CoreMS 4.0.0__py3-none-any.whl

corems/molecular_id/calc/MolecularFilter.py

@@ -0,0 +1,122 @@
+from corems.molecular_id.calc.ClusterFilter import ClusteringFilter
+
+
+class MolecularFormulaSearchFilters:
+    """Class containing static methods for filtering molecular formulas in a mass spectrum.
+
+    Methods
+    -------
+    * filter_kendrick(ms_peak_indexes, mass_spectrum_obj).
+        Apply Kendrick filter to the mass spectrum.
+    * check_min_peaks(ms_peak_indexes, mass_spectrum_obj).
+        Check if the number of peaks per class meets the minimum requirement.
+    * filter_isotopologue(ms_peak_indexes, mass_spectrum_obj).
+        Apply isotopologue filter to the mass spectrum.
+
+    """
+
+    @staticmethod
+    def filter_kendrick(ms_peak_indexes, mass_spectrum_obj):
+        """Apply Kendrick filter to the mass spectrum.
+
+        Parameters
+        ----------
+        ms_peak_indexes : list
+            List of peak indexes and their associated molecular formula objects.
+        mass_spectrum_obj : MassSpectrum
+            The mass spectrum object.
+
+        Returns
+        -------
+        filtered_ms_peak_indexes : list
+            List of peak indexes and their associated molecular formula objects after applying the Kendrick filter.
+        """
+        index_to_remove = []
+
+        if mass_spectrum_obj.molecular_search_settings.use_runtime_kendrick_filter:
+            index_to_remove = ClusteringFilter().filter_kendrick_by_index(
+                ms_peak_indexes, mass_spectrum_obj
+            )
+
+            # for index in noise_indexes: self.mass_spectrum_obj[index].clear_molecular_formulas()
+
+        all_index_to_remove = []
+
+        for peak_index, mf_obj in index_to_remove:
+            ms_peak_indexes.remove((peak_index, mf_obj))
+
+            all_index_to_remove.extend(mf_obj.mspeak_mf_isotopologues_indexes)
+
+        all_index_to_remove = list(set(all_index_to_remove + index_to_remove))
+
+        for peak_index, mf_obj in all_index_to_remove:
+            mass_spectrum_obj[peak_index].remove_molecular_formula(mf_obj)
+
+        return ms_peak_indexes
+
+    @staticmethod
+    def check_min_peaks(ms_peak_indexes, mass_spectrum):
+        """Check if the number of peaks per class meets the minimum requirement.
+
+        Parameters
+        --------
+        ms_peak_indexes : list
+            List of peak indexes and their associated molecular formula objects.
+        mass_spectrum_obj : MassSpectrum
+            The mass spectrum object.
+
+        """
+        if mass_spectrum.molecular_search_settings.use_min_peaks_filter:
+            if (
+                not len(ms_peak_indexes)
+                >= mass_spectrum.molecular_search_settings.min_peaks_per_class
+            ):
+                for peak_index, mf_obj in ms_peak_indexes:
+                    mass_spectrum[peak_index].remove_molecular_formula(mf_obj)
+
+    @staticmethod
+    def filter_isotopologue(ms_peak_indexes, mass_spectrum):
+        """Apply isotopologue filter to the mass spectrum.
+
+        Parameters
+        --------
+        ms_peak_indexes : list
+            List of peak indexes and their associated molecular formula objects.
+        mass_spectrum_obj : MassSpectrum
+            The mass spectrum object.
+
+        Returns
+        ------------
+        filtered_ms_peak_indexes : list
+            List of peak indexes and their associated molecular formula objects after applying the isotopologue filter.
+        """
+        index_to_remove = []
+        # print(len(ms_peak_indexes))
+        if mass_spectrum.molecular_search_settings.use_isotopologue_filter:
+            atoms_iso_filter = (
+                mass_spectrum.molecular_search_settings.isotopologue_filter_atoms
+            )
+
+            isotopologue_count_threshold = (
+                mass_spectrum.molecular_search_settings.isotopologue_filter_threshold
+            )
+
+            for mspeak_index, mf_obj in ms_peak_indexes:
+                if mf_obj.isotopologue_count_percentile < isotopologue_count_threshold:
+                    if set(mf_obj.atoms).intersection(atoms_iso_filter):
+                        # removes tuple obj from initial list to be used on next filter steps
+                        ms_peak_indexes.remove((mspeak_index, mf_obj))
+
+                        # current mf_obj
+                        index_to_remove.append((mspeak_index, mf_obj))
+                        # all other associated isotopolgues
+                        index_to_remove.extend(mf_obj.mspeak_mf_isotopologues_indexes)
+
+        # iterate over all indexes to be remove and remove the mf from the mspeak
+
+        # print(len(ms_peak_indexes))
+        for peak_index, mf_obj in index_to_remove:
+            # print(peak_index, mf_obj)
+            mass_spectrum[peak_index].remove_molecular_formula(mf_obj)
+
+        return ms_peak_indexes