| | |
- builtins.object
-
- BestMatchesCollection
- DownstreamCoordinateKinemageWriter
-
- SingleDownstreamResidueWriter
- MatchEvaluator
-
- DownstreamRMSEvaluator
- MatchFilter
-
- MatchCollisionFilter
-
- UpstreamCollisionFilter
- UpstreamDownstreamCollisionFilter
- StateAccumulatingMatchFilter
-
- LimitHitsPerRotamerFilter
- MatchGrouper
-
- SameChiBinComboGrouper
- SameRotamerComboGrouper
- SameSequenceGrouper
-
- SameSequenceAndDSPositionGrouper
- MatchProcessor
-
- MatchConsolidator
- MatchOutputter
- MatchScoreWriter
- OutputWriter
-
- PDBWriter
-
- CloudPDBWriter
-
- PoseMatchOutputWriter
- WriteKinemageOutputter
- ProcessorFactory
- ResidueKinemageWriter
- rosetta.protocols.match.downstream.DownstreamAlgorithm(builtins.object)
-
- WriteUpstreamCoordinateKinemage
- rosetta.protocols.match.upstream.UpstreamResidueProcessor(builtins.object)
-
- PoseInserter
- UpstreamHitCacher
- WriteUpstreamHitKinemage
class BestMatchesCollection(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.match.output.BestMatchesCollection, int) -> NoneType
doc
2. __init__(self : rosetta.protocols.match.output.BestMatchesCollection, n_to_keep : int, dspos1_mode : bool) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_match(...) from builtins.PyCapsule
- add_match(self : rosetta.protocols.match.output.BestMatchesCollection, m : rosetta.utility.vector1_protocols_match_Hit, score : float) -> NoneType
- add_match_dspos1(...) from builtins.PyCapsule
- add_match_dspos1(self : rosetta.protocols.match.output.BestMatchesCollection, m : rosetta.protocols.match.match_dspos1, score : float) -> NoneType
- dspos1_mode(...) from builtins.PyCapsule
- dspos1_mode(rosetta.protocols.match.output.BestMatchesCollection) -> bool
- kept_match(...) from builtins.PyCapsule
- kept_match(self : rosetta.protocols.match.output.BestMatchesCollection, which_match : int) -> rosetta.utility.vector1_protocols_match_Hit
- kept_match_dspos1(...) from builtins.PyCapsule
- kept_match_dspos1(self : rosetta.protocols.match.output.BestMatchesCollection, which_match : int) -> rosetta.protocols.match.match_dspos1
- n_kept_matches(...) from builtins.PyCapsule
- n_kept_matches(rosetta.protocols.match.output.BestMatchesCollection) -> int
|
class CloudPDBWriter(PDBWriter) |
| |
an output writer that uses a grouper to group matches and
then writes out one pdb file per group, with the different hits
from the group in different MODEL sections
|
| |
- Method resolution order:
- CloudPDBWriter
- PDBWriter
- OutputWriter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, grouper : rosetta.protocols.match.output.MatchGrouper) -> NoneType
2. __init__(handle, rosetta.protocols.match.output.CloudPDBWriter) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.output.CloudPDBWriter, : rosetta.protocols.match.output.CloudPDBWriter) -> rosetta.protocols.match.output.CloudPDBWriter
- ds_hitset_end_its(...) from builtins.PyCapsule
- ds_hitset_end_its(rosetta.protocols.match.output.CloudPDBWriter) -> rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t
- ds_hitset_its(...) from builtins.PyCapsule
- ds_hitset_its(rosetta.protocols.match.output.CloudPDBWriter) -> rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t
- end_output_writing(...) from builtins.PyCapsule
- end_output_writing(rosetta.protocols.match.output.CloudPDBWriter) -> NoneType
- prepare_for_output_writing(...) from builtins.PyCapsule
- prepare_for_output_writing(rosetta.protocols.match.output.CloudPDBWriter) -> NoneType
- record_match(...) from builtins.PyCapsule
- record_match(*args, **kwargs)
Overloaded function.
1. record_match(self : rosetta.protocols.match.output.CloudPDBWriter, m : rosetta.utility.vector1_protocols_match_Hit, evaluator : rosetta.protocols.match.output.MatchEvaluator, match_score_writer : rosetta.protocols.match.output.MatchScoreWriter) -> NoneType
no writing in this function, only saving the hits according
to what group they belong to
2. record_match(self : rosetta.protocols.match.output.CloudPDBWriter, m : rosetta.protocols.match.match_dspos1) -> NoneType
- representative_group_matches(...) from builtins.PyCapsule
- representative_group_matches(rosetta.protocols.match.output.CloudPDBWriter) -> rosetta.utility.vector1_protocols_match_match_dspos1
- write_match_groups(...) from builtins.PyCapsule
- write_match_groups(rosetta.protocols.match.output.CloudPDBWriter) -> NoneType
this is where the actual writing happens
Methods inherited from PDBWriter:
- assemble_remark_lines(...) from builtins.PyCapsule
- assemble_remark_lines(self : rosetta.protocols.match.output.PDBWriter, outpose : rosetta.core.pose.Pose, upstream_matchres : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, redundant_upstream_res : rosetta.std.map_unsigned_long_unsigned_long, ex_geom_ids_for_upstream_res : rosetta.utility.vector1_unsigned_long) -> NoneType
- create_output_upstream_pose(...) from builtins.PyCapsule
- create_output_upstream_pose(self : rosetta.protocols.match.output.PDBWriter, upstream_matchres : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, redundant_upstream_res : rosetta.std.map_unsigned_long_unsigned_long, ex_geom_ids_for_upstream_res : rosetta.utility.vector1_unsigned_long) -> rosetta.core.pose.Pose
- cstfile_name(...) from builtins.PyCapsule
- cstfile_name(rosetta.protocols.match.output.PDBWriter) -> str
- initialize_from_matcher_task(...) from builtins.PyCapsule
- initialize_from_matcher_task(self : rosetta.protocols.match.output.PDBWriter, mtask : rosetta.protocols.match.MatcherTask) -> NoneType
- num_geom_cst(...) from builtins.PyCapsule
- num_geom_cst(rosetta.protocols.match.output.PDBWriter) -> int
- prefix(...) from builtins.PyCapsule
- prefix(rosetta.protocols.match.output.PDBWriter) -> str
- scaf_name(...) from builtins.PyCapsule
- scaf_name(rosetta.protocols.match.output.PDBWriter) -> str
- set_coordinate_cacher(...) from builtins.PyCapsule
- set_coordinate_cacher(self : rosetta.protocols.match.output.PDBWriter, : protocols::match::output::UpstreamHitCacher) -> NoneType
- set_downstream_builder(...) from builtins.PyCapsule
- set_downstream_builder(self : rosetta.protocols.match.output.PDBWriter, geomcst_id : int, dsbuilder : rosetta.protocols.match.downstream.DownstreamBuilder) -> NoneType
- set_prefix(...) from builtins.PyCapsule
- set_prefix(self : rosetta.protocols.match.output.PDBWriter, prefix : str) -> NoneType
- signature_string(...) from builtins.PyCapsule
- signature_string(self : rosetta.protocols.match.output.PDBWriter, upstream_matchres : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> str
Methods inherited from OutputWriter:
- cst_io(...) from builtins.PyCapsule
- cst_io(rosetta.protocols.match.output.OutputWriter) -> rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO
- determine_redundant_upstream_matchres(...) from builtins.PyCapsule
- determine_redundant_upstream_matchres(self : rosetta.protocols.match.output.OutputWriter, m : rosetta.protocols.match.match_dspos1, redundant_upstream_res : rosetta.std.map_unsigned_long_unsigned_long) -> NoneType
determine if any upstream res are at the same scaffold
position, i.e. if one of them is a backbone interaction
the redundant_upstream_res map is a mapping from the redundant
geometric constraint id of the redundant residue to the geomcst_id of
the "nonredundant" res i.e. if cstres 1 happens to be a cys at
position 10 and cstres 3 is a gly at position 10 (and it's backbone is
used in satisfying constraint 3), the mapping will contain the 3,1 pair.
|
class DownstreamRMSEvaluator(MatchEvaluator) |
| |
In the best of all possible worlds, this class would be sufficiently
generic such that I could compare RMS for arbitrary subsets of atoms on
the downstream partner, but in my first pass implementation, I'm writing
while aiming at the RigidLigandBuilder -- 1 residue -- and I'll compare
all heavy atoms.
|
| |
- Method resolution order:
- DownstreamRMSEvaluator
- MatchEvaluator
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.output.DownstreamRMSEvaluator, : rosetta.protocols.match.output.DownstreamRMSEvaluator) -> rosetta.protocols.match.output.DownstreamRMSEvaluator
- score(...) from builtins.PyCapsule
- score(*args, **kwargs)
Overloaded function.
1. score(self : rosetta.protocols.match.output.DownstreamRMSEvaluator, m : rosetta.utility.vector1_protocols_match_Hit) -> float
2. score(self : rosetta.protocols.match.output.DownstreamRMSEvaluator, m : rosetta.protocols.match.match_dspos1) -> float
Causes a graceful exit. The DownstreamRMSEvaluator is incompatible with
the match_dspos1 match definition!
- set_downstream_builder(...) from builtins.PyCapsule
- set_downstream_builder(self : rosetta.protocols.match.output.DownstreamRMSEvaluator, which_geom_cst : int, ds_builder : rosetta.protocols.match.downstream.DownstreamBuilder) -> NoneType
- set_downstream_pose(...) from builtins.PyCapsule
- set_downstream_pose(self : rosetta.protocols.match.output.DownstreamRMSEvaluator, dspose : rosetta.core.pose.Pose) -> NoneType
- set_n_geometric_constraints(...) from builtins.PyCapsule
- set_n_geometric_constraints(self : rosetta.protocols.match.output.DownstreamRMSEvaluator, setting : int) -> NoneType
|
class MatchCollisionFilter(MatchFilter) |
| | |
- Method resolution order:
- MatchCollisionFilter
- MatchFilter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.match.output.MatchCollisionFilter, filter_name : str, coordinate_cacher : protocols::match::output::UpstreamHitCacher) -> NoneType
2. __init__(rosetta.protocols.match.output.MatchCollisionFilter, rosetta.protocols.match.output.MatchCollisionFilter) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.output.MatchCollisionFilter, : rosetta.protocols.match.output.MatchCollisionFilter) -> rosetta.protocols.match.output.MatchCollisionFilter
- bump_grid(...) from builtins.PyCapsule
- bump_grid(rosetta.protocols.match.output.MatchCollisionFilter) -> rosetta.protocols.match.BumpGrid
- empty_pose(...) from builtins.PyCapsule
- empty_pose(rosetta.protocols.match.output.MatchCollisionFilter) -> rosetta.core.pose.Pose
- empty_sfxn(...) from builtins.PyCapsule
- empty_sfxn(rosetta.protocols.match.output.MatchCollisionFilter) -> rosetta.core.scoring.ScoreFunction
- etable_energy(...) from builtins.PyCapsule
- etable_energy(rosetta.protocols.match.output.MatchCollisionFilter) -> rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy
- filter_by_lj(...) from builtins.PyCapsule
- filter_by_lj(rosetta.protocols.match.output.MatchCollisionFilter) -> bool
- lj_cutoff(...) from builtins.PyCapsule
- lj_cutoff(rosetta.protocols.match.output.MatchCollisionFilter) -> float
- passes_filter(...) from builtins.PyCapsule
- passes_filter(*args, **kwargs)
Overloaded function.
1. passes_filter(self : rosetta.protocols.match.output.MatchCollisionFilter, m : rosetta.utility.vector1_protocols_match_Hit) -> bool
2. passes_filter(self : rosetta.protocols.match.output.MatchCollisionFilter, m : rosetta.protocols.match.match_dspos1) -> bool
- set_filter_by_lj(...) from builtins.PyCapsule
- set_filter_by_lj(self : rosetta.protocols.match.output.MatchCollisionFilter, setting : bool) -> NoneType
- set_lj_atr_weight(...) from builtins.PyCapsule
- set_lj_atr_weight(self : rosetta.protocols.match.output.MatchCollisionFilter, setting : float) -> NoneType
- set_lj_cutoff(...) from builtins.PyCapsule
- set_lj_cutoff(self : rosetta.protocols.match.output.MatchCollisionFilter, setting : float) -> NoneType
- set_lj_rep_weight(...) from builtins.PyCapsule
- set_lj_rep_weight(self : rosetta.protocols.match.output.MatchCollisionFilter, setting : float) -> NoneType
- set_lj_sol_weight(...) from builtins.PyCapsule
- set_lj_sol_weight(self : rosetta.protocols.match.output.MatchCollisionFilter, setting : float) -> NoneType
- set_tolerated_overlap(...) from builtins.PyCapsule
- set_tolerated_overlap(self : rosetta.protocols.match.output.MatchCollisionFilter, setting : float) -> NoneType
- tolerated_overlap(...) from builtins.PyCapsule
- tolerated_overlap(rosetta.protocols.match.output.MatchCollisionFilter) -> float
- wfa_atr(...) from builtins.PyCapsule
- wfa_atr(rosetta.protocols.match.output.MatchCollisionFilter) -> float
- wfa_rep(...) from builtins.PyCapsule
- wfa_rep(rosetta.protocols.match.output.MatchCollisionFilter) -> float
- wfa_sol(...) from builtins.PyCapsule
- wfa_sol(rosetta.protocols.match.output.MatchCollisionFilter) -> float
Methods inherited from MatchFilter:
- filter_name(...) from builtins.PyCapsule
- filter_name(rosetta.protocols.match.output.MatchFilter) -> str
|
class MatchConsolidator(MatchProcessor) |
| | |
- Method resolution order:
- MatchConsolidator
- MatchProcessor
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.output.MatchConsolidator, : rosetta.protocols.match.output.MatchConsolidator) -> rosetta.protocols.match.output.MatchConsolidator
- begin_processing(...) from builtins.PyCapsule
- begin_processing(rosetta.protocols.match.output.MatchConsolidator) -> NoneType
- end_processing(...) from builtins.PyCapsule
- end_processing(rosetta.protocols.match.output.MatchConsolidator) -> NoneType
- process_match(...) from builtins.PyCapsule
- process_match(*args, **kwargs)
Overloaded function.
1. process_match(self : rosetta.protocols.match.output.MatchConsolidator, m : rosetta.utility.vector1_protocols_match_Hit) -> NoneType
2. process_match(self : rosetta.protocols.match.output.MatchConsolidator, m : rosetta.protocols.match.match_dspos1) -> NoneType
- reset_grouper(...) from builtins.PyCapsule
- reset_grouper(rosetta.protocols.match.output.MatchConsolidator) -> NoneType
- set_grouper(...) from builtins.PyCapsule
- set_grouper(self : rosetta.protocols.match.output.MatchConsolidator, grouper : protocols::match::output::MatchGrouper) -> NoneType
- set_n_to_output_per_group(...) from builtins.PyCapsule
- set_n_to_output_per_group(self : rosetta.protocols.match.output.MatchConsolidator, setting : int) -> NoneType
Methods inherited from MatchProcessor:
- add_filter(...) from builtins.PyCapsule
- add_filter(self : rosetta.protocols.match.output.MatchProcessor, filter : rosetta.protocols.match.output.MatchFilter) -> NoneType
- clear_filters(...) from builtins.PyCapsule
- clear_filters(rosetta.protocols.match.output.MatchProcessor) -> NoneType
- match_processing_successful(...) from builtins.PyCapsule
- match_processing_successful(rosetta.protocols.match.output.MatchProcessor) -> bool
- output_writer(...) from builtins.PyCapsule
- output_writer(rosetta.protocols.match.output.MatchProcessor) -> protocols::match::output::OutputWriter
const access to the output writer, e.g.
for the MatcherMover when incorporating matches
into the pose
- reset_filters(...) from builtins.PyCapsule
- reset_filters(rosetta.protocols.match.output.MatchProcessor) -> NoneType
- set_evaluator(...) from builtins.PyCapsule
- set_evaluator(self : rosetta.protocols.match.output.MatchProcessor, evaluator : rosetta.protocols.match.output.MatchEvaluator) -> NoneType
- set_match_score_writer(...) from builtins.PyCapsule
- set_match_score_writer(self : rosetta.protocols.match.output.MatchProcessor, scorewriter : protocols::match::output::MatchScoreWriter) -> NoneType
- set_output_writer(...) from builtins.PyCapsule
- set_output_writer(self : rosetta.protocols.match.output.MatchProcessor, writer : protocols::match::output::OutputWriter) -> NoneType
- up_coll_filt(...) from builtins.PyCapsule
- up_coll_filt(rosetta.protocols.match.output.MatchProcessor) -> protocols::match::output::UpstreamCollisionFilter
- up_down_filt(...) from builtins.PyCapsule
- up_down_filt(rosetta.protocols.match.output.MatchProcessor) -> protocols::match::output::UpstreamDownstreamCollisionFilter
|
class MatchOutputter(MatchProcessor) |
| | |
- Method resolution order:
- MatchOutputter
- MatchProcessor
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.output.MatchOutputter, : rosetta.protocols.match.output.MatchOutputter) -> rosetta.protocols.match.output.MatchOutputter
- begin_processing(...) from builtins.PyCapsule
- begin_processing(rosetta.protocols.match.output.MatchOutputter) -> NoneType
- end_processing(...) from builtins.PyCapsule
- end_processing(rosetta.protocols.match.output.MatchOutputter) -> NoneType
- process_match(...) from builtins.PyCapsule
- process_match(*args, **kwargs)
Overloaded function.
1. process_match(self : rosetta.protocols.match.output.MatchOutputter, m : rosetta.utility.vector1_protocols_match_Hit) -> NoneType
2. process_match(self : rosetta.protocols.match.output.MatchOutputter, m : rosetta.protocols.match.match_dspos1) -> NoneType
Methods inherited from MatchProcessor:
- add_filter(...) from builtins.PyCapsule
- add_filter(self : rosetta.protocols.match.output.MatchProcessor, filter : rosetta.protocols.match.output.MatchFilter) -> NoneType
- clear_filters(...) from builtins.PyCapsule
- clear_filters(rosetta.protocols.match.output.MatchProcessor) -> NoneType
- match_processing_successful(...) from builtins.PyCapsule
- match_processing_successful(rosetta.protocols.match.output.MatchProcessor) -> bool
- output_writer(...) from builtins.PyCapsule
- output_writer(rosetta.protocols.match.output.MatchProcessor) -> protocols::match::output::OutputWriter
const access to the output writer, e.g.
for the MatcherMover when incorporating matches
into the pose
- reset_filters(...) from builtins.PyCapsule
- reset_filters(rosetta.protocols.match.output.MatchProcessor) -> NoneType
- set_evaluator(...) from builtins.PyCapsule
- set_evaluator(self : rosetta.protocols.match.output.MatchProcessor, evaluator : rosetta.protocols.match.output.MatchEvaluator) -> NoneType
- set_match_score_writer(...) from builtins.PyCapsule
- set_match_score_writer(self : rosetta.protocols.match.output.MatchProcessor, scorewriter : protocols::match::output::MatchScoreWriter) -> NoneType
- set_output_writer(...) from builtins.PyCapsule
- set_output_writer(self : rosetta.protocols.match.output.MatchProcessor, writer : protocols::match::output::OutputWriter) -> NoneType
- up_coll_filt(...) from builtins.PyCapsule
- up_coll_filt(rosetta.protocols.match.output.MatchProcessor) -> protocols::match::output::UpstreamCollisionFilter
- up_down_filt(...) from builtins.PyCapsule
- up_down_filt(rosetta.protocols.match.output.MatchProcessor) -> protocols::match::output::UpstreamDownstreamCollisionFilter
|
class MatchProcessor(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.match.output.MatchProcessor) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_filter(...) from builtins.PyCapsule
- add_filter(self : rosetta.protocols.match.output.MatchProcessor, filter : rosetta.protocols.match.output.MatchFilter) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.output.MatchProcessor, : rosetta.protocols.match.output.MatchProcessor) -> rosetta.protocols.match.output.MatchProcessor
- begin_processing(...) from builtins.PyCapsule
- begin_processing(rosetta.protocols.match.output.MatchProcessor) -> NoneType
Invoked by the Matcher before it begins feeding matches to the processor.
Base-class has a no-op implementation.
- clear_filters(...) from builtins.PyCapsule
- clear_filters(rosetta.protocols.match.output.MatchProcessor) -> NoneType
- end_processing(...) from builtins.PyCapsule
- end_processing(rosetta.protocols.match.output.MatchProcessor) -> NoneType
Invoked by the Matcher after it finishes feeding matches to the processor.
Base-class has a no-op implementation.
- match_processing_successful(...) from builtins.PyCapsule
- match_processing_successful(rosetta.protocols.match.output.MatchProcessor) -> bool
- output_writer(...) from builtins.PyCapsule
- output_writer(rosetta.protocols.match.output.MatchProcessor) -> protocols::match::output::OutputWriter
const access to the output writer, e.g.
for the MatcherMover when incorporating matches
into the pose
- process_match(...) from builtins.PyCapsule
- process_match(*args, **kwargs)
Overloaded function.
1. process_match(self : rosetta.protocols.match.output.MatchProcessor, m : rosetta.utility.vector1_protocols_match_Hit) -> NoneType
2. process_match(self : rosetta.protocols.match.output.MatchProcessor, m : rosetta.protocols.match.match_dspos1) -> NoneType
- reset_filters(...) from builtins.PyCapsule
- reset_filters(rosetta.protocols.match.output.MatchProcessor) -> NoneType
- set_evaluator(...) from builtins.PyCapsule
- set_evaluator(self : rosetta.protocols.match.output.MatchProcessor, evaluator : rosetta.protocols.match.output.MatchEvaluator) -> NoneType
- set_match_score_writer(...) from builtins.PyCapsule
- set_match_score_writer(self : rosetta.protocols.match.output.MatchProcessor, scorewriter : protocols::match::output::MatchScoreWriter) -> NoneType
- set_output_writer(...) from builtins.PyCapsule
- set_output_writer(self : rosetta.protocols.match.output.MatchProcessor, writer : protocols::match::output::OutputWriter) -> NoneType
- up_coll_filt(...) from builtins.PyCapsule
- up_coll_filt(rosetta.protocols.match.output.MatchProcessor) -> protocols::match::output::UpstreamCollisionFilter
- up_down_filt(...) from builtins.PyCapsule
- up_down_filt(rosetta.protocols.match.output.MatchProcessor) -> protocols::match::output::UpstreamDownstreamCollisionFilter
|
class MatchScoreWriter(builtins.object) |
| |
Writes out a score file based on the sum of RMS of geometric constrainst satisfaction with the desired ligan positioning
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.match.output.MatchScoreWriter) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.match.output.MatchScoreWriter) -> str
- add_match(...) from builtins.PyCapsule
- add_match(*args, **kwargs)
Overloaded function.
1. add_match(self : rosetta.protocols.match.output.MatchScoreWriter, match_name : str, score : float) -> NoneType
Add a match name (along with score) to be outputed in score file
2. add_match(self : rosetta.protocols.match.output.MatchScoreWriter, score : float) -> NoneType
Add an unnamed match (along with score) to be outputed in score file
Each additional match will have an incremented name
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.output.MatchScoreWriter, object_to_copy : rosetta.protocols.match.output.MatchScoreWriter) -> rosetta.protocols.match.output.MatchScoreWriter
- set_output(...) from builtins.PyCapsule
- set_output(self : rosetta.protocols.match.output.MatchScoreWriter, output_on : bool) -> NoneType
Set whether or not to output
- set_output_filename(...) from builtins.PyCapsule
- set_output_filename(self : rosetta.protocols.match.output.MatchScoreWriter, output_filename : str) -> NoneType
Set output filename, which also turns on output
- write_match_scores(...) from builtins.PyCapsule
- write_match_scores(rosetta.protocols.match.output.MatchScoreWriter) -> NoneType
Write out the match scores once all scores have been added
|
class OutputWriter(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.match.output.OutputWriter) -> NoneType
2. __init__(rosetta.protocols.match.output.OutputWriter, rosetta.protocols.match.output.OutputWriter) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.output.OutputWriter, : rosetta.protocols.match.output.OutputWriter) -> rosetta.protocols.match.output.OutputWriter
- cst_io(...) from builtins.PyCapsule
- cst_io(rosetta.protocols.match.output.OutputWriter) -> rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO
- determine_redundant_upstream_matchres(...) from builtins.PyCapsule
- determine_redundant_upstream_matchres(self : rosetta.protocols.match.output.OutputWriter, m : rosetta.protocols.match.match_dspos1, redundant_upstream_res : rosetta.std.map_unsigned_long_unsigned_long) -> NoneType
determine if any upstream res are at the same scaffold
position, i.e. if one of them is a backbone interaction
the redundant_upstream_res map is a mapping from the redundant
geometric constraint id of the redundant residue to the geomcst_id of
the "nonredundant" res i.e. if cstres 1 happens to be a cys at
position 10 and cstres 3 is a gly at position 10 (and it's backbone is
used in satisfying constraint 3), the mapping will contain the 3,1 pair.
- end_output_writing(...) from builtins.PyCapsule
- end_output_writing(rosetta.protocols.match.output.OutputWriter) -> NoneType
- initialize_from_matcher_task(...) from builtins.PyCapsule
- initialize_from_matcher_task(self : rosetta.protocols.match.output.OutputWriter, mtask : rosetta.protocols.match.MatcherTask) -> NoneType
- prepare_for_output_writing(...) from builtins.PyCapsule
- prepare_for_output_writing(rosetta.protocols.match.output.OutputWriter) -> NoneType
- record_match(...) from builtins.PyCapsule
- record_match(*args, **kwargs)
Overloaded function.
1. record_match(self : rosetta.protocols.match.output.OutputWriter, m : rosetta.utility.vector1_protocols_match_Hit, evaluator : rosetta.protocols.match.output.MatchEvaluator, match_score_writer : rosetta.protocols.match.output.MatchScoreWriter) -> NoneType
2. record_match(self : rosetta.protocols.match.output.OutputWriter, m : rosetta.protocols.match.match_dspos1) -> NoneType
evaluator and score writer are not passed in because single-downstream-position match
currently have no way of being evaluated
|
class PDBWriter(OutputWriter) |
| | |
- Method resolution order:
- PDBWriter
- OutputWriter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.match.output.PDBWriter) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assemble_remark_lines(...) from builtins.PyCapsule
- assemble_remark_lines(self : rosetta.protocols.match.output.PDBWriter, outpose : rosetta.core.pose.Pose, upstream_matchres : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, redundant_upstream_res : rosetta.std.map_unsigned_long_unsigned_long, ex_geom_ids_for_upstream_res : rosetta.utility.vector1_unsigned_long) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.output.PDBWriter, : rosetta.protocols.match.output.PDBWriter) -> rosetta.protocols.match.output.PDBWriter
- create_output_upstream_pose(...) from builtins.PyCapsule
- create_output_upstream_pose(self : rosetta.protocols.match.output.PDBWriter, upstream_matchres : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, redundant_upstream_res : rosetta.std.map_unsigned_long_unsigned_long, ex_geom_ids_for_upstream_res : rosetta.utility.vector1_unsigned_long) -> rosetta.core.pose.Pose
- cstfile_name(...) from builtins.PyCapsule
- cstfile_name(rosetta.protocols.match.output.PDBWriter) -> str
- initialize_from_matcher_task(...) from builtins.PyCapsule
- initialize_from_matcher_task(self : rosetta.protocols.match.output.PDBWriter, mtask : rosetta.protocols.match.MatcherTask) -> NoneType
- num_geom_cst(...) from builtins.PyCapsule
- num_geom_cst(rosetta.protocols.match.output.PDBWriter) -> int
- prefix(...) from builtins.PyCapsule
- prefix(rosetta.protocols.match.output.PDBWriter) -> str
- prepare_for_output_writing(...) from builtins.PyCapsule
- prepare_for_output_writing(rosetta.protocols.match.output.PDBWriter) -> NoneType
- record_match(...) from builtins.PyCapsule
- record_match(*args, **kwargs)
Overloaded function.
1. record_match(self : rosetta.protocols.match.output.PDBWriter, m : rosetta.utility.vector1_protocols_match_Hit, evaluator : rosetta.protocols.match.output.MatchEvaluator, match_score_writer : rosetta.protocols.match.output.MatchScoreWriter) -> NoneType
2. record_match(self : rosetta.protocols.match.output.PDBWriter, m : rosetta.protocols.match.match_dspos1) -> NoneType
evaluator and score writer are not passed in because single-downstream-position match
currently have no way of being evaluated
- scaf_name(...) from builtins.PyCapsule
- scaf_name(rosetta.protocols.match.output.PDBWriter) -> str
- set_coordinate_cacher(...) from builtins.PyCapsule
- set_coordinate_cacher(self : rosetta.protocols.match.output.PDBWriter, : protocols::match::output::UpstreamHitCacher) -> NoneType
- set_downstream_builder(...) from builtins.PyCapsule
- set_downstream_builder(self : rosetta.protocols.match.output.PDBWriter, geomcst_id : int, dsbuilder : rosetta.protocols.match.downstream.DownstreamBuilder) -> NoneType
- set_prefix(...) from builtins.PyCapsule
- set_prefix(self : rosetta.protocols.match.output.PDBWriter, prefix : str) -> NoneType
- signature_string(...) from builtins.PyCapsule
- signature_string(self : rosetta.protocols.match.output.PDBWriter, upstream_matchres : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> str
Methods inherited from OutputWriter:
- cst_io(...) from builtins.PyCapsule
- cst_io(rosetta.protocols.match.output.OutputWriter) -> rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO
- determine_redundant_upstream_matchres(...) from builtins.PyCapsule
- determine_redundant_upstream_matchres(self : rosetta.protocols.match.output.OutputWriter, m : rosetta.protocols.match.match_dspos1, redundant_upstream_res : rosetta.std.map_unsigned_long_unsigned_long) -> NoneType
determine if any upstream res are at the same scaffold
position, i.e. if one of them is a backbone interaction
the redundant_upstream_res map is a mapping from the redundant
geometric constraint id of the redundant residue to the geomcst_id of
the "nonredundant" res i.e. if cstres 1 happens to be a cys at
position 10 and cstres 3 is a gly at position 10 (and it's backbone is
used in satisfying constraint 3), the mapping will contain the 3,1 pair.
- end_output_writing(...) from builtins.PyCapsule
- end_output_writing(rosetta.protocols.match.output.OutputWriter) -> NoneType
|
class PoseMatchOutputWriter(CloudPDBWriter) |
| |
helper class for the MatcherMover that will put a match
into a supplied pose
|
| |
- Method resolution order:
- PoseMatchOutputWriter
- CloudPDBWriter
- PDBWriter
- OutputWriter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, grouper : rosetta.protocols.match.output.MatchGrouper) -> NoneType
2. __init__(handle, rosetta.protocols.match.output.PoseMatchOutputWriter) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.output.PoseMatchOutputWriter, : rosetta.protocols.match.output.PoseMatchOutputWriter) -> rosetta.protocols.match.output.PoseMatchOutputWriter
- end_output_writing(...) from builtins.PyCapsule
- end_output_writing(rosetta.protocols.match.output.PoseMatchOutputWriter) -> NoneType
- insert_match_into_pose(...) from builtins.PyCapsule
- insert_match_into_pose(*args, **kwargs)
Overloaded function.
1. insert_match_into_pose(self : rosetta.protocols.match.output.PoseMatchOutputWriter, pose : rosetta.core.pose.Pose, match_group : int) -> NoneType
2. insert_match_into_pose(self : rosetta.protocols.match.output.PoseMatchOutputWriter, pose : rosetta.core.pose.Pose) -> NoneType
Methods inherited from CloudPDBWriter:
- ds_hitset_end_its(...) from builtins.PyCapsule
- ds_hitset_end_its(rosetta.protocols.match.output.CloudPDBWriter) -> rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t
- ds_hitset_its(...) from builtins.PyCapsule
- ds_hitset_its(rosetta.protocols.match.output.CloudPDBWriter) -> rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t
- prepare_for_output_writing(...) from builtins.PyCapsule
- prepare_for_output_writing(rosetta.protocols.match.output.CloudPDBWriter) -> NoneType
- record_match(...) from builtins.PyCapsule
- record_match(*args, **kwargs)
Overloaded function.
1. record_match(self : rosetta.protocols.match.output.CloudPDBWriter, m : rosetta.utility.vector1_protocols_match_Hit, evaluator : rosetta.protocols.match.output.MatchEvaluator, match_score_writer : rosetta.protocols.match.output.MatchScoreWriter) -> NoneType
no writing in this function, only saving the hits according
to what group they belong to
2. record_match(self : rosetta.protocols.match.output.CloudPDBWriter, m : rosetta.protocols.match.match_dspos1) -> NoneType
- representative_group_matches(...) from builtins.PyCapsule
- representative_group_matches(rosetta.protocols.match.output.CloudPDBWriter) -> rosetta.utility.vector1_protocols_match_match_dspos1
- write_match_groups(...) from builtins.PyCapsule
- write_match_groups(rosetta.protocols.match.output.CloudPDBWriter) -> NoneType
this is where the actual writing happens
Methods inherited from PDBWriter:
- assemble_remark_lines(...) from builtins.PyCapsule
- assemble_remark_lines(self : rosetta.protocols.match.output.PDBWriter, outpose : rosetta.core.pose.Pose, upstream_matchres : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, redundant_upstream_res : rosetta.std.map_unsigned_long_unsigned_long, ex_geom_ids_for_upstream_res : rosetta.utility.vector1_unsigned_long) -> NoneType
- create_output_upstream_pose(...) from builtins.PyCapsule
- create_output_upstream_pose(self : rosetta.protocols.match.output.PDBWriter, upstream_matchres : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, redundant_upstream_res : rosetta.std.map_unsigned_long_unsigned_long, ex_geom_ids_for_upstream_res : rosetta.utility.vector1_unsigned_long) -> rosetta.core.pose.Pose
- cstfile_name(...) from builtins.PyCapsule
- cstfile_name(rosetta.protocols.match.output.PDBWriter) -> str
- initialize_from_matcher_task(...) from builtins.PyCapsule
- initialize_from_matcher_task(self : rosetta.protocols.match.output.PDBWriter, mtask : rosetta.protocols.match.MatcherTask) -> NoneType
- num_geom_cst(...) from builtins.PyCapsule
- num_geom_cst(rosetta.protocols.match.output.PDBWriter) -> int
- prefix(...) from builtins.PyCapsule
- prefix(rosetta.protocols.match.output.PDBWriter) -> str
- scaf_name(...) from builtins.PyCapsule
- scaf_name(rosetta.protocols.match.output.PDBWriter) -> str
- set_coordinate_cacher(...) from builtins.PyCapsule
- set_coordinate_cacher(self : rosetta.protocols.match.output.PDBWriter, : protocols::match::output::UpstreamHitCacher) -> NoneType
- set_downstream_builder(...) from builtins.PyCapsule
- set_downstream_builder(self : rosetta.protocols.match.output.PDBWriter, geomcst_id : int, dsbuilder : rosetta.protocols.match.downstream.DownstreamBuilder) -> NoneType
- set_prefix(...) from builtins.PyCapsule
- set_prefix(self : rosetta.protocols.match.output.PDBWriter, prefix : str) -> NoneType
- signature_string(...) from builtins.PyCapsule
- signature_string(self : rosetta.protocols.match.output.PDBWriter, upstream_matchres : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> str
Methods inherited from OutputWriter:
- cst_io(...) from builtins.PyCapsule
- cst_io(rosetta.protocols.match.output.OutputWriter) -> rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO
- determine_redundant_upstream_matchres(...) from builtins.PyCapsule
- determine_redundant_upstream_matchres(self : rosetta.protocols.match.output.OutputWriter, m : rosetta.protocols.match.match_dspos1, redundant_upstream_res : rosetta.std.map_unsigned_long_unsigned_long) -> NoneType
determine if any upstream res are at the same scaffold
position, i.e. if one of them is a backbone interaction
the redundant_upstream_res map is a mapping from the redundant
geometric constraint id of the redundant residue to the geomcst_id of
the "nonredundant" res i.e. if cstres 1 happens to be a cys at
position 10 and cstres 3 is a gly at position 10 (and it's backbone is
used in satisfying constraint 3), the mapping will contain the 3,1 pair.
|
class SameSequenceAndDSPositionGrouper(SameSequenceGrouper) |
| |
class that groups based on same sequence and proximity of the downstream object (based on rms )
NOTE: right now only the downstream position according to the first geomcst id upstream residue is
taken into account
|
| |
- Method resolution order:
- SameSequenceAndDSPositionGrouper
- SameSequenceGrouper
- MatchGrouper
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, ncst : int) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper, : rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper) -> rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper
- assign_group_for_match(...) from builtins.PyCapsule
- assign_group_for_match(self : rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper, m : rosetta.protocols.match.match_dspos1) -> int
- reset(...) from builtins.PyCapsule
- reset(rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper) -> NoneType
- set_downstream_builder(...) from builtins.PyCapsule
- set_downstream_builder(self : rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper, geomcst_id : int, dsbuilder : rosetta.protocols.match.downstream.DownstreamBuilder) -> NoneType
- set_n_geometric_constraints(...) from builtins.PyCapsule
- set_n_geometric_constraints(self : rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper, n_csts : int) -> NoneType
- set_relevant_atom_ids(...) from builtins.PyCapsule
- set_relevant_atom_ids(self : rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper, relevant_atom_ids : rosetta.utility.vector1_core_id_AtomID) -> NoneType
- set_rms_group_cutoff(...) from builtins.PyCapsule
- set_rms_group_cutoff(self : rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper, cutoff : float) -> NoneType
Methods inherited from SameSequenceGrouper:
- set_hit_cacher(...) from builtins.PyCapsule
- set_hit_cacher(self : rosetta.protocols.match.output.SameSequenceGrouper, cacher : protocols::match::output::UpstreamHitCacher) -> NoneType
|
class SameSequenceGrouper(MatchGrouper) |
| |
Class to group matches that represent the same amino acids at
the same launch points. E.g. Two matches that both put a cys at launch
point #33, a ser a launch point #42 and another ser at launch point
#80 would be grouped together -- even if they are different rotamers.
|
| |
- Method resolution order:
- SameSequenceGrouper
- MatchGrouper
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, ncst : int) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.output.SameSequenceGrouper, : rosetta.protocols.match.output.SameSequenceGrouper) -> rosetta.protocols.match.output.SameSequenceGrouper
- assign_group_for_match(...) from builtins.PyCapsule
- assign_group_for_match(*args, **kwargs)
Overloaded function.
1. assign_group_for_match(self : rosetta.protocols.match.output.SameSequenceGrouper, m : rosetta.utility.vector1_protocols_match_Hit) -> int
2. assign_group_for_match(self : rosetta.protocols.match.output.SameSequenceGrouper, m : rosetta.protocols.match.match_dspos1) -> int
- reset(...) from builtins.PyCapsule
- reset(rosetta.protocols.match.output.SameSequenceGrouper) -> NoneType
- set_hit_cacher(...) from builtins.PyCapsule
- set_hit_cacher(self : rosetta.protocols.match.output.SameSequenceGrouper, cacher : protocols::match::output::UpstreamHitCacher) -> NoneType
- set_n_geometric_constraints(...) from builtins.PyCapsule
- set_n_geometric_constraints(self : rosetta.protocols.match.output.SameSequenceGrouper, n_csts : int) -> NoneType
|
class StateAccumulatingMatchFilter(MatchFilter) |
| | |
- Method resolution order:
- StateAccumulatingMatchFilter
- MatchFilter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.match.output.StateAccumulatingMatchFilter, filter_name : str) -> NoneType
2. __init__(rosetta.protocols.match.output.StateAccumulatingMatchFilter, rosetta.protocols.match.output.StateAccumulatingMatchFilter) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.output.StateAccumulatingMatchFilter, : rosetta.protocols.match.output.StateAccumulatingMatchFilter) -> rosetta.protocols.match.output.StateAccumulatingMatchFilter
- note_match_accepted(...) from builtins.PyCapsule
- note_match_accepted(*args, **kwargs)
Overloaded function.
1. note_match_accepted(self : rosetta.protocols.match.output.StateAccumulatingMatchFilter, m : rosetta.utility.vector1_protocols_match_Hit) -> NoneType
Note that a particular match has passed all the filters and will be output.
2. note_match_accepted(self : rosetta.protocols.match.output.StateAccumulatingMatchFilter, m : rosetta.protocols.match.match_dspos1) -> bool
- passes_filter(...) from builtins.PyCapsule
- passes_filter(*args, **kwargs)
Overloaded function.
1. passes_filter(self : rosetta.protocols.match.output.StateAccumulatingMatchFilter, m : rosetta.utility.vector1_protocols_match_Hit) -> bool
Returns true if the given match passes this filter
2. passes_filter(self : rosetta.protocols.match.output.StateAccumulatingMatchFilter, m : rosetta.protocols.match.match_dspos1) -> bool
- reset(...) from builtins.PyCapsule
- reset(rosetta.protocols.match.output.StateAccumulatingMatchFilter) -> NoneType
Erase all tracking data on which matches have already been output.
Methods inherited from MatchFilter:
- filter_name(...) from builtins.PyCapsule
- filter_name(rosetta.protocols.match.output.MatchFilter) -> str
|
class UpstreamCollisionFilter(MatchCollisionFilter) |
| |
This class is used to detect collisions between the upstream residues
and filter out matches that have too much collision. It can perform either
hard-sphere collision detection, or score-function (Etable) driven collision
detection. Four command-line flags are read by the MatcherTask to initialize
this class:
match::filter_colliding_upstream_residues
match::upstream_residue_collision_tolerance
match::upstream_residue_collision_score_cutoff
match::upstream_residue_collision_Wfa_atr
match::upstream_residue_collision_Wfa_rep
match::upstream_residue_collision_Wfa_sol
|
| |
- Method resolution order:
- UpstreamCollisionFilter
- MatchCollisionFilter
- MatchFilter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, filter_name : str, coordinate_cacher : protocols::match::output::UpstreamHitCacher) -> NoneType
2. __init__(handle, rosetta.protocols.match.output.UpstreamCollisionFilter) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.output.UpstreamCollisionFilter, : rosetta.protocols.match.output.UpstreamCollisionFilter) -> rosetta.protocols.match.output.UpstreamCollisionFilter
- passes_filter(...) from builtins.PyCapsule
- passes_filter(*args, **kwargs)
Overloaded function.
1. passes_filter(self : rosetta.protocols.match.output.UpstreamCollisionFilter, m : rosetta.utility.vector1_protocols_match_Hit) -> bool
Returns true if the given match does not contain too much residue-pair collision.
2. passes_filter(self : rosetta.protocols.match.output.UpstreamCollisionFilter, m : rosetta.protocols.match.match_dspos1) -> bool
Returns true if the given match does not contain too much residue-pair collision.
- passes_hardsphere_filter(...) from builtins.PyCapsule
- passes_hardsphere_filter(*args, **kwargs)
Overloaded function.
1. passes_hardsphere_filter(self : rosetta.protocols.match.output.UpstreamCollisionFilter, geomcst_a : int, geomcst_b : int, upstream_hit_a : rosetta.protocols.match.Hit, upstream_hit_b : rosetta.protocols.match.Hit) -> bool
2. passes_hardsphere_filter(self : rosetta.protocols.match.output.UpstreamCollisionFilter, resA : rosetta.core.conformation.Residue, resB : rosetta.core.conformation.Residue) -> bool
Methods inherited from MatchCollisionFilter:
- bump_grid(...) from builtins.PyCapsule
- bump_grid(rosetta.protocols.match.output.MatchCollisionFilter) -> rosetta.protocols.match.BumpGrid
- empty_pose(...) from builtins.PyCapsule
- empty_pose(rosetta.protocols.match.output.MatchCollisionFilter) -> rosetta.core.pose.Pose
- empty_sfxn(...) from builtins.PyCapsule
- empty_sfxn(rosetta.protocols.match.output.MatchCollisionFilter) -> rosetta.core.scoring.ScoreFunction
- etable_energy(...) from builtins.PyCapsule
- etable_energy(rosetta.protocols.match.output.MatchCollisionFilter) -> rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy
- filter_by_lj(...) from builtins.PyCapsule
- filter_by_lj(rosetta.protocols.match.output.MatchCollisionFilter) -> bool
- lj_cutoff(...) from builtins.PyCapsule
- lj_cutoff(rosetta.protocols.match.output.MatchCollisionFilter) -> float
- set_filter_by_lj(...) from builtins.PyCapsule
- set_filter_by_lj(self : rosetta.protocols.match.output.MatchCollisionFilter, setting : bool) -> NoneType
- set_lj_atr_weight(...) from builtins.PyCapsule
- set_lj_atr_weight(self : rosetta.protocols.match.output.MatchCollisionFilter, setting : float) -> NoneType
- set_lj_cutoff(...) from builtins.PyCapsule
- set_lj_cutoff(self : rosetta.protocols.match.output.MatchCollisionFilter, setting : float) -> NoneType
- set_lj_rep_weight(...) from builtins.PyCapsule
- set_lj_rep_weight(self : rosetta.protocols.match.output.MatchCollisionFilter, setting : float) -> NoneType
- set_lj_sol_weight(...) from builtins.PyCapsule
- set_lj_sol_weight(self : rosetta.protocols.match.output.MatchCollisionFilter, setting : float) -> NoneType
- set_tolerated_overlap(...) from builtins.PyCapsule
- set_tolerated_overlap(self : rosetta.protocols.match.output.MatchCollisionFilter, setting : float) -> NoneType
- tolerated_overlap(...) from builtins.PyCapsule
- tolerated_overlap(rosetta.protocols.match.output.MatchCollisionFilter) -> float
- wfa_atr(...) from builtins.PyCapsule
- wfa_atr(rosetta.protocols.match.output.MatchCollisionFilter) -> float
- wfa_rep(...) from builtins.PyCapsule
- wfa_rep(rosetta.protocols.match.output.MatchCollisionFilter) -> float
- wfa_sol(...) from builtins.PyCapsule
- wfa_sol(rosetta.protocols.match.output.MatchCollisionFilter) -> float
Methods inherited from MatchFilter:
- filter_name(...) from builtins.PyCapsule
- filter_name(rosetta.protocols.match.output.MatchFilter) -> str
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class UpstreamDownstreamCollisionFilter(MatchCollisionFilter) |
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This class is used to detect collisions between upstream residues
and downstream poses.
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- Method resolution order:
- UpstreamDownstreamCollisionFilter
- MatchCollisionFilter
- MatchFilter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, filter_name : str, coordinate_cacher : rosetta.protocols.match.output.UpstreamHitCacher) -> NoneType
2. __init__(handle, rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, : rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter) -> rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter
- passes_filter(...) from builtins.PyCapsule
- passes_filter(*args, **kwargs)
Overloaded function.
1. passes_filter(self : rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, m : rosetta.utility.vector1_protocols_match_Hit) -> bool
Returns true if there is at least one placement of the
downstream partner which does not exceed the collision tolerance
with any of the upstream residues.
2. passes_filter(self : rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, m : rosetta.protocols.match.match_dspos1) -> bool
Returns true if the specified downstream position does not
collide more than tolerated with any of the upstream residues
- passes_hardsphere_filter(...) from builtins.PyCapsule
- passes_hardsphere_filter(*args, **kwargs)
Overloaded function.
1. passes_hardsphere_filter(self : rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, geomcst_up : int, geomcst_down : int, upstream_hit : rosetta.protocols.match.Hit, downstream_hit : rosetta.protocols.match.Hit) -> bool
2. passes_hardsphere_filter(self : rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, geomcst : int, upstream_hit : rosetta.protocols.match.Hit, coords : rosetta.utility.vector1_numeric_xyzVector_double_t) -> bool
- set_chemical_bond_from_upstream_to_downstream(...) from builtins.PyCapsule
- set_chemical_bond_from_upstream_to_downstream(self : rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, geomcst_id : int) -> NoneType
Do not perform any collision detection between an upstream residue and the downstream
pose if there is a chemical bond between them
- set_downstream_builder(...) from builtins.PyCapsule
- set_downstream_builder(self : rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, geomcst_id : int, builder : rosetta.protocols.match.downstream.DownstreamBuilder) -> NoneType
- set_downstream_pose(...) from builtins.PyCapsule
- set_downstream_pose(self : rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, downstream_pose : rosetta.core.pose.Pose) -> NoneType
- set_num_geometric_constraints(...) from builtins.PyCapsule
- set_num_geometric_constraints(self : rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, n_geomcst : int) -> NoneType
- set_tolerated_overlap(...) from builtins.PyCapsule
- set_tolerated_overlap(self : rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, setting : float) -> NoneType
Methods inherited from MatchCollisionFilter:
- bump_grid(...) from builtins.PyCapsule
- bump_grid(rosetta.protocols.match.output.MatchCollisionFilter) -> rosetta.protocols.match.BumpGrid
- empty_pose(...) from builtins.PyCapsule
- empty_pose(rosetta.protocols.match.output.MatchCollisionFilter) -> rosetta.core.pose.Pose
- empty_sfxn(...) from builtins.PyCapsule
- empty_sfxn(rosetta.protocols.match.output.MatchCollisionFilter) -> rosetta.core.scoring.ScoreFunction
- etable_energy(...) from builtins.PyCapsule
- etable_energy(rosetta.protocols.match.output.MatchCollisionFilter) -> rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy
- filter_by_lj(...) from builtins.PyCapsule
- filter_by_lj(rosetta.protocols.match.output.MatchCollisionFilter) -> bool
- lj_cutoff(...) from builtins.PyCapsule
- lj_cutoff(rosetta.protocols.match.output.MatchCollisionFilter) -> float
- set_filter_by_lj(...) from builtins.PyCapsule
- set_filter_by_lj(self : rosetta.protocols.match.output.MatchCollisionFilter, setting : bool) -> NoneType
- set_lj_atr_weight(...) from builtins.PyCapsule
- set_lj_atr_weight(self : rosetta.protocols.match.output.MatchCollisionFilter, setting : float) -> NoneType
- set_lj_cutoff(...) from builtins.PyCapsule
- set_lj_cutoff(self : rosetta.protocols.match.output.MatchCollisionFilter, setting : float) -> NoneType
- set_lj_rep_weight(...) from builtins.PyCapsule
- set_lj_rep_weight(self : rosetta.protocols.match.output.MatchCollisionFilter, setting : float) -> NoneType
- set_lj_sol_weight(...) from builtins.PyCapsule
- set_lj_sol_weight(self : rosetta.protocols.match.output.MatchCollisionFilter, setting : float) -> NoneType
- tolerated_overlap(...) from builtins.PyCapsule
- tolerated_overlap(rosetta.protocols.match.output.MatchCollisionFilter) -> float
- wfa_atr(...) from builtins.PyCapsule
- wfa_atr(rosetta.protocols.match.output.MatchCollisionFilter) -> float
- wfa_rep(...) from builtins.PyCapsule
- wfa_rep(rosetta.protocols.match.output.MatchCollisionFilter) -> float
- wfa_sol(...) from builtins.PyCapsule
- wfa_sol(rosetta.protocols.match.output.MatchCollisionFilter) -> float
Methods inherited from MatchFilter:
- filter_name(...) from builtins.PyCapsule
- filter_name(rosetta.protocols.match.output.MatchFilter) -> str
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class WriteKinemageOutputter(OutputWriter) |
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- Method resolution order:
- WriteKinemageOutputter
- OutputWriter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.output.WriteKinemageOutputter, : rosetta.protocols.match.output.WriteKinemageOutputter) -> rosetta.protocols.match.output.WriteKinemageOutputter
- record_match(...) from builtins.PyCapsule
- record_match(*args, **kwargs)
Overloaded function.
1. record_match(self : rosetta.protocols.match.output.WriteKinemageOutputter, m : rosetta.utility.vector1_protocols_match_Hit, evaluator : rosetta.protocols.match.output.MatchEvaluator, match_score_writer : rosetta.protocols.match.output.MatchScoreWriter) -> NoneType
2. record_match(self : rosetta.protocols.match.output.WriteKinemageOutputter, m : rosetta.protocols.match.match_dspos1) -> NoneType
evaluator and score writer are not passed in because single-downstream-position match
currently have no way of being evaluated
- set_coordinate_cacher(...) from builtins.PyCapsule
- set_coordinate_cacher(self : rosetta.protocols.match.output.WriteKinemageOutputter, : rosetta.protocols.match.output.UpstreamHitCacher) -> NoneType
- set_downstream_writer(...) from builtins.PyCapsule
- set_downstream_writer(self : rosetta.protocols.match.output.WriteKinemageOutputter, geomcst_id : int, ds_writer : protocols::match::output::DownstreamCoordinateKinemageWriter) -> NoneType
- set_kin_writer(...) from builtins.PyCapsule
- set_kin_writer(self : rosetta.protocols.match.output.WriteKinemageOutputter, us_writer : protocols::match::output::WriteUpstreamHitKinemage) -> NoneType
- set_n_geomcst(...) from builtins.PyCapsule
- set_n_geomcst(self : rosetta.protocols.match.output.WriteKinemageOutputter, n_geomcst : int) -> NoneType
Methods inherited from OutputWriter:
- cst_io(...) from builtins.PyCapsule
- cst_io(rosetta.protocols.match.output.OutputWriter) -> rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO
- determine_redundant_upstream_matchres(...) from builtins.PyCapsule
- determine_redundant_upstream_matchres(self : rosetta.protocols.match.output.OutputWriter, m : rosetta.protocols.match.match_dspos1, redundant_upstream_res : rosetta.std.map_unsigned_long_unsigned_long) -> NoneType
determine if any upstream res are at the same scaffold
position, i.e. if one of them is a backbone interaction
the redundant_upstream_res map is a mapping from the redundant
geometric constraint id of the redundant residue to the geomcst_id of
the "nonredundant" res i.e. if cstres 1 happens to be a cys at
position 10 and cstres 3 is a gly at position 10 (and it's backbone is
used in satisfying constraint 3), the mapping will contain the 3,1 pair.
- end_output_writing(...) from builtins.PyCapsule
- end_output_writing(rosetta.protocols.match.output.OutputWriter) -> NoneType
- initialize_from_matcher_task(...) from builtins.PyCapsule
- initialize_from_matcher_task(self : rosetta.protocols.match.output.OutputWriter, mtask : rosetta.protocols.match.MatcherTask) -> NoneType
- prepare_for_output_writing(...) from builtins.PyCapsule
- prepare_for_output_writing(rosetta.protocols.match.output.OutputWriter) -> NoneType
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class WriteUpstreamCoordinateKinemage(rosetta.protocols.match.downstream.DownstreamAlgorithm) |
| | |
- Method resolution order:
- WriteUpstreamCoordinateKinemage
- rosetta.protocols.match.downstream.DownstreamAlgorithm
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, fname : str) -> NoneType
3. __init__(self : handle, ostr : std::ostream) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- build(...) from builtins.PyCapsule
- build(self : rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage, scaffold_build_point_id : int, upstream_conf_id : int, upstream_residue : rosetta.core.conformation.Residue) -> rosetta.std.list_protocols_match_Hit_std_allocator_protocols_match_Hit_t
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage) -> rosetta.protocols.match.downstream.DownstreamAlgorithm
- generates_primary_hits(...) from builtins.PyCapsule
- generates_primary_hits(rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage) -> bool
This method returns 'true' since when it does return hits, it's those generated
by the ClassicMatchAlgorithm
- n_possible_hits_per_upstream_conformation(...) from builtins.PyCapsule
- n_possible_hits_per_upstream_conformation(rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage) -> int
- return_pseudo_hits(...) from builtins.PyCapsule
- return_pseudo_hits(*args, **kwargs)
Overloaded function.
1. return_pseudo_hits(rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage) -> bool
2. return_pseudo_hits(self : rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage, setting : bool) -> NoneType
- set_downstream_writer(...) from builtins.PyCapsule
- set_downstream_writer(self : rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage, dswriter : protocols::match::output::DownstreamCoordinateKinemageWriter) -> NoneType
- set_kinemage_file_name(...) from builtins.PyCapsule
- set_kinemage_file_name(self : rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage, filename : str) -> NoneType
- set_match_algorithm(...) from builtins.PyCapsule
- set_match_algorithm(self : rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage, algorithm : rosetta.protocols.match.downstream.ClassicMatchAlgorithm) -> NoneType
- set_n_downstream_to_output(...) from builtins.PyCapsule
- set_n_downstream_to_output(self : rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage, n_downstream_to_output : int) -> NoneType
- upstream_only(...) from builtins.PyCapsule
- upstream_only(rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage) -> bool
This method returns 'true' whether or not it's ClassicMatchAlgorithm is set
as it should not have its hits_to_include_with_partial_match method invoked.
Methods inherited from rosetta.protocols.match.downstream.DownstreamAlgorithm:
- are_colliding(...) from builtins.PyCapsule
- are_colliding(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, us_res : rosetta.core.conformation.Residue, ds_res : rosetta.core.conformation.Residue, ds_atoms : rosetta.utility.vector1_core_id_AtomID, catalytic_atoms : rosetta.utility.vector1_unsigned_long) -> bool
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, : rosetta.protocols.match.downstream.DownstreamAlgorithm) -> rosetta.protocols.match.downstream.DownstreamAlgorithm
- build_hits_at_all_positions(...) from builtins.PyCapsule
- build_hits_at_all_positions(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, matcher : rosetta.protocols.match.Matcher) -> rosetta.std.list_protocols_match_Hit_std_allocator_protocols_match_Hit_t
Main driver function for hit generation. The algorithm
is responsible for generating hits at all scaffold build points that
are valid for this geometric constraint. The base class provides an
iterate-across-all-positions-and-splice-together-hit-lists implementation,
however, derived classes may overload this function. The base class
function is parallelizable with OpenMP. The returned hit list must be in sorted
order by 1) hit.scaffold_build_id() and then by 2) hit.upstream_conf_id().
- geom_cst_id(...) from builtins.PyCapsule
- geom_cst_id(rosetta.protocols.match.downstream.DownstreamAlgorithm) -> int
- get_dsbuilder(...) from builtins.PyCapsule
- get_dsbuilder(rosetta.protocols.match.downstream.DownstreamAlgorithm) -> protocols::match::downstream::DownstreamBuilder
- prepare_for_match_enumeration(...) from builtins.PyCapsule
- prepare_for_match_enumeration(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, : rosetta.protocols.match.Matcher) -> NoneType
Called at the conclusion of matching, the Matcher signals
to the downstream algorithm that it's time to prepare for
match generation; if the downstream algorithm needs to enumerate
compatible hits in response to the invokation of its
hits_to_include_with_partial_match method, then now is the time
to prepare for those calls. Base class has a noop implementation.
- respond_to_peripheral_hitlist_change(...) from builtins.PyCapsule
- respond_to_peripheral_hitlist_change(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, matcher : rosetta.protocols.match.Matcher) -> NoneType
Following the change in the number of hits of some other round -- either
from the conclusion of that round in which a new set of hits has been generated,
or from the cascading change to the hits from round A which were deleted after the
conclusion of round B.
- respond_to_primary_hitlist_change(...) from builtins.PyCapsule
- respond_to_primary_hitlist_change(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, matcher : rosetta.protocols.match.Matcher, round_just_completed : int) -> NoneType
Reset appropriate Matcher data to spawn the deletion of hits from other rounds
following either hit generation by this geometric constraint, or
following hit generation by another geometric constraint which caused the deletion
of hits from this geometric constraint. The classic match algorithm, for example,
resets the occupied-space hash so that other classic-match algorithms can delete their
non-viable hits in subsequent calls to respond_to_peripheral_hitlist_change.
- set_active_site_grid(...) from builtins.PyCapsule
- set_active_site_grid(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, active_site_grid : rosetta.protocols.match.downstream.ActiveSiteGrid) -> NoneType
- set_bb_grid(...) from builtins.PyCapsule
- set_bb_grid(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, bbgrid : rosetta.protocols.match.BumpGrid) -> NoneType
- set_dsbuilder(...) from builtins.PyCapsule
- set_dsbuilder(self : rosetta.protocols.match.downstream.DownstreamAlgorithm, dsbuilder : protocols::match::downstream::DownstreamBuilder) -> NoneType
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class WriteUpstreamHitKinemage(rosetta.protocols.match.upstream.UpstreamResidueProcessor) |
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- Method resolution order:
- WriteUpstreamHitKinemage
- rosetta.protocols.match.upstream.UpstreamResidueProcessor
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, fname : str) -> NoneType
3. __init__(self : handle, ostr : std::ostream) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- animate(...) from builtins.PyCapsule
- animate(self : rosetta.protocols.match.output.WriteUpstreamHitKinemage, setting : bool) -> NoneType
- default_master(...) from builtins.PyCapsule
- default_master(*args, **kwargs)
Overloaded function.
1. default_master(self : rosetta.protocols.match.output.WriteUpstreamHitKinemage, setting : bool) -> NoneType
Set whether the default master should be used, or whether the
user-defined master should be used. If the user defined master is the
empty string, no master will be writen.
2. default_master(rosetta.protocols.match.output.WriteUpstreamHitKinemage) -> bool
Returns whether or not the default master is being used.
- dominant(...) from builtins.PyCapsule
- dominant(self : rosetta.protocols.match.output.WriteUpstreamHitKinemage, setting : bool) -> NoneType
- geom_id(...) from builtins.PyCapsule
- geom_id(self : rosetta.protocols.match.output.WriteUpstreamHitKinemage, setting : int) -> NoneType
- group(...) from builtins.PyCapsule
- group(self : rosetta.protocols.match.output.WriteUpstreamHitKinemage, setting : bool) -> NoneType
- output_hit(...) from builtins.PyCapsule
- output_hit(self : rosetta.protocols.match.output.WriteUpstreamHitKinemage, hit : rosetta.protocols.match.Hit, upstream_conformation : rosetta.core.conformation.Residue) -> NoneType
Non-virtual method to write out a kinemage for an upstream residue
- output_upstream_coordinates(...) from builtins.PyCapsule
- output_upstream_coordinates(self : rosetta.protocols.match.output.WriteUpstreamHitKinemage, hit : rosetta.protocols.match.upstream_hit, upstream_conformation : rosetta.core.conformation.Residue) -> NoneType
non-virtual method to write out a kinemage for an upstream residue;
without invoking dswriter_->write_downstream_coordinates().
Only information about the upstream portion of the hit is needed.
- process_hit(...) from builtins.PyCapsule
- process_hit(self : rosetta.protocols.match.output.WriteUpstreamHitKinemage, hit : rosetta.protocols.match.Hit, upstream_conformation : rosetta.core.conformation.Residue) -> NoneType
- set_dswriter(...) from builtins.PyCapsule
- set_dswriter(self : rosetta.protocols.match.output.WriteUpstreamHitKinemage, dswriter : protocols::match::output::DownstreamCoordinateKinemageWriter) -> NoneType
- set_kinemage_file(...) from builtins.PyCapsule
- set_kinemage_file(self : rosetta.protocols.match.output.WriteUpstreamHitKinemage, fname : str) -> NoneType
- set_master(...) from builtins.PyCapsule
- set_master(self : rosetta.protocols.match.output.WriteUpstreamHitKinemage, master : str) -> NoneType
Set the kinemage master for the upstream residue, overriding
the default master, which is "geom#"
- start_new_match(...) from builtins.PyCapsule
- start_new_match(rosetta.protocols.match.output.WriteUpstreamHitKinemage) -> NoneType
- write_virtual_atoms(...) from builtins.PyCapsule
- write_virtual_atoms(self : rosetta.protocols.match.output.WriteUpstreamHitKinemage, setting : bool) -> NoneType
Methods inherited from rosetta.protocols.match.upstream.UpstreamResidueProcessor:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.match.upstream.UpstreamResidueProcessor, : rosetta.protocols.match.upstream.UpstreamResidueProcessor) -> rosetta.protocols.match.upstream.UpstreamResidueProcessor
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