) -> str
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_label(...) from builtins.PyCapsule
- set_label(self : rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector, label_str : str) -> NoneType
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class ResidueRanges(rosetta.utility.vector1_core_select_residue_selector_ResidueRange) |
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- Method resolution order:
- ResidueRanges
- rosetta.utility.vector1_core_select_residue_selector_ResidueRange
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.select.residue_selector.ResidueRanges) -> NoneType
2. __init__(self : rosetta.core.select.residue_selector.ResidueRanges, subset : rosetta.utility.vector1_bool) -> 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.select.residue_selector.ResidueRanges, : rosetta.core.select.residue_selector.ResidueRanges) -> rosetta.core.select.residue_selector.ResidueRanges
- from_subset(...) from builtins.PyCapsule
- from_subset(self : rosetta.core.select.residue_selector.ResidueRanges, subset : rosetta.utility.vector1_bool) -> NoneType
Clears the ranges and uses the provided ResidueSubset to create new ranges
: residue subset from which contiguous ranges of residues will be derived
ResidueRanges created via this method are guaranteed
to be ordered in ascending order by start resid and
contain no duplicates
Methods inherited from rosetta.utility.vector1_core_select_residue_selector_ResidueRange:
- __bool__(...) from builtins.PyCapsule
- __bool__(rosetta.utility.vector1_core_select_residue_selector_ResidueRange) -> bool
Check whether the list is nonempty
- __getitem__(...) from builtins.PyCapsule
- __getitem__(rosetta.utility.vector1_core_select_residue_selector_ResidueRange, int) -> core::select::residue_selector::ResidueRange
- __iter__(...) from builtins.PyCapsule
- __iter__(rosetta.utility.vector1_core_select_residue_selector_ResidueRange) -> iterator
- __len__(...) from builtins.PyCapsule
- __len__(rosetta.utility.vector1_core_select_residue_selector_ResidueRange) -> int
- __setitem__(...) from builtins.PyCapsule
- __setitem__(rosetta.utility.vector1_core_select_residue_selector_ResidueRange, int, core::select::residue_selector::ResidueRange) -> NoneType
- append(...) from builtins.PyCapsule
- append(rosetta.utility.vector1_core_select_residue_selector_ResidueRange, core::select::residue_selector::ResidueRange) -> NoneType
adds an element to the end
- back(...) from builtins.PyCapsule
- back(rosetta.utility.vector1_core_select_residue_selector_ResidueRange) -> core::select::residue_selector::ResidueRange
access the last element
- capacity(...) from builtins.PyCapsule
- capacity(std::vector<core::select::residue_selector::ResidueRange, std::allocator<core::select::residue_selector::ResidueRange> >) -> int
returns the number of elements that can be held in currently allocated storage
- clear(...) from builtins.PyCapsule
- clear(std::vector<core::select::residue_selector::ResidueRange, std::allocator<core::select::residue_selector::ResidueRange> >) -> NoneType
clears the contents
- erase(...) from builtins.PyCapsule
- erase(rosetta.utility.vector1_core_select_residue_selector_ResidueRange, int) -> NoneType
erases element at index
- extend = _vector_extend_func(vec, othervec)
- # Vector compatibility: Adding 'extend' to all utility.vector* functions
- front(...) from builtins.PyCapsule
- front(rosetta.utility.vector1_core_select_residue_selector_ResidueRange) -> core::select::residue_selector::ResidueRange
access the first element
- l(...) from builtins.PyCapsule
- l(rosetta.utility.vector1_core_select_residue_selector_ResidueRange) -> int
lower index
- max_size(...) from builtins.PyCapsule
- max_size(std::vector<core::select::residue_selector::ResidueRange, std::allocator<core::select::residue_selector::ResidueRange> >) -> int
returns the maximum possible number of elements
- pop(...) from builtins.PyCapsule
- pop(*args, **kwargs)
Overloaded function.
1. pop(rosetta.utility.vector1_core_select_residue_selector_ResidueRange) -> core::select::residue_selector::ResidueRange
remove and return last item
2. pop(rosetta.utility.vector1_core_select_residue_selector_ResidueRange, int) -> core::select::residue_selector::ResidueRange
remove and return item at index
- reserve(...) from builtins.PyCapsule
- reserve(std::vector<core::select::residue_selector::ResidueRange, std::allocator<core::select::residue_selector::ResidueRange> >, int) -> NoneType
reserves storage
- resize(...) from builtins.PyCapsule
- resize(rosetta.utility.vector1_core_select_residue_selector_ResidueRange, int) -> NoneType
changes the number of elements stored
- shrink_to_fit(...) from builtins.PyCapsule
- shrink_to_fit(std::vector<core::select::residue_selector::ResidueRange, std::allocator<core::select::residue_selector::ResidueRange> >) -> NoneType
reduces memory usage by freeing unused memory
- u(...) from builtins.PyCapsule
- u(rosetta.utility.vector1_core_select_residue_selector_ResidueRange) -> int
upper index
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class ResidueSelector(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.select.residue_selector.ResidueSelector) -> NoneType
2. __init__(rosetta.core.select.residue_selector.ResidueSelector, rosetta.core.select.residue_selector.ResidueSelector) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.select.residue_selector.ResidueSelector, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
Return a ResidueSubset indicating a selection of Residues from the
input Pose; the ResidueSubset is an array of booleans where a value of
"true" for position i indicates that residue i is a part of the selected
subset -- and a value of "false" would indicate that it is not.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.residue_selector.ResidueSelector, : rosetta.core.select.residue_selector.ResidueSelector) -> rosetta.core.select.residue_selector.ResidueSelector
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.ResidueSelector) -> rosetta.core.select.residue_selector.ResidueSelector
Clone operator.
All ResidueSelectors must implement a clone() operator. This must create a copy of the object and
return a ResidueSelectorOP to the original object.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.core.select.residue_selector.ResidueSelector) -> str
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.select.residue_selector.ResidueSelector, tag : rosetta.utility.tag.Tag, datacache : rosetta.basic.datacache.DataMap) -> NoneType
Initialize any data members of this instance from an input tag
and a DataMap object
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class ResidueSelectorFactory(builtins.object) |
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Methods defined here:
- __init__(self, /, *args, **kwargs)
- Initialize self. See help(type(self)) for accurate signature.
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- define_residue_selector_xml_schema(...) from builtins.PyCapsule
- define_residue_selector_xml_schema(self : rosetta.core.select.residue_selector.ResidueSelectorFactory, xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
The %ResidueSelectorFactory is the point of entry for the definition of the XML Schemas
for every ResidueSelector that may be instantiated from a file. It is responsible for defining
an xs:group named "residue_selector" listing each of the residue-selector-complex types that may
be initialized using the %ResidueSelectorFactory and to iterate across each of the
ResidueSelectorCreators it contains asking them for the XML schema of the ResidueSelector they
are responsible for creating.
- factory_register(...) from builtins.PyCapsule
- factory_register(self : rosetta.core.select.residue_selector.ResidueSelectorFactory, creator : rosetta.core.select.residue_selector.ResidueSelectorCreator) -> NoneType
- get_instance(...) from builtins.PyCapsule
- get_instance() -> rosetta.core.select.residue_selector.ResidueSelectorFactory
- has_type(...) from builtins.PyCapsule
- has_type(self : rosetta.core.select.residue_selector.ResidueSelectorFactory, : str) -> bool
- new_residue_selector(...) from builtins.PyCapsule
- new_residue_selector(self : rosetta.core.select.residue_selector.ResidueSelectorFactory, selector_name : str, tag : rosetta.utility.tag.Tag, datamap : rosetta.basic.datacache.DataMap) -> rosetta.core.select.residue_selector.ResidueSelector
- residue_selector_xml_schema_group_name(...) from builtins.PyCapsule
- residue_selector_xml_schema_group_name() -> str
- set_throw_on_double_registration(...) from builtins.PyCapsule
- set_throw_on_double_registration(rosetta.core.select.residue_selector.ResidueSelectorFactory) -> NoneType
Should the Factory throw an exception or call utility::exit when it encounters the
second of two ResidueSelctorCreators with the same keyname? It's default behavior is to
call utility::exit, but this method allows you to set it so that it will throw an
exception instead (which is unit testable).
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class ResidueVector(rosetta.utility.vector1_unsigned_long) |
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- Method resolution order:
- ResidueVector
- rosetta.utility.vector1_unsigned_long
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.select.residue_selector.ResidueVector) -> NoneType
2. __init__(self : rosetta.core.select.residue_selector.ResidueVector, subset : rosetta.utility.vector1_bool) -> NoneType
3. __init__(self : rosetta.core.select.residue_selector.ResidueVector, vec : rosetta.utility.vector1_unsigned_long) -> 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.select.residue_selector.ResidueVector, : rosetta.core.select.residue_selector.ResidueVector) -> rosetta.core.select.residue_selector.ResidueVector
- from_subset(...) from builtins.PyCapsule
- from_subset(self : rosetta.core.select.residue_selector.ResidueVector, subset : rosetta.utility.vector1_bool) -> NoneType
Methods inherited from rosetta.utility.vector1_unsigned_long:
- __bool__(...) from builtins.PyCapsule
- __bool__(rosetta.utility.vector1_unsigned_long) -> bool
Check whether the list is nonempty
- __contains__(...) from builtins.PyCapsule
- __contains__(rosetta.utility.vector1_unsigned_long, int) -> bool
return true if item in the container
- __eq__(...) from builtins.PyCapsule
- __eq__(rosetta.utility.vector1_unsigned_long, rosetta.utility.vector1_unsigned_long) -> bool
- __getitem__(...) from builtins.PyCapsule
- __getitem__(rosetta.utility.vector1_unsigned_long, int) -> int
- __iter__(...) from builtins.PyCapsule
- __iter__(rosetta.utility.vector1_unsigned_long) -> iterator
- __len__(...) from builtins.PyCapsule
- __len__(rosetta.utility.vector1_unsigned_long) -> int
- __ne__(...) from builtins.PyCapsule
- __ne__(rosetta.utility.vector1_unsigned_long, rosetta.utility.vector1_unsigned_long) -> bool
- __repr__(...) from builtins.PyCapsule
- __repr__(rosetta.utility.vector1_unsigned_long) -> str
- __setitem__(...) from builtins.PyCapsule
- __setitem__(rosetta.utility.vector1_unsigned_long, int, int) -> NoneType
- append(...) from builtins.PyCapsule
- append(rosetta.utility.vector1_unsigned_long, int) -> NoneType
adds an element to the end
- back(...) from builtins.PyCapsule
- back(rosetta.utility.vector1_unsigned_long) -> int
access the last element
- capacity(...) from builtins.PyCapsule
- capacity(rosetta.std.vector_unsigned_long) -> int
returns the number of elements that can be held in currently allocated storage
- clear(...) from builtins.PyCapsule
- clear(rosetta.std.vector_unsigned_long) -> NoneType
clears the contents
- count(...) from builtins.PyCapsule
- count(rosetta.utility.vector1_unsigned_long, int) -> int
counts the elements that are equal to value
- erase(...) from builtins.PyCapsule
- erase(rosetta.utility.vector1_unsigned_long, int) -> NoneType
erases element at index
- extend = _vector_extend_func(vec, othervec)
- # Vector compatibility: Adding 'extend' to all utility.vector* functions
- front(...) from builtins.PyCapsule
- front(rosetta.utility.vector1_unsigned_long) -> int
access the first element
- l(...) from builtins.PyCapsule
- l(rosetta.utility.vector1_unsigned_long) -> int
lower index
- max_size(...) from builtins.PyCapsule
- max_size(rosetta.std.vector_unsigned_long) -> int
returns the maximum possible number of elements
- pop(...) from builtins.PyCapsule
- pop(*args, **kwargs)
Overloaded function.
1. pop(rosetta.utility.vector1_unsigned_long) -> int
remove and return last item
2. pop(rosetta.utility.vector1_unsigned_long, int) -> int
remove and return item at index
- remove(...) from builtins.PyCapsule
- remove(rosetta.utility.vector1_unsigned_long, int) -> NoneType
Remove the first item from the list whose value is x. It is an error if there is no such item.
- reserve(...) from builtins.PyCapsule
- reserve(rosetta.std.vector_unsigned_long, int) -> NoneType
reserves storage
- resize(...) from builtins.PyCapsule
- resize(rosetta.utility.vector1_unsigned_long, int) -> NoneType
changes the number of elements stored
- shrink_to_fit(...) from builtins.PyCapsule
- shrink_to_fit(rosetta.std.vector_unsigned_long) -> NoneType
reduces memory usage by freeing unused memory
- u(...) from builtins.PyCapsule
- u(rosetta.utility.vector1_unsigned_long) -> int
upper index
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class SecondaryStructureSelector(ResidueSelector) |
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- Method resolution order:
- SecondaryStructureSelector
- ResidueSelector
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, selected : str) -> NoneType
3. __init__(handle, rosetta.core.select.residue_selector.SecondaryStructureSelector) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.select.residue_selector.SecondaryStructureSelector, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.residue_selector.SecondaryStructureSelector, : rosetta.core.select.residue_selector.SecondaryStructureSelector) -> rosetta.core.select.residue_selector.SecondaryStructureSelector
- class_name(...) from builtins.PyCapsule
- class_name() -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.residue_selector.SecondaryStructureSelector) -> rosetta.core.select.residue_selector.ResidueSelector
Clone operator.
Copy this object and return an owning pointer to the new object.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.core.select.residue_selector.SecondaryStructureSelector) -> str
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.select.residue_selector.SecondaryStructureSelector, tag : rosetta.utility.tag.Tag, datamap : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_always_use_dssp(...) from builtins.PyCapsule
- set_always_use_dssp(self : rosetta.core.select.residue_selector.SecondaryStructureSelector, always_use_dssp : bool) -> NoneType
If set, dssp will be used to determine secondary structure. Otherwise, the pose SS will
be used IF it's not poly-L or empty (default=true)
- set_include_terminal_loops(...) from builtins.PyCapsule
- set_include_terminal_loops(self : rosetta.core.select.residue_selector.SecondaryStructureSelector, inc_term : bool) -> NoneType
if true, one-residue terminal "loops" will be included (default=false)
- set_overlap(...) from builtins.PyCapsule
- set_overlap(self : rosetta.core.select.residue_selector.SecondaryStructureSelector, overlapval : int) -> NoneType
sets number of residues around the given SS elements to select (default=0)
- set_pose_secstruct(...) from builtins.PyCapsule
- set_pose_secstruct(self : rosetta.core.select.residue_selector.SecondaryStructureSelector, ss : str) -> NoneType
Use this secstruct instead of the one found in the pose or DSSP, if set (default = not set)
- set_selected_ss(...) from builtins.PyCapsule
- set_selected_ss(self : rosetta.core.select.residue_selector.SecondaryStructureSelector, selected : str) -> NoneType
sets ss characters to select -- must be set prior to apply()
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