corems.mass_spectra.calc.GC_RI_Calibration 

 1from corems.molecular_id.search.compoundSearch import LowResMassSpectralMatch
 2
 3
 4def get_rt_ri_pairs(gcms_ref_obj, sql_obj=None):
 5    lowResSearch = LowResMassSpectralMatch(
 6        gcms_ref_obj, sql_obj=sql_obj, calibration=True
 7    )
 8
 9    lowResSearch.run()
10
11    dict_ri_rt = {}
12
13    list_of_compound_obj = {}
14
15    for gcms_peak in gcms_ref_obj:
16        # has a compound matched
17        if gcms_peak:
18            compound_obj = gcms_peak.highest_ss_compound
19
20            if not compound_obj.ri in dict_ri_rt.keys():
21                dict_ri_rt[compound_obj.ri] = [
22                    (gcms_peak.mass_spectrum.retention_time, compound_obj)
23                ]
24
25            else:
26                dict_ri_rt[compound_obj.ri].append(
27                    (gcms_peak.mass_spectrum.retention_time, compound_obj)
28                )
29            if gcms_ref_obj.parameters.gc_ms.verbose_processing:
30                print(
31                    compound_obj.name,
32                    gcms_peak.mass_spectrum.retention_time,
33                    compound_obj.spectral_similarity_score,
34                )
35
36    ris = [i for i in dict_ri_rt.keys()]
37    rts = [
38        max(i, key=lambda c: c[1].spectral_similarity_score)[0]
39        for i in dict_ri_rt.values()
40    ]
41
42    rt_ri_pairs = list(zip(rts, ris))
43
44    return rt_ri_pairs
def get_rt_ri_pairs(gcms_ref_obj, sql_obj=None): 
 5def get_rt_ri_pairs(gcms_ref_obj, sql_obj=None):
 6    lowResSearch = LowResMassSpectralMatch(
 7        gcms_ref_obj, sql_obj=sql_obj, calibration=True
 8    )
 9
10    lowResSearch.run()
11
12    dict_ri_rt = {}
13
14    list_of_compound_obj = {}
15
16    for gcms_peak in gcms_ref_obj:
17        # has a compound matched
18        if gcms_peak:
19            compound_obj = gcms_peak.highest_ss_compound
20
21            if not compound_obj.ri in dict_ri_rt.keys():
22                dict_ri_rt[compound_obj.ri] = [
23                    (gcms_peak.mass_spectrum.retention_time, compound_obj)
24                ]
25
26            else:
27                dict_ri_rt[compound_obj.ri].append(
28                    (gcms_peak.mass_spectrum.retention_time, compound_obj)
29                )
30            if gcms_ref_obj.parameters.gc_ms.verbose_processing:
31                print(
32                    compound_obj.name,
33                    gcms_peak.mass_spectrum.retention_time,
34                    compound_obj.spectral_similarity_score,
35                )
36
37    ris = [i for i in dict_ri_rt.keys()]
38    rts = [
39        max(i, key=lambda c: c[1].spectral_similarity_score)[0]
40        for i in dict_ri_rt.values()
41    ]
42
43    rt_ri_pairs = list(zip(rts, ris))
44
45    return rt_ri_pairs