CoreMS 2.0.6__tar.gz → 2.0.8__tar.gz

{CoreMS-2.0.6 → CoreMS-2.0.8}/CoreMS.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CoreMS
-Version: 2.0.6
+Version: 2.0.8
 Summary: Mass Spectrometry Framework for Small Molecules Analysis
 Home-page: https://github.com/EMSL-Computing/CoreMS
 Author: Corilo, Yuri
@@ -66,7 +66,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `2.0.6`
+ `2.0.8`
 
 ***
 
@@ -339,7 +339,7 @@ UML (unified modeling language) diagrams for Direct Infusion FT-MS and GC-MS cla
 
 If you use CoreMS in your work, please use the following citation:
 
-Version [2.0.6 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.0.6), archived on Zenodo:  
+Version [2.0.8 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.0.8), archived on Zenodo:  
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
 

{CoreMS-2.0.6 → CoreMS-2.0.8}/CoreMS.egg-info/SOURCES.txt

@@ -128,6 +128,24 @@ ext_lib/ThermoFisher.CommonCore.MassPrecisionEstimator.dll
 ext_lib/ThermoFisher.CommonCore.RawFileReader.dll
 ext_lib/ThermoFisher.CommonCore.RawFileReader.xml
 ext_lib/__init__.py
+ext_lib/dotnet/OpenMcdf.Extensions.dll
+ext_lib/dotnet/OpenMcdf.dll
+ext_lib/dotnet/OpenMcdf.xml
+ext_lib/dotnet/System.IO.FileSystem.AccessControl.dll
+ext_lib/dotnet/System.IO.FileSystem.AccessControl.xml
+ext_lib/dotnet/System.Security.AccessControl.dll
+ext_lib/dotnet/System.Security.AccessControl.xml
+ext_lib/dotnet/System.Security.Principal.Windows.dll
+ext_lib/dotnet/System.Security.Principal.Windows.xml
+ext_lib/dotnet/ThermoFisher.CommonCore.BackgroundSubtraction.dll
+ext_lib/dotnet/ThermoFisher.CommonCore.BackgroundSubtraction.xml
+ext_lib/dotnet/ThermoFisher.CommonCore.Data.dll
+ext_lib/dotnet/ThermoFisher.CommonCore.Data.xml
+ext_lib/dotnet/ThermoFisher.CommonCore.MassPrecisionEstimator.dll
+ext_lib/dotnet/ThermoFisher.CommonCore.MassPrecisionEstimator.xml
+ext_lib/dotnet/ThermoFisher.CommonCore.RawFileReader.dll
+ext_lib/dotnet/ThermoFisher.CommonCore.RawFileReader.xml
+ext_lib/dotnet/__init__.py
 tests/test.py
 tests/test_LossFinder.py
 tests/test_assembly_identification.py

{CoreMS-2.0.6 → CoreMS-2.0.8}/CoreMS.egg-info/requires.txt

@@ -2,7 +2,7 @@ beautifulsoup4~=4.12.0
 chardet~=5.1.0
 comtypes~=1.1.14
 h5py~=3.8.0
-IsoSpecPy~=2.0.2
+IsoSpecPy~=2.2.2
 lmfit~=1.1.0
 lxml~=4.9.3
 matplotlib~=3.7.0

{CoreMS-2.0.6 → CoreMS-2.0.8}/MANIFEST.in

@@ -1,4 +1,5 @@
 include requirements.txt
 include disclaimer.txt
 include Dockerfile
-include ext_lib/*
+include ext_lib/*
+include ext_lib/dotnet/*

{CoreMS-2.0.6 → CoreMS-2.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CoreMS
-Version: 2.0.6
+Version: 2.0.8
 Summary: Mass Spectrometry Framework for Small Molecules Analysis
 Home-page: https://github.com/EMSL-Computing/CoreMS
 Author: Corilo, Yuri
@@ -66,7 +66,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `2.0.6`
+ `2.0.8`
 
 ***
 
@@ -339,7 +339,7 @@ UML (unified modeling language) diagrams for Direct Infusion FT-MS and GC-MS cla
 
 If you use CoreMS in your work, please use the following citation:
 
-Version [2.0.6 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.0.6), archived on Zenodo:  
+Version [2.0.8 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.0.8), archived on Zenodo:  
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
 

{CoreMS-2.0.6 → CoreMS-2.0.8}/README.md

@@ -50,7 +50,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `2.0.6`
+ `2.0.8`
 
 ***
 
@@ -323,7 +323,7 @@ UML (unified modeling language) diagrams for Direct Infusion FT-MS and GC-MS cla
 
 If you use CoreMS in your work, please use the following citation:
 
-Version [2.0.6 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.0.6), archived on Zenodo:  
+Version [2.0.8 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.0.8), archived on Zenodo:  
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
 

{CoreMS-2.0.6 → CoreMS-2.0.8}/corems/__init__.py

@@ -1,5 +1,5 @@
 __author__ = 'Yuri E. Corilo'
-__version__ = '2.0.6'
+__version__ = '2.0.8'
 __doc__ = '''
 <div align="left">
 

{CoreMS-2.0.6 → CoreMS-2.0.8}/corems/mass_spectra/input/brukerSolarix.py

@@ -1,7 +1,6 @@
 __author__ = "Yuri E. Corilo"
 __date__ = "Oct 29, 2019"
 
-from future import __annotations__
 from threading import Thread
 from pathlib import Path
 from s3path import S3Path

{CoreMS-2.0.6 → CoreMS-2.0.8}/corems/mass_spectrum/calc/NoiseCalc.py

@@ -79,7 +79,7 @@ class NoiseThresholdCalc:
 
             elif self.settings.noise_threshold_method == 'signal_noise':
 
-                normalized_threshold = (self.max_abundance * self.settings.s2n_threshold )/self.max_signal_to_noise
+                normalized_threshold = (self.max_abundance * self.settings.noise_threshold_min_s2n )/self.max_signal_to_noise
                 y = (normalized_threshold, normalized_threshold)
             
             elif self.settings.noise_threshold_method == "relative_abundance":
@@ -115,7 +115,7 @@ class NoiseThresholdCalc:
 
                     max_sn = self.abundance_profile.max()/self.baseline_noise_std
 
-                    normalized_threshold = (self.abundance_profile.max() * self.settings.s2n_threshold )/max_sn
+                    normalized_threshold = (self.abundance_profile.max() * self.settings.noise_threshold_min_s2n )/max_sn
                     y = (normalized_threshold, normalized_threshold)
 
                 elif self.settings.noise_threshold_method == "relative_abundance":

{CoreMS-2.0.6 → CoreMS-2.0.8}/corems/mass_spectrum/calc/PeakPicking.py

@@ -452,7 +452,7 @@ class PeakPicking:
 
         elif noise_threshold_method == 'signal_noise':
 
-            abundance_threshold = self.settings.s2n_threshold
+            abundance_threshold = self.settings.noise_threshold_min_s2n
             factor = self.baseline_noise_std
 
         elif noise_threshold_method == "relative_abundance":

{CoreMS-2.0.6 → CoreMS-2.0.8}/corems/molecular_formula/calc/MolecularFormulaCalc.py

@@ -1,8 +1,8 @@
 __author__ = "Yuri E. Corilo"
 __date__ = "Jun 24, 2019"
 
-from IsoSpecPy import IsoSpecPy
-from numpy import isnan, power, exp, nextafter
+
+from numpy import isnan, power, exp, nextafter, array
 from pandas import DataFrame
 from scipy.stats import pearsonr, spearmanr, kendalltau
 
@@ -11,6 +11,19 @@ from corems.encapsulation.constant import Labels
 from corems.encapsulation.factory.parameters import MSParameters
 from corems.molecular_id.calc.SpectralSimilarity import SpectralSimilarity
 
+# this is to handle both versions of IsoSpecPy, 2.0.2 and 2.2.2
+# TODO in a future release remove support for legacy isospecpy
+from packaging import version
+import IsoSpecPy
+isospec_version = IsoSpecPy.__version__
+if version.parse(isospec_version) > version.parse('2.0.2'): 
+    legacy_isospec = False
+else: legacy_isospec = True
+if legacy_isospec:
+    from IsoSpecPy import IsoSpecPy
+    print(f"IsoSpecPy version {isospec_version} is installed, and support is deprecated. Please update to 2.2.2")
+
+
 class MolecularFormulaCalc:
     """Class of calculations related to molecular formula
 
@@ -645,15 +658,31 @@ class MolecularFormulaCalc:
                 atoms_count.append(formula_dict.get(atom_label))
                 masses_list_tuples.append(masses)
                 props_list_tuples.append(props)
-        
-        iso = IsoSpecPy.IsoSpec(atoms_count,masses_list_tuples,props_list_tuples, cut_off_to_IsoSpeccPy)
-        
-        conf = iso.getConfs()
-        masses = conf[0]
-        probs = exp(conf[1])
-        molecular_formulas = conf[2]
-        #print('conf', conf)
-        #print('probs', conf[1])
+        if legacy_isospec:
+            iso = IsoSpecPy.IsoSpec(atoms_count,masses_list_tuples,props_list_tuples, cut_off_to_IsoSpeccPy)
+            conf = iso.getConfs()
+            masses = conf[0]
+            probs = exp(conf[1])
+            molecular_formulas = conf[2]
+            #print('conf', conf)
+            #print('probs', conf[1])
+        else:
+            # This syntax in IsoSpecPy 2.2.2 yields the same information as the legacy approach
+            iso = IsoSpecPy.IsoTotalProb(atomCounts = atoms_count, isotopeMasses = masses_list_tuples, 
+                           isotopeProbabilities = props_list_tuples, prob_to_cover =cut_off_to_IsoSpeccPy, get_confs=True)
+            masses = list(iso.masses)
+            probs = array(list(iso.probs))
+            confs = list(iso.confs)
+
+            molecular_formulas = []
+            for x in confs:
+                tmplist = []
+                for y in x:
+                    tmplist.extend(list(y))
+                molecular_formulas.append(tmplist)
+
+
+
         
         new_formulas = []
         

{CoreMS-2.0.6 → CoreMS-2.0.8}/corems/molecular_formula/factory/MolecularFormulaFactory.py

@@ -406,9 +406,14 @@ class MolecularFormulaBase(MolecularFormulaCalc):
         -----
         This calculation ignores the hydrogen isotopes.
         """
-        
+        isotopologues = []
         for mf in self._cal_isotopologues(self._d_molecular_formula, min_abundance, current_mono_abundance, dynamic_range ):
-             
+            isotopologues.append(mf)
+        
+        # To account for differences in how the isotopologue outputs are sorted between IsoSpec versions. 
+        sorted_isotopologues = sorted(isotopologues, key=lambda mf: mf[1], reverse=True)
+
+        for mf in sorted_isotopologues:
             yield MolecularFormulaIsotopologue(
                 *mf, 
                 current_mono_abundance,