src.serena.utilities.local_minima_variation
File to hold the local minima variation code
1""" 2File to hold the local minima variation code 3""" 4import attrs 5from typing import List 6from dataclasses import dataclass 7 8from serena.utilities.ensemble_groups import MultipleEnsembleGroups, SingleEnsembleGroup 9from serena.utilities.ensemble_structures import Sara2SecondaryStructure 10from serena.utilities.ensemble_variation import EVToken, EV, EVResult 11from serena.utilities.thread_manager import EV_ThreadProcessor 12 13@dataclass 14class ComparisonLMV(): 15 """ 16 Holds the LMV's for the comparison structure 17 algorithm 18 """ 19 lmv_comp:EV = EV() 20 lmv_mfe:EV = EV() 21 lmv_rel:EV = EV() 22 23@attrs.define 24class ComparisonLMVResponse(): 25 """ 26 Holds the LMV's responses for the comparison structure 27 algorithm 28 """ 29 lmv_comps:List[ComparisonLMV] = [] 30 31class LocalMinimaVariation(): 32 """ 33 Local Minima Variation main algorithm access point. 34 This is teh base for finding the many flavors of LMV 35 """ 36 def __init__(self) -> None: 37 pass 38 39 def get_multi_group_lmv_single_ref(self, ensemble: MultipleEnsembleGroups, reference_structure:Sara2SecondaryStructure):#pylint: disable=line-too-long 40 """ 41 Return the lmv for a provided MultipleEnsemble Groups with seconfary structure as reference 42 """ 43 lmv_thread: EV_ThreadProcessor = EV_ThreadProcessor(stuctures=ensemble.raw_groups, 44 comp_structure=reference_structure) 45 result_thread_lmv:EVToken = lmv_thread.run_EV() 46 lmv_results: EVResult = result_thread_lmv.ev_results 47 return lmv_results 48 49 def get_single_group_lmv_single_ref(self, ensemble_group: SingleEnsembleGroup, reference_structure:Sara2SecondaryStructure):#pylint: disable=line-too-long 50 """ 51 Return the lmv for a provided SingleEnsembleGroup with seconfary structure as reference 52 """ 53 lmv_thread: EV_ThreadProcessor = EV_ThreadProcessor(stuctures=[ensemble_group.group], 54 comp_structure=reference_structure) 55 result_thread_lmv:EVToken = lmv_thread.run_EV() 56 lmv_results: EVResult = result_thread_lmv.ev_results 57 return lmv_results 58 59 def get_multi_group_lmv_list_ref(self, ensemble: MultipleEnsembleGroups, reference_list:List[Sara2SecondaryStructure]):#pylint: disable=line-too-long 60 """ 61 Return the lmv for a provided MultipleEnsemble Groups with seconfary structure as reference 62 """ 63 lmv_thread: EV_ThreadProcessor = EV_ThreadProcessor(stuctures=ensemble.raw_groups, 64 comp_struct_list_option=reference_list) 65 result_thread_lmv:EVToken = lmv_thread.run_EV() 66 lmv_results: EVResult = result_thread_lmv.ev_results 67 return lmv_results
@dataclass
class
ComparisonLMV:
14@dataclass 15class ComparisonLMV(): 16 """ 17 Holds the LMV's for the comparison structure 18 algorithm 19 """ 20 lmv_comp:EV = EV() 21 lmv_mfe:EV = EV() 22 lmv_rel:EV = EV()
Holds the LMV's for the comparison structure algorithm
ComparisonLMV( lmv_comp: serena.utilities.ensemble_variation.EV = EV(ev_normalized=-1, ev_threshold_norm=-1, ev_structure=-1), lmv_mfe: serena.utilities.ensemble_variation.EV = EV(ev_normalized=-1, ev_threshold_norm=-1, ev_structure=-1), lmv_rel: serena.utilities.ensemble_variation.EV = EV(ev_normalized=-1, ev_threshold_norm=-1, ev_structure=-1))
lmv_comp: serena.utilities.ensemble_variation.EV =
EV(ev_normalized=-1, ev_threshold_norm=-1, ev_structure=-1)
@attrs.define
class
ComparisonLMVResponse:
24@attrs.define 25class ComparisonLMVResponse(): 26 """ 27 Holds the LMV's responses for the comparison structure 28 algorithm 29 """ 30 lmv_comps:List[ComparisonLMV] = []
Holds the LMV's responses for the comparison structure algorithm
ComparisonLMVResponse( lmv_comps: List[src.serena.utilities.local_minima_variation.ComparisonLMV] = [])
Method generated by attrs for class ComparisonLMVResponse.
lmv_comps: List[src.serena.utilities.local_minima_variation.ComparisonLMV]
class
LocalMinimaVariation:
32class LocalMinimaVariation(): 33 """ 34 Local Minima Variation main algorithm access point. 35 This is teh base for finding the many flavors of LMV 36 """ 37 def __init__(self) -> None: 38 pass 39 40 def get_multi_group_lmv_single_ref(self, ensemble: MultipleEnsembleGroups, reference_structure:Sara2SecondaryStructure):#pylint: disable=line-too-long 41 """ 42 Return the lmv for a provided MultipleEnsemble Groups with seconfary structure as reference 43 """ 44 lmv_thread: EV_ThreadProcessor = EV_ThreadProcessor(stuctures=ensemble.raw_groups, 45 comp_structure=reference_structure) 46 result_thread_lmv:EVToken = lmv_thread.run_EV() 47 lmv_results: EVResult = result_thread_lmv.ev_results 48 return lmv_results 49 50 def get_single_group_lmv_single_ref(self, ensemble_group: SingleEnsembleGroup, reference_structure:Sara2SecondaryStructure):#pylint: disable=line-too-long 51 """ 52 Return the lmv for a provided SingleEnsembleGroup with seconfary structure as reference 53 """ 54 lmv_thread: EV_ThreadProcessor = EV_ThreadProcessor(stuctures=[ensemble_group.group], 55 comp_structure=reference_structure) 56 result_thread_lmv:EVToken = lmv_thread.run_EV() 57 lmv_results: EVResult = result_thread_lmv.ev_results 58 return lmv_results 59 60 def get_multi_group_lmv_list_ref(self, ensemble: MultipleEnsembleGroups, reference_list:List[Sara2SecondaryStructure]):#pylint: disable=line-too-long 61 """ 62 Return the lmv for a provided MultipleEnsemble Groups with seconfary structure as reference 63 """ 64 lmv_thread: EV_ThreadProcessor = EV_ThreadProcessor(stuctures=ensemble.raw_groups, 65 comp_struct_list_option=reference_list) 66 result_thread_lmv:EVToken = lmv_thread.run_EV() 67 lmv_results: EVResult = result_thread_lmv.ev_results 68 return lmv_results
Local Minima Variation main algorithm access point. This is teh base for finding the many flavors of LMV
def
get_multi_group_lmv_single_ref( self, ensemble: serena.utilities.ensemble_groups.MultipleEnsembleGroups, reference_structure: serena.utilities.ensemble_structures.Sara2SecondaryStructure):
40 def get_multi_group_lmv_single_ref(self, ensemble: MultipleEnsembleGroups, reference_structure:Sara2SecondaryStructure):#pylint: disable=line-too-long 41 """ 42 Return the lmv for a provided MultipleEnsemble Groups with seconfary structure as reference 43 """ 44 lmv_thread: EV_ThreadProcessor = EV_ThreadProcessor(stuctures=ensemble.raw_groups, 45 comp_structure=reference_structure) 46 result_thread_lmv:EVToken = lmv_thread.run_EV() 47 lmv_results: EVResult = result_thread_lmv.ev_results 48 return lmv_results
Return the lmv for a provided MultipleEnsemble Groups with seconfary structure as reference
def
get_single_group_lmv_single_ref( self, ensemble_group: serena.utilities.ensemble_groups.SingleEnsembleGroup, reference_structure: serena.utilities.ensemble_structures.Sara2SecondaryStructure):
50 def get_single_group_lmv_single_ref(self, ensemble_group: SingleEnsembleGroup, reference_structure:Sara2SecondaryStructure):#pylint: disable=line-too-long 51 """ 52 Return the lmv for a provided SingleEnsembleGroup with seconfary structure as reference 53 """ 54 lmv_thread: EV_ThreadProcessor = EV_ThreadProcessor(stuctures=[ensemble_group.group], 55 comp_structure=reference_structure) 56 result_thread_lmv:EVToken = lmv_thread.run_EV() 57 lmv_results: EVResult = result_thread_lmv.ev_results 58 return lmv_results
Return the lmv for a provided SingleEnsembleGroup with seconfary structure as reference
def
get_multi_group_lmv_list_ref( self, ensemble: serena.utilities.ensemble_groups.MultipleEnsembleGroups, reference_list: List[serena.utilities.ensemble_structures.Sara2SecondaryStructure]):
60 def get_multi_group_lmv_list_ref(self, ensemble: MultipleEnsembleGroups, reference_list:List[Sara2SecondaryStructure]):#pylint: disable=line-too-long 61 """ 62 Return the lmv for a provided MultipleEnsemble Groups with seconfary structure as reference 63 """ 64 lmv_thread: EV_ThreadProcessor = EV_ThreadProcessor(stuctures=ensemble.raw_groups, 65 comp_struct_list_option=reference_list) 66 result_thread_lmv:EVToken = lmv_thread.run_EV() 67 lmv_results: EVResult = result_thread_lmv.ev_results 68 return lmv_results
Return the lmv for a provided MultipleEnsemble Groups with seconfary structure as reference