CoreMS 2.0.3__tar.gz → 2.0.6__tar.gz

{CoreMS-2.0.3 → CoreMS-2.0.6}/CoreMS.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CoreMS
-Version: 2.0.3
+Version: 2.0.6
 Summary: Mass Spectrometry Framework for Small Molecules Analysis
 Home-page: https://github.com/EMSL-Computing/CoreMS
 Author: Corilo, Yuri
@@ -14,7 +14,7 @@ Classifier: Development Status :: 4 - Beta
 Description-Content-Type: text/markdown
 License-File: LICENSE
 
-![CoreMS Logo](https://github.com/EMSL-Computing/CoreMS/blob/v2.0.1/docs/CoreMS.COLOR_small.png?raw=true)  
+![CoreMS Logo](https://github.com/EMSL-Computing/CoreMS/tree/master/docs/CoreMS.COLOR_small.png?raw=true)  
 
 <div align="left">
 
@@ -66,7 +66,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `2.0.3`
+ `2.0.6`
 
 ***
 
@@ -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 [2.0.3 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.0.3), archived on Zenodo:  
+Version [2.0.6 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.0.6), archived on Zenodo:  
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
 

{CoreMS-2.0.3 → CoreMS-2.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CoreMS
-Version: 2.0.3
+Version: 2.0.6
 Summary: Mass Spectrometry Framework for Small Molecules Analysis
 Home-page: https://github.com/EMSL-Computing/CoreMS
 Author: Corilo, Yuri
@@ -14,7 +14,7 @@ Classifier: Development Status :: 4 - Beta
 Description-Content-Type: text/markdown
 License-File: LICENSE
 
-![CoreMS Logo](https://github.com/EMSL-Computing/CoreMS/blob/v2.0.1/docs/CoreMS.COLOR_small.png?raw=true)  
+![CoreMS Logo](https://github.com/EMSL-Computing/CoreMS/tree/master/docs/CoreMS.COLOR_small.png?raw=true)  
 
 <div align="left">
 
@@ -66,7 +66,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `2.0.3`
+ `2.0.6`
 
 ***
 
@@ -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 [2.0.3 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.0.3), archived on Zenodo:  
+Version [2.0.6 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.0.6), archived on Zenodo:  
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
 

{CoreMS-2.0.3 → CoreMS-2.0.6}/README.md

@@ -1,4 +1,4 @@
-![CoreMS Logo](https://github.com/EMSL-Computing/CoreMS/blob/v2.0.1/docs/CoreMS.COLOR_small.png?raw=true)  
+![CoreMS Logo](https://github.com/EMSL-Computing/CoreMS/tree/master/docs/CoreMS.COLOR_small.png?raw=true)  
 
 <div align="left">
 
@@ -50,7 +50,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `2.0.3`
+ `2.0.6`
 
 ***
 
@@ -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 [2.0.3 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.0.3), archived on Zenodo:  
+Version [2.0.6 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.0.6), archived on Zenodo:  
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
 

{CoreMS-2.0.3 → CoreMS-2.0.6}/corems/__init__.py

@@ -1,5 +1,5 @@
 __author__ = 'Yuri E. Corilo'
-__version__ = '2.0.3'
+__version__ = '2.0.6'
 __doc__ = '''
 <div align="left">
 

{CoreMS-2.0.3 → CoreMS-2.0.6}/corems/encapsulation/constant.py

@@ -36,7 +36,8 @@ class Labels: #pragma: no cover
     ion_type_translate = { 'protonated': 'DE_OR_PROTONATED',
                           'de-protonated': 'DE_OR_PROTONATED',
                           'radical': 'RADICAL',
-                          'adduct': 'ADDUCT'}
+                          'adduct': 'ADDUCT',
+                          'ADDUCT': 'ADDUCT'}
     
 class Atoms: #pragma: no cover
     """ Class for Atoms in CoreMS

{CoreMS-2.0.3 → CoreMS-2.0.6}/corems/encapsulation/factory/parameters.py

@@ -100,11 +100,17 @@ def default_parameters(file_location):  # pragma: no cover
 
     parameters["exc_low_freq"] = 0
 
+    parameters["mw_low"] = 0
+        
+    parameters["mw_high"] = 0
+
+    parameters["qpd_enabled"] = 0
+
     parameters["bandwidth"] = 0
 
     parameters['analyzer'] = 'Unknown'
 
-    parameters['aquisition_time'] = None
+    parameters['acquisition_time'] = None
 
     parameters['instrument_label'] = 'Unknown' 
 

{CoreMS-2.0.3 → CoreMS-2.0.6}/corems/encapsulation/factory/processingSetting.py

@@ -252,7 +252,7 @@ class MassSpectrumSetting:
     # How many data points (in each direction) to extrapolate the mz axis and 0 pad the abundance axis
     # This will fix peak picking at spectrum limit issues
     #  0 to keep normal behaviour, typical value 3 to fix
-    picking_point_extrapolate: int = 3 
+    picking_point_extrapolate: int = 0 
 
     calib_minimize_method: str = 'Powell'
     calib_pol_order: int = 2

{CoreMS-2.0.3 → CoreMS-2.0.6}/corems/mass_spectra/input/rawFileReader.py

@@ -759,7 +759,7 @@ class ThermoBaseClass:
 
         d_params["analyzer"] = self.iRawDataPlus.GetInstrumentData().Model
 
-        d_params["aquisition_time"] = self.iRawDataPlus.GetInstrumentData().Model
+        d_params["acquisition_time"] = self.get_creation_time()
 
         d_params["instrument_label"] = self.iRawDataPlus.GetInstrumentData().Name
 

{CoreMS-2.0.3 → CoreMS-2.0.6}/corems/mass_spectrum/calc/PeakPicking.py

@@ -147,10 +147,11 @@ class PeakPicking:
         self.abundance_profile = abundance
         self.freq_exp_profile = freq
         
-        mz, abundance, freq = self.extrapolate_axes_for_pp()
-        self.mz_exp_profile = mz
-        self.abundance_profile = abundance
-        self.freq_exp_profile = freq
+        if self.settings.picking_point_extrapolate > 0:
+            mz, abundance, freq = self.extrapolate_axes_for_pp()
+            self.mz_exp_profile = mz
+            self.abundance_profile = abundance
+            self.freq_exp_profile = freq
         
         if self.label == Labels.bruker_frequency or self.label == Labels.midas_frequency:
 

{CoreMS-2.0.3 → CoreMS-2.0.6}/corems/mass_spectrum/factory/MassSpectrumClasses.py

@@ -3,7 +3,7 @@ from copy import deepcopy
 
 
 #from matplotlib import rcParamsDefault, rcParams
-from numpy import array, power, float64, where, histogram
+from numpy import array, power, float64, where, histogram, trapz
 
 from pandas import DataFrame
 from lmfit.models import GaussianModel
@@ -217,7 +217,7 @@ class MassSpecBase(MassSpecCalc, KendrickGrouping):
         - _calibration_terms
         - label
         - analyzer
-        - aquisition_time
+        - acquisition_time
         - instrument_label
         - polarity
         - scan_number
@@ -240,7 +240,7 @@ class MassSpecBase(MassSpecCalc, KendrickGrouping):
 
         self.analyzer = d_params.get('analyzer')
 
-        self.aquisition_time = d_params.get('aquisition_time')
+        self.acquisition_time = d_params.get('acquisition_time')
 
         self.instrument_label = d_params.get('instrument_label')
 
@@ -612,7 +612,7 @@ class MassSpecBase(MassSpecCalc, KendrickGrouping):
     @property
     def tic(self):
         """Return the total ion current of the mass spectrum."""
-        return sum(self.abundance_profile)
+        return trapz(self.abundance_profile, self.mz_exp_profile)
 
     def check_mspeaks_warning(self):
         """Check if the mass spectrum has MSpeaks objects.
@@ -1263,6 +1263,7 @@ class MassSpecfromFreq(MassSpecBase):
         if self._mz_exp[0] > self._mz_exp[-1]:
             self._mz_exp = self._mz_exp[::-1]
             self._abundance = self._abundance[::-1]
+            self._frequency_domain = self._frequency_domain[::-1]
 
     def _set_mz_domain(self):
         """Set the m/z domain of the mass spectrum based on the settings of d_params."""
@@ -1375,6 +1376,8 @@ class MassSpecCentroid(MassSpecBase):
 
         self.is_centroid = True
         self.data_dict = data_dict
+        self._mz_exp = data_dict[Labels.mz]
+        self._abundance = data_dict[Labels.abundance]
 
         if auto_process:
             self.process_mass_spec()

{CoreMS-2.0.3 → CoreMS-2.0.6}/corems/mass_spectrum/input/massList.py

@@ -83,6 +83,10 @@ class ReadCoremsMasslist(MassListBaseClass):
             ion_type_df = dataframe["Ion Type"]
             ion_charge_df = dataframe["Ion Charge"]
             is_isotopologue_df = dataframe['Is Isotopologue']
+            if 'Adduct' in dataframe:
+                adduct_df = dataframe['Adduct']
+            else:
+                adduct_df = None
 
         mass_spec_mz_exp_list = mass_spec_obj.mz_exp
 
@@ -102,7 +106,11 @@ class ReadCoremsMasslist(MassListBaseClass):
             if sum(counts) > 0:
 
                 ion_type = str(Labels.ion_type_translate.get(ion_type_df[df_index]))
-                mfobj = MolecularFormula(formula_list, int(ion_charge_df[df_index]), mspeak_parent=mass_spec_obj[ms_peak_index] , ion_type=ion_type)
+                if adduct_df is not None:
+                    adduct_atom = str(adduct_df[df_index])
+                else:
+                    adduct_atom = None
+                mfobj = MolecularFormula(formula_list, int(ion_charge_df[df_index]), mspeak_parent=mass_spec_obj[ms_peak_index] , ion_type=ion_type, adduct_atom=adduct_atom)
                 mfobj.is_isotopologue = bool(is_isotopologue_df[df_index])
                 mass_spec_obj[ms_peak_index].add_molecular_formula(mfobj)
 

CoreMS-2.0.6/corems/mass_spectrum/input/numpyArray.py

@@ -0,0 +1,108 @@
+
+__author__ = "Yuri E. Corilo"
+__date__ = "Oct 23, 2019"
+
+from corems.mass_spectrum.factory.MassSpectrumClasses import MassSpecProfile, MassSpecCentroid
+from corems.encapsulation.factory.parameters import default_parameters
+from corems.encapsulation.constant import Labels
+
+def ms_from_array_profile(mz, abundance, dataname:str, polarity:int = -1, auto_process:bool = True, data_type:str = Labels.simulated_profile):
+    """Create a MassSpecProfile object from an array of m/z values and abundance values.
+
+    Parameters
+    ----------
+    mz : numpy.ndarray
+        Array of m/z values.
+    abundance : numpy.ndarray
+        Array of abundance values.
+    dataname : str
+        Name of the data.
+    polarity : int, optional
+        Polarity of the data. The default is -1.
+    auto_process : bool, optional
+        Flag to automatically process the data. The default is True.
+    data_type : str, optional
+        Type of the data. The default is Labels.simulated_profile.
+
+    Returns
+    -------
+    MassSpecProfile
+        The created MassSpecProfile object.
+    """
+    data_dict = {Labels.mz: mz, Labels.abundance: abundance}
+    
+    output_parameters = get_output_parameters(polarity, dataname)
+    
+    output_parameters[Labels.label] = data_type
+
+    ms = MassSpecProfile(data_dict, output_parameters, auto_process=auto_process)
+    
+    return ms
+
+def ms_from_array_centroid(mz, abundance, rp:list[float], s2n:list[float], dataname:str, polarity:int=-1, auto_process:bool=True):
+    """Create a MassSpecCentroid object from an array of m/z values, abundance values, resolution power, and signal-to-noise ratio.
+
+    Parameters
+    ----------
+    mz : numpy.ndarray
+        Array of m/z values.
+    abundance : numpy.ndarray
+        Array of abundance values.
+    rp : list(float)
+        List of resolving power values.
+    s2n : list(float)
+        List of signal-to-noise ratio values.
+    dataname : str
+        Name of the data.
+    polarity : int, optional
+        Polarity of the data. The default is -1.
+    auto_process : bool, optional
+
+    Returns
+    -------
+    MassSpecCentroid
+        The created MassSpecCentroid object.
+    """
+    data_dict = {Labels.mz: mz, Labels.abundance: abundance, Labels.s2n : s2n, Labels.rp: rp}
+    
+    output_parameters = get_output_parameters(polarity, dataname)
+    output_parameters[Labels.label] = Labels.corems_centroid
+    
+    return MassSpecCentroid(data_dict, output_parameters, auto_process)
+    
+def get_output_parameters(polarity:int, file_location:str):
+    """Generate the output parameters for creating a MassSpecProfile or MassSpecCentroid object.
+
+    Parameters
+    ----------
+    polarity : int
+        Polarity of the data.
+    file_location : str
+        File location.
+
+    Returns
+    -------
+    dict
+        Output parameters.
+    """
+    d_params = default_parameters(file_location)
+    
+    d_params['analyzer'] = 'Generic Simulated'
+
+    d_params['instrument_label'] = 'Generic Simulated'
+
+    d_params["polarity"] = polarity
+    
+    d_params["filename_path"] = file_location
+    
+    d_params["mobility_scan"] = 0
+    
+    d_params["mobility_rt"] = 0
+    
+    d_params["scan_number"] = 0
+    
+    d_params["rt"] = 0
+
+    d_params[Labels.label] = Labels.simulated_profile
+    
+    return d_params

{CoreMS-2.0.3 → CoreMS-2.0.6}/corems/mass_spectrum/output/export.py

@@ -111,6 +111,7 @@ class HighResMassSpecExport(Thread):
                               'O/C',
                               'Heteroatom Class',
                               'Ion Type',
+                              'Adduct',
                               'Is Isotopologue',
                               'Mono Isotopic Index',
                               'Molecular Formula'
@@ -160,7 +161,6 @@ class HighResMassSpecExport(Thread):
 
     def get_pandas_df(self):
         """Returns the mass spectrum data as a pandas DataFrame."""
-
         columns = self.columns_label + self.get_all_used_atoms_in_order(self.mass_spectrum)
         dict_data_list = self.get_list_dict_data(self.mass_spectrum)
         df = DataFrame(dict_data_list, columns=columns)
@@ -563,6 +563,9 @@ class HighResMassSpecExport(Thread):
                            'Is Isotopologue': int(mformula.is_isotopologue),
                            'Molecular Formula': eval("mformula.string{}".format(encode))
                            }
+            
+            if mformula.adduct_atom:
+                dict_result['Adduct'] = eval("mformula.adduct_atom{}".format(encode))
 
             if mformula.is_isotopologue:
                 dict_result['Mono Isotopic Index'] = mformula.mspeak_index_mono_isotopic

{CoreMS-2.0.3 → CoreMS-2.0.6}/corems/molecular_formula/factory/MolecularFormulaFactory.py

@@ -98,9 +98,7 @@ class MolecularFormulaBase(MolecularFormulaCalc):
 
     def __init__(self, molecular_formula, ion_charge, ion_type=None, 
                 adduct_atom=None, mspeak_parent=None, external_mz=None):
-        
         # clear dictionary of atoms with 0 value
-        
         if  type(molecular_formula) is dict:
                 self._from_dict(molecular_formula, ion_type, adduct_atom)   
         
@@ -110,7 +108,6 @@ class MolecularFormulaBase(MolecularFormulaCalc):
         elif type(molecular_formula) is str:
                 self._from_str(molecular_formula, ion_type, adduct_atom)   
 
-        
         self._ion_charge = ion_charge
         self._external_mz = external_mz
         self._confidence_score = None        
@@ -176,13 +173,14 @@ class MolecularFormulaBase(MolecularFormulaCalc):
         
         self._d_molecular_formula = {key:val for key, val in molecular_formula.items() if val != 0}
         
-        if ion_type:
+        if ion_type is not None:
             self._d_molecular_formula[Labels.ion_type] = ion_type
             
         if adduct_atom:
             if adduct_atom in self._d_molecular_formula:
                 self._d_molecular_formula[adduct_atom] += 1 
             else: self._d_molecular_formula[adduct_atom] = 1 
+        self.adduct_atom = adduct_atom
 
     def _from_list(self, molecular_formula_list, ion_type, adduct_atom):
         # list has to be in the format 
@@ -198,9 +196,12 @@ class MolecularFormulaBase(MolecularFormulaCalc):
         
         self._d_molecular_formula[Labels.ion_type] = ion_type
         if adduct_atom:
+            self.adduct_atom = adduct_atom
             if adduct_atom in self._d_molecular_formula:
                 self._d_molecular_formula[adduct_atom] += 1 
             else: self._d_molecular_formula[adduct_atom] = 1 
+        else:
+            self.adduct_atom = None
 
     def _from_str(self, molecular_formula_str,  ion_type, adduct_atom):
         # string has to be in the format 
@@ -317,7 +318,16 @@ class MolecularFormulaBase(MolecularFormulaCalc):
     def ion_charge(self): return self._ion_charge
     
     @property
-    def atoms(self): return [key for key in self._d_molecular_formula.keys() if key != Labels.ion_type]
+    def atoms(self): 
+        """Get the atoms in the molecular formula."""
+        # if there is an adduct_atom, them reduce it from the atoms list
+        if self.adduct_atom is None:
+            return [key for key in self._d_molecular_formula.keys() if key != Labels.ion_type]
+        else:
+            temp_dict = self._d_molecular_formula.copy()
+            temp_dict[self.adduct_atom] -= 1
+            return [key for key,val in temp_dict.items() if key != Labels.ion_type and val > 0]
+
     
     @property
     def confidence_score(self): 
@@ -399,7 +409,13 @@ class MolecularFormulaBase(MolecularFormulaCalc):
         
         for mf in self._cal_isotopologues(self._d_molecular_formula, min_abundance, current_mono_abundance, dynamic_range ):
              
-            yield MolecularFormulaIsotopologue(*mf, current_mono_abundance, self.ion_charge)
+            yield MolecularFormulaIsotopologue(
+                *mf, 
+                current_mono_abundance, 
+                self.ion_charge, 
+                ion_type=self.ion_type, 
+                adduct_atom=self.adduct_atom
+                )
     
     def atoms_qnt(self,atom): 
         """Get the atom quantity of a specific atom in the molecular formula."""
@@ -414,12 +430,20 @@ class MolecularFormulaBase(MolecularFormulaCalc):
 
     @property       
     def string(self):
-        
+        """Returns the molecular formula as a string."""
         if self._d_molecular_formula:
+            if self.adduct_atom is None:
+                mol_form_dict = self._d_molecular_formula
+            else:
+                mol_form_dict = self._d_molecular_formula.copy()
+                if self.adduct_atom not in mol_form_dict.keys():
+                    raise Exception("Adduct atom not found in molecular formula dict")
+                mol_form_dict[self.adduct_atom] -= 1
+                mol_form_dict = {key:val for key, val in mol_form_dict.items() if val != 0}
             formula_srt = ''
             for atom in Atoms.atoms_order:
-                if atom in self.to_dict().keys():
-                    formula_srt += atom + str(int(self.to_dict().get(atom))) + ' '
+                if atom in mol_form_dict.keys():
+                    formula_srt += atom + str(int(mol_form_dict.get(atom))) + ' '
             return formula_srt.strip()
         
         else:
@@ -547,6 +571,10 @@ class MolecularFormulaIsotopologue(MolecularFormulaBase):
         The ion charge.
     mspeak_parent : object, optional
         The parent mass spectrum peak object instance. Defaults to None.
+    ion_type : str, optional
+        The ion type. Defaults to None.
+    adduct_atom : str, optional
+        The adduct atom. Defaults to None.
     
     Attributes
     ----------
@@ -565,9 +593,48 @@ class MolecularFormulaIsotopologue(MolecularFormulaBase):
     mono_isotopic_formula_index : int
         The index of the monoisotopic formula in the molecular formula list. Defaults to None.
     """
-    def __init__(self, _d_molecular_formula, prob_ratio, mono_abundance, ion_charge, mspeak_parent=None):
+    def __init__(
+            self, 
+            _d_molecular_formula, 
+            prob_ratio, 
+            mono_abundance, 
+            ion_charge, 
+            mspeak_parent=None,
+            ion_type = None,
+            adduct_atom = None
+            ):
+        
+        if ion_type is None:
+            # check if ion type or adduct_atom is in the molecular formula dict
+            if Labels.ion_type in _d_molecular_formula:
+                ion_type = _d_molecular_formula.get(Labels.ion_type)
+            else:
+                ion_type = None
+        else:
+            ion_type = Labels.ion_type_translate.get(ion_type)
         
-        super().__init__(_d_molecular_formula,  ion_charge)
+        if ion_type == Labels.adduct_ion:
+            adduct_atom_int = None
+            if adduct_atom in _d_molecular_formula.keys():
+                adduct_atom_int = adduct_atom
+            else:
+                # Check to see if adduct_atom should actually be an isotope of the adduct atom
+                for adduct_iso in Atoms.isotopes.get(adduct_atom)[1]:
+                    if adduct_iso in _d_molecular_formula.keys():
+                        adduct_atom_int = adduct_iso
+            adduct_atom = adduct_atom_int
+            if adduct_atom is None:
+                raise Exception("adduct_atom is required for adduct ion")
+            _d_molecular_formula[adduct_atom] -= 1
+            _d_molecular_formula = {key:val for key, val in _d_molecular_formula.items() if val != 0}
+
+        
+        super().__init__(
+            molecular_formula =_d_molecular_formula, 
+            ion_charge = ion_charge, 
+            ion_type=ion_type,
+            adduct_atom=adduct_atom
+            )
         #prob_ratio is relative to the monoisotopic peak p_isotopologue/p_mono_isotopic
         
         self.prob_ratio = prob_ratio

{CoreMS-2.0.3 → CoreMS-2.0.6}/corems/molecular_id/search/compoundSearch.py

@@ -49,9 +49,7 @@ class LowResMassSpectralMatch(Thread):
         self.calibration = calibration
         # reading local file for now,
         if not sql_obj:
-            
             self.sql_obj = EI_LowRes_SQLite(url=self.gcms_obj.molecular_search_settings.url_database)
-        
         else:
             self.sql_obj = sql_obj
 

{CoreMS-2.0.3 → CoreMS-2.0.6}/corems/ms_peak/calc/MSPeakCalc.py

@@ -717,9 +717,11 @@ class MSPeakCalculation:
         """
         
         candidates = list(filter(lambda mf: mf.get("O") > 0 and mf.get("N") <=3 and mf.get("P") <= 2 and (3 * mf.get("P")) <= mf.get("O"), self.molecular_formulas))
-
-        if lowest_error:
-            return min(candidates, key=lambda m: abs(m.mz_error))
+        if len(candidates) >0:
+            if lowest_error:
+                return min(candidates, key=lambda m: abs(m.mz_error))
+            else:
+                return candidates
         else:
             return candidates
 
@@ -752,9 +754,11 @@ class MSPeakCalculation:
         """
        
         candidates = list(filter(lambda mf: mf.get("O") > 0 and mf.get("N") <=3 and mf.get("S") <=2 and  mf.get("P") <= 2, self.molecular_formulas))
-
-        if lowest_error:
-            return min(candidates, key=lambda m: abs(m.mz_error))
+        if len(candidates) >0:
+            if lowest_error:
+                return min(candidates, key=lambda m: abs(m.mz_error))
+            else:
+                return candidates
         else:
             return candidates
     
@@ -789,8 +793,11 @@ class MSPeakCalculation:
        
         candidates = list(filter(lambda mf: mf.get("O") > 0 and mf.get("N") <=2 and mf.get("S") <=1 and  mf.get("P") == 0 and 3* (mf.get("S") + mf.get("N")) <= mf.get("O"), self.molecular_formulas))
         
-        if lowest_error:
-            return min(candidates, key=lambda m: abs(m.mz_error))
+        if len(candidates) >0:
+            if lowest_error:
+                return min(candidates, key=lambda m: abs(m.mz_error))
+            else:
+                return candidates
         else:
             return candidates
 

{CoreMS-2.0.3 → CoreMS-2.0.6}/corems/transient/calc/TransientCalc.py

@@ -238,18 +238,35 @@ class TransientCalculations(object):
         
         
         """
+        # If the mw_low and mw_high are set, the frequency domain is cut to the mw range
+        # this accounts for the detection settings, not the excitation settings.
+        # TODO: Implement this - right now the f to mz function is in the ms class, not the transient class, so it doesnt work.
+        #if (self._mw_low != 0) & (self._mw_high != 0):
+        #    high_freq = self._f_to_mz(self._mw_high)
+        #    low_freq = self._f_to_mz(self._mw_low)
+        #
+        #    final =  where(freqdomain_X < high_freq)[-1][-1]
+        #      start =  where(freqdomain_X > low_freq)[0][0]
+        #else:
+        if self._qpd_enabled == 1:
+            low_freq = self._exc_low_freq *2
+            high_freq = self._exc_high_freq *2
+        else:
+            low_freq = self._exc_low_freq
+            high_freq = self._exc_high_freq 
 
-      
         if self._exc_low_freq > self._exc_high_freq:
-            
-            final =  where(freqdomain_X > self._exc_high_freq)[-1][-1]
-            start =  where(freqdomain_X > self._exc_high_freq())[0][0]
-        
+            # TODO: This needs to be tested
+            # I'm not sure that this is relevant anyway - the excitation pulse is ramped in frequency but the detection is simulatenous
+            print("This is not tested. Please check the results.")
+            final =  where(freqdomain_X > low_freq)[0][0]
+            start =  where(freqdomain_X > high_freq)[0][0]
+
         else:
             
-            final =  where(freqdomain_X > self._exc_low_freq)[-1][-1]
-            start =  where(freqdomain_X > self._exc_low_freq)[0][0]
-            
+            final =  where(freqdomain_X < high_freq)[-1][-1]
+            start =  where(freqdomain_X > low_freq)[0][0]
+        
         
         return freqdomain_X[start:final], freqdomain_Y[start:final]
         #del freqdomain_X, freqdomain_Y

{CoreMS-2.0.3 → CoreMS-2.0.6}/corems/transient/factory/TransientClasses.py

@@ -119,6 +119,12 @@ class Transient(TransientCalculations):
 
         self._exc_low_freq = d_params.get("exc_low_freq")
 
+        self._qpd_enabled = d_params.get("qpd_enabled") #Quadrupolar detection enabled
+
+        self._mw_low = d_params.get("mw_low") # low mass for detection
+
+        self._mw_high = d_params.get("mw_high") # high mass for detection
+
         self.bandwidth = d_params.get("bandwidth")
 
         self.number_data_points = d_params.get("number_data_points")