src.serena.ensemble_variation

This is the file to just get plain old ensemble variation for a list of structures that make up an ensemble

 1"""
 2This is the file to just get plain old ensemble variation for a list
 3of structures that make up an ensemble
 4"""
 5
 6from serena.utilities.ensemble_structures import Sara2SecondaryStructure, Sara2StructureList
 7from serena.utilities.ensemble_variation import EV, EnsembleVariation
 8from serena.interfaces.nupack4_0_28_wsl2_interface import NUPACK4Interface, MaterialParameter
 9
10class RunEnsembleVariation(EnsembleVariation):
11    """
12    Class to get the ensemble variation
13    """
14    def ev_from_structures_list(self, structures_list:Sara2StructureList, mfe_structure:Sara2SecondaryStructure):#pylint: disable=line-too-long
15        """
16        Get the Ensemble Variation for a sara2Structure List amd reference mfe structure
17        """
18        e_v:EV = self.ensemble_variation_algorithm(kcal_group_structures_list=structures_list,
19                                                        ref_structure=mfe_structure)
20        return e_v.ev_normalized
21
22    def ev_from_nupack4(self, material:MaterialParameter, temp_c:int, span_from_mfe:int, sequence:str):#pylint: disable=line-too-long
23        """
24        Get the Ensemble Variation for an ensemble after folding in silico with nupack
25        """
26        nupack4: NUPACK4Interface = NUPACK4Interface()
27        structs:Sara2StructureList = nupack4.get_subopt_energy_gap(material_param=material,
28                                  temp_C=temp_c,
29                                  sequence_string=sequence,
30                                  energy_delta_from_MFE=span_from_mfe,
31                                  )
32        ensemble_variation:float = self.ev_from_structures_list(structures_list=structs,
33                                                                mfe_structure=structs.sara_stuctures[0])#pylint: disable=line-too-long
34        return ensemble_variation
class RunEnsembleVariation(serena.utilities.ensemble_variation.EnsembleVariation): 
11class RunEnsembleVariation(EnsembleVariation):
12    """
13    Class to get the ensemble variation
14    """
15    def ev_from_structures_list(self, structures_list:Sara2StructureList, mfe_structure:Sara2SecondaryStructure):#pylint: disable=line-too-long
16        """
17        Get the Ensemble Variation for a sara2Structure List amd reference mfe structure
18        """
19        e_v:EV = self.ensemble_variation_algorithm(kcal_group_structures_list=structures_list,
20                                                        ref_structure=mfe_structure)
21        return e_v.ev_normalized
22
23    def ev_from_nupack4(self, material:MaterialParameter, temp_c:int, span_from_mfe:int, sequence:str):#pylint: disable=line-too-long
24        """
25        Get the Ensemble Variation for an ensemble after folding in silico with nupack
26        """
27        nupack4: NUPACK4Interface = NUPACK4Interface()
28        structs:Sara2StructureList = nupack4.get_subopt_energy_gap(material_param=material,
29                                  temp_C=temp_c,
30                                  sequence_string=sequence,
31                                  energy_delta_from_MFE=span_from_mfe,
32                                  )
33        ensemble_variation:float = self.ev_from_structures_list(structures_list=structs,
34                                                                mfe_structure=structs.sara_stuctures[0])#pylint: disable=line-too-long
35        return ensemble_variation

Class to get the ensemble variation

def ev_from_structures_list( self, structures_list: serena.utilities.ensemble_structures.Sara2StructureList, mfe_structure: serena.utilities.ensemble_structures.Sara2SecondaryStructure): 
15    def ev_from_structures_list(self, structures_list:Sara2StructureList, mfe_structure:Sara2SecondaryStructure):#pylint: disable=line-too-long
16        """
17        Get the Ensemble Variation for a sara2Structure List amd reference mfe structure
18        """
19        e_v:EV = self.ensemble_variation_algorithm(kcal_group_structures_list=structures_list,
20                                                        ref_structure=mfe_structure)
21        return e_v.ev_normalized

Get the Ensemble Variation for a sara2Structure List amd reference mfe structure

def ev_from_nupack4( self, material: serena.interfaces.nupack4_0_28_wsl2_interface.MaterialParameter, temp_c: int, span_from_mfe: int, sequence: str): 
23    def ev_from_nupack4(self, material:MaterialParameter, temp_c:int, span_from_mfe:int, sequence:str):#pylint: disable=line-too-long
24        """
25        Get the Ensemble Variation for an ensemble after folding in silico with nupack
26        """
27        nupack4: NUPACK4Interface = NUPACK4Interface()
28        structs:Sara2StructureList = nupack4.get_subopt_energy_gap(material_param=material,
29                                  temp_C=temp_c,
30                                  sequence_string=sequence,
31                                  energy_delta_from_MFE=span_from_mfe,
32                                  )
33        ensemble_variation:float = self.ev_from_structures_list(structures_list=structs,
34                                                                mfe_structure=structs.sara_stuctures[0])#pylint: disable=line-too-long
35        return ensemble_variation

Get the Ensemble Variation for an ensemble after folding in silico with nupack

Inherited Members
serena.utilities.ensemble_variation.EnsembleVariation
thread_ev
ensemble_variation_algorithm