| | |
- rosetta.core.pack.task.operation.TaskOperation(builtins.object)
-
- AddCDRProfileSetsOperation
- AddCDRProfilesOperation
- DisableAntibodyRegionOperation
- DisableCDRsOperation
- RestrictToCDRsAndNeighbors
- rosetta.core.pack.task.operation.TaskOperationCreator(builtins.object)
-
- AddCDRProfileSetsOperationCreator
- AddCDRProfilesOperationCreator
- DisableAntibodyRegionOperationCreator
- DisableCDRsOperationCreator
- RestrictToCDRsAndNeighborsCreator
class AddCDRProfileSetsOperation(rosetta.core.pack.task.operation.TaskOperation) |
| |
Add Cluster-based sets of mutations as a TaskOperation.
Essentially samples full sequences of CDRs within a particular CDR cluster randomly each time the packer is called.
Does this for each CDR.
See protocols/toolbox/task_operations/MutationSetDesignOperation for more info.
If a CDR has an unknown cluster or there are no data for that particular CDR, will skip that CDR.
CDR definitions used are North/Dunbrack as the clusters are defined using it.
Note that by default, a data cutoff of 10 is set. If the cluster has less than 10 sequences it will be skipped.
Use the set_cutoff function to change this.
|
| |
- Method resolution order:
- AddCDRProfileSetsOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType
3. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo, cdrs : rosetta.utility.vector1_bool) -> NoneType
4. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo, cdrs : rosetta.utility.vector1_bool, limit_only_to_length : bool) -> NoneType
5. __init__(handle, rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation) -> 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.protocols.antibody.task_operations.AddCDRProfileSetsOperation, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
////////////////////
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, : rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation) -> rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
Configure from a RosettaScripts XML tag.
- pre_load_data(...) from builtins.PyCapsule
- pre_load_data(self : rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
Pre load the data according to options instead of at each apply.
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_add_to_current(...) from builtins.PyCapsule
- set_add_to_current(self : rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, add_to_current : bool) -> NoneType
Add to the current set of amino acids in the task or replace them?
Default False
- set_cdr_only(...) from builtins.PyCapsule
- set_cdr_only(self : rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, cdr : rosetta.protocols.antibody.CDRNameEnum) -> NoneType
Set a single CDR with which to use this task op on.
Default is all of them.
- set_cdrs(...) from builtins.PyCapsule
- set_cdrs(self : rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, cdrs : rosetta.utility.vector1_bool) -> NoneType
Set the CDRs with which to use this task op on.
Default is all of them.
- set_cutoff(...) from builtins.PyCapsule
- set_cutoff(self : rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, cutoff : int) -> NoneType
Set the cutoff. Will not add the profile set if the total is less than or equal to this number.
Default is 10.
- set_defaults(...) from builtins.PyCapsule
- set_defaults(rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation) -> NoneType
- set_force_north_paper_db(...) from builtins.PyCapsule
- set_force_north_paper_db(self : rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, force_north_db : bool) -> NoneType
Force the use of the antibody database that houses only the North data.
This is the db distributed with Rosetta. If a current one is present in the database, it will use that instead.
Default False.
- set_include_native_type(...) from builtins.PyCapsule
- set_include_native_type(self : rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, use_native : bool) -> NoneType
Include the poses current residue type in the allowed amino acids.
Default True.
- set_limit_only_to_length(...) from builtins.PyCapsule
- set_limit_only_to_length(self : rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, limit_only_to_length : bool) -> NoneType
Set the class to sample all CDR sequences within a particular length,
instead of by cluster, which is the default.
Default False.
- set_picking_rounds(...) from builtins.PyCapsule
- set_picking_rounds(self : rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, rounds : int) -> NoneType
Set the number of times a sequence each chosen. Increase this number to increase variability of design.
Default 1 round
- set_use_light_chain_type(...) from builtins.PyCapsule
- set_use_light_chain_type(self : rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, use_light_chain_type : bool) -> NoneType
Use the light chain type if held by AntibodyInfo.
Default is true.
- set_use_outliers(...) from builtins.PyCapsule
- set_use_outliers(self : rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, use_outliers : bool) -> NoneType
Use cluster outliers as defined using DihedralDistance and RMSD.
Default false.
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class AddCDRProfilesOperation(rosetta.core.pack.task.operation.TaskOperation) |
| |
Add Cluster-based CDR Profiles as the task operation for the set of CDRs by default.
See protocols/toolbox/task_operations/ResidueProbTaskOperation for more.
CDR definitions used are North/Dunbrack as the clusters are defined using it.
If Cluster-based profiles cannot be used, will use the fallback strategy.
This can happen if the the CDR is of an unknown cluster or there is too little data
about the cluster to use profiles.
See protocols/antibody/design/AntibodyDesignEnum; SeqDesignStrategyEnum
for possible fallback strategies. Right now, only conservative or basic/none are implemented.
FALLBACK STRATEGIES:
seq_design_conservative adds a conservative mutation set to the possible residue types (blosum62 default),
seq_design_basic will do nothing (as the default for design is to allow all residue positions);
seq_design_none will disable design for that CDR (essentially your saying that if it doesn't have profiles, don't design it)
Due to constness of the apply method, cannot store which CDRs used the fall back strategy.
Functions in antibody/database/util can be used to query the database for the number of datapoints
Functions in AntibodyInfo can query what the CDR cluster is (NA for unknown clusters)
This TaskOperation is not currently recommended for H3 as it does not cluster well.
Optionally sample whole CDR sequences via the primary strategy of:
seq_design_profile_sets (use sets instead of profile probability)
seq_design_profile_sets_combined (use profile sets and profile probability)
|
| |
- Method resolution order:
- AddCDRProfilesOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType
3. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo, cdrs : rosetta.utility.vector1_bool) -> NoneType
4. __init__(handle, rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation) -> 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.protocols.antibody.task_operations.AddCDRProfilesOperation, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, : rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation) -> rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
Configure from a RosettaScripts XML tag.
- pre_load_data(...) from builtins.PyCapsule
- pre_load_data(self : rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, pose : rosetta.core.pose.Pose) -> NoneType
Pre load the profile data with this function instead of loading it when we apply.
Use this function after all settings are ready to save time with each apply.
This is needed due to const apply for TaskOps
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_add_to_current(...) from builtins.PyCapsule
- set_add_to_current(self : rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, add_to_current : bool) -> NoneType
Add to the current set of amino acids in the task or replace them?
Default False
- set_cdr_only(...) from builtins.PyCapsule
- set_cdr_only(self : rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, cdr : rosetta.protocols.antibody.CDRNameEnum) -> NoneType
- set_cdrs(...) from builtins.PyCapsule
- set_cdrs(self : rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, cdrs : rosetta.utility.vector1_bool) -> NoneType
- set_cons_design_data_source(...) from builtins.PyCapsule
- set_cons_design_data_source(self : rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, data_source : str) -> NoneType
Set the data source for conservative design. Default is blosum62. Increased blosum are more stringent, more conservative design.
legal = 'chothia_1976', 'BLOSUM30', 'blosum30', 'BLOSUM35', 'blosum35', 'BLOSUM40', 'blosum40',
'BLOSUM45', 'blosum45', 'BLOSUM50', 'blosum50', 'BLOSUM55', 'blosum55', 'BLOSUM60', 'blosum60',
'BLOSUM62', 'blosum62', 'BLOSUM65', 'blosum65', 'BLOSUM70', 'blosum70', 'BLOSUM75', 'blosum75',
'BLOSUM80', 'blosum80', 'BLOSUM85', 'blosum85', 'BLOSUM90', 'blosum90', 'BLOSUM100', 'blosum100'
- set_defaults(...) from builtins.PyCapsule
- set_defaults(rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation) -> NoneType
- set_design_options(...) from builtins.PyCapsule
- set_design_options(self : rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, seq_design_options : rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRSeqDesignOptions_t) -> NoneType
Set the CDR-level options as opposed to the defaults.
- set_fallback_strategy(...) from builtins.PyCapsule
- set_fallback_strategy(self : rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, fallback_strategy : rosetta.protocols.antibody.design.SeqDesignStrategyEnum) -> NoneType
Set the fallback strategy for all CDRs. If the primary strategy could not be
completed due to lack of data, will use this fallback strategy.
See AntibodyDesignEnum.hh for more
Default is Design using the set of Conservative Mutations for each position (Blosum-62) - seq_design_conservative
Set to seq_design_none to disable CDRs as the fallback instead of designing them.
- set_force_north_paper_db(...) from builtins.PyCapsule
- set_force_north_paper_db(self : rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, force_north_db : bool) -> NoneType
Force the use of the north paper DB. Used for benchmarking and Unit Tests.
- set_include_native_type(...) from builtins.PyCapsule
- set_include_native_type(self : rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, use_native : bool) -> NoneType
Include the poses current residue type in the allowed amino acids.
Default True.
- set_picking_rounds(...) from builtins.PyCapsule
- set_picking_rounds(self : rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, rounds : int) -> NoneType
Set the number of times a sequence each chosen. Increase this number to increase variability of design.
Default 1 round
- set_primary_strategy(...) from builtins.PyCapsule
- set_primary_strategy(self : rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, primary_strategy : rosetta.protocols.antibody.design.SeqDesignStrategyEnum) -> NoneType
Set the primary strategy for all CDRs. See AntibodyDesignEnum.hh for more
Default is Cluster-based Sequence Probabilities - seq_design_profiles
- set_sample_zero_probs_at(...) from builtins.PyCapsule
- set_sample_zero_probs_at(self : rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, zero_prob_sample : float) -> NoneType
For residue types that have a probability of 0, use this setting
to give a probability to them that is not zero.
Used to increase variability of designs.
- set_stats_cutoff(...) from builtins.PyCapsule
- set_stats_cutoff(self : rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, stats_cutoff : int) -> NoneType
Set the cutoff. Will not add the profile set if the total is less than or equal to this number.
Default is 10.
- set_use_outliers(...) from builtins.PyCapsule
- set_use_outliers(self : rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, use_outliers : bool) -> NoneType
Use cluster outliers as defined using DihedralDistance and RMSD.
Default false.
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class DisableAntibodyRegionOperation(rosetta.core.pack.task.operation.TaskOperation) |
| |
A TaskOperation that Disables packing +/or design of a particular antibody region.
By Default, disables packing and design of the cdr_region. Make sure to set the region you want disabled.
|
| |
- Method resolution order:
- DisableAntibodyRegionOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType
3. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo, region : rosetta.protocols.antibody.AntibodyRegionEnum) -> NoneType
4. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo, region : rosetta.protocols.antibody.AntibodyRegionEnum, disable_packing_and_design : bool) -> NoneType
5. __init__(handle, rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation) -> 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.protocols.antibody.task_operations.DisableAntibodyRegionOperation, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
///////////////////
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation, : rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation) -> rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
Configure from a RosettaScripts XML tag.
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_defaults(...) from builtins.PyCapsule
- set_defaults(rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation) -> NoneType
- set_disable_packing_and_design(...) from builtins.PyCapsule
- set_disable_packing_and_design(self : rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation, disable_packing_and_design : bool) -> NoneType
If disable_packing_and_design is set to False, will only disable design.
- set_region(...) from builtins.PyCapsule
- set_region(self : rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation, region : rosetta.protocols.antibody.AntibodyRegionEnum) -> NoneType
|
class DisableCDRsOperation(rosetta.core.pack.task.operation.TaskOperation) |
| |
TaskOperation to Disable Packing and/or design of a set of CDRs.
By default, disables both Packing and Design of all CDRs.
See options for setting specific CDRs and whether to only disable design.
|
| |
- Method resolution order:
- DisableCDRsOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType
3. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo, cdrs : rosetta.utility.vector1_bool) -> NoneType
4. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo, cdrs : rosetta.utility.vector1_bool, disable_packing_and_design : bool) -> NoneType
5. __init__(handle, rosetta.protocols.antibody.task_operations.DisableCDRsOperation) -> 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.protocols.antibody.task_operations.DisableCDRsOperation, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
///////////////////
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.antibody.task_operations.DisableCDRsOperation, : rosetta.protocols.antibody.task_operations.DisableCDRsOperation) -> rosetta.protocols.antibody.task_operations.DisableCDRsOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.antibody.task_operations.DisableCDRsOperation) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.antibody.task_operations.DisableCDRsOperation, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
Configure from a RosettaScripts XML tag.
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_cdr_only(...) from builtins.PyCapsule
- set_cdr_only(self : rosetta.protocols.antibody.task_operations.DisableCDRsOperation, cdr : rosetta.protocols.antibody.CDRNameEnum) -> NoneType
Set only a single CDR to disable.
- set_cdrs(...) from builtins.PyCapsule
- set_cdrs(self : rosetta.protocols.antibody.task_operations.DisableCDRsOperation, cdrs : rosetta.utility.vector1_bool) -> NoneType
Set the CDRs we will be disabling - 6/8 long vector corresponding to Enum.
- set_defaults(...) from builtins.PyCapsule
- set_defaults(rosetta.protocols.antibody.task_operations.DisableCDRsOperation) -> NoneType
- set_disable_packing_and_design(...) from builtins.PyCapsule
- set_disable_packing_and_design(self : rosetta.protocols.antibody.task_operations.DisableCDRsOperation, disable_packing_and_design : bool) -> NoneType
Set to disable packing and design, or only just design.
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class RestrictToCDRsAndNeighbors(rosetta.core.pack.task.operation.TaskOperation) |
| |
Task Operation to restrict packing/design to specific CDRs and neighbors.
See DisableAntibodyRegionOperation and DisableCDRsOperation further restrict TaskFactory.
See options for control of the design of CDRs, antigen, and framework.
By default, restricts to all packing of all CDRs and neighbors.
See options for control of which CDRs, including whether to only restrict design and control of whether we design
neighbor antigen and/or framework residues.
|
| |
- Method resolution order:
- RestrictToCDRsAndNeighbors
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType
3. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo, cdrs : rosetta.utility.vector1_bool) -> NoneType
4. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo, cdrs : rosetta.utility.vector1_bool, allow_cdr_design : bool) -> NoneType
5. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo, cdrs : rosetta.utility.vector1_bool, allow_cdr_design : bool, allow_neighbor_framework_design : bool, allow_neighbor_antigen_design : bool) -> NoneType
6. __init__(handle, rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors) -> 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.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
///////////////////////
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors, : rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors) -> rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
Configure from a RosettaScripts XML tag.
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_allow_design_cdr(...) from builtins.PyCapsule
- set_allow_design_cdr(self : rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors, allow_cdr_design : bool) -> NoneType
Allow design of CDRs?
- set_allow_design_neighbor_antigen(...) from builtins.PyCapsule
- set_allow_design_neighbor_antigen(self : rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors, allow_antigen_design : bool) -> NoneType
Allow design of neighbor antigen residues?
- set_allow_design_neighbor_framework(...) from builtins.PyCapsule
- set_allow_design_neighbor_framework(self : rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors, allow_framework_design : bool) -> NoneType
Allow design of neighbor framework residues?
- set_cdr_only(...) from builtins.PyCapsule
- set_cdr_only(self : rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors, cdr : rosetta.protocols.antibody.CDRNameEnum) -> NoneType
- set_cdrs(...) from builtins.PyCapsule
- set_cdrs(self : rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors, cdrs : rosetta.utility.vector1_bool) -> NoneType
- set_defaults(...) from builtins.PyCapsule
- set_defaults(rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors) -> NoneType
- set_neighbor_distance(...) from builtins.PyCapsule
- set_neighbor_distance(self : rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors, neighbor_dis : float) -> NoneType
Set the distance for the detection of neighbor residues. 6A default
- set_stem_size(...) from builtins.PyCapsule
- set_stem_size(self : rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors, stem_size : int) -> NoneType
Set the size of the stem - the number of residues going into the framework. This will be included as part of the loop when determining neighbors.
However, the residues of the stem itself count as part of the framework
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