IsoSpecPy 2.3.0.dev11__cp313-cp313-win_arm64.whl

IsoSpecPy/isoFFI.py

@@ -0,0 +1,223 @@
+import cffi
+import platform
+import sys
+import glob
+from pathlib import Path
+if False:
+    import IsoSpecCppPy
+
+class IsoFFI:
+    def __init__(self):
+        self.ffi = cffi.FFI()
+        self.ffi.cdef('''
+        void * setupIso(int dimNumber,
+                const int* isotopeNumbers,
+                const int* atomCounts,
+                const double* isotopeMasses,
+                const double* isotopeProbabilities);
+
+        void * isoFromFasta(const char* fasta, bool use_nominal_masses, bool add_water);
+
+        double getLightestPeakMassIso(void* iso);
+        double getHeaviestPeakMassIso(void* iso);
+        double getMonoisotopicPeakMassIso(void* iso);
+        double getModeLProbIso(void* iso);
+        double getModeMassIso(void* iso);
+        double getTheoreticalAverageMassIso(void* iso);
+        double getIsoVariance(void* iso);
+        double getIsoStddev(void* iso);
+        double* getMarginalLogSizeEstimates(void* iso, double target_total_prob);
+
+        void deleteIso(void* iso);
+
+        void* setupIsoThresholdGenerator(void* iso,
+                                         double threshold,
+                                         bool _absolute,
+                                         int _tabSize,
+                                         int _hashSize,
+                                         bool reorder_marginals);
+        double massIsoThresholdGenerator(void* generator);
+        double lprobIsoThresholdGenerator(void* generator);
+        double probIsoThresholdGenerator(void* generator);
+        bool advanceToNextConfigurationIsoThresholdGenerator(void* generator);
+        void deleteIsoThresholdGenerator(void* generator);
+        void get_conf_signatureIsoThresholdGenerator(void* generator, int* space);
+
+
+
+        void* setupIsoLayeredGenerator(void* iso,
+                                       int _tabSize,
+                                       int _hashSize,
+                                       bool reorder_marginals,
+                                       double t_prob_hint);
+        double massIsoLayeredGenerator(void* generator);
+        double lprobIsoLayeredGenerator(void* generator);
+        double probIsoLayeredGenerator(void* generator);
+        bool advanceToNextConfigurationIsoLayeredGenerator(void* generator);
+        void deleteIsoLayeredGenerator(void* generator);
+        void get_conf_signatureIsoLayeredGenerator(void* generator, int* space);
+
+
+        void* setupIsoOrderedGenerator(void* iso,
+                                       int _tabSize,
+                                       int _hashSize);
+        double massIsoOrderedGenerator(void* generator);
+        double lprobIsoOrderedGenerator(void* generator);
+        double probIsoOrderedGenerator(void* generator);
+        bool advanceToNextConfigurationIsoOrderedGenerator(void* generator);
+        void deleteIsoOrderedGenerator(void* generator);
+        void get_conf_signatureIsoOrderedGenerator(void* generator, int* space);
+
+        void* setupIsoStochasticGenerator(void* iso,
+                                   size_t no_molecules,
+                                   double precision,
+                                   double beta_bias);
+        double massIsoStochasticGenerator(void* generator);
+        double lprobIsoStochasticGenerator(void* generator);
+        double probIsoStochasticGenerator(void* generator);
+        bool advanceToNextConfigurationIsoStochasticGenerator(void* generator);
+        void deleteIsoStochasticGenerator(void* generator);
+        void get_conf_signatureIsoStochasticGenerator(void* generator, int* space);
+
+        void* setupThresholdFixedEnvelope(void* iso,
+                                    double threshold,
+                                    bool absolute,
+                                    bool get_confs);
+
+        void* setupTotalProbFixedEnvelope(void* iso,
+                                      double taget_coverage,
+                                      bool optimize,
+                                      bool get_confs);
+
+        void* setupStochasticFixedEnvelope(void* iso,
+                                     size_t no_molecules,
+                                     double precision,
+                                     double beta_bias,
+                                     bool get_confs);
+
+        void* setupBinnedFixedEnvelope(void* iso,
+                            double target_total_prob,
+                            double bin_width,
+                            double bin_middle);
+
+        void* setupFixedEnvelope(double* masses, double* probs, size_t size, bool mass_sorted, bool prob_sorted, double total_prob);
+        void* copyFixedEnvelope(void* other);
+        void deleteFixedEnvelope(void* tabulator, bool releaseEverything);
+
+        const double* massesFixedEnvelope(void* tabulator);
+        const double* probsFixedEnvelope(void* tabulator);
+        const int*    confsFixedEnvelope(void* tabulator);
+        size_t confs_noFixedEnvelope(void* tabulator);
+
+        double empiricAverageMass(void* tabulator);
+        double empiricVariance(void* tabulator);
+        double empiricStddev(void* tabulator);
+
+        double wassersteinDistance(void* tabulator1, void* tabulator2);
+        double orientedWassersteinDistance(void* tabulator1, void* tabulator2);
+        double abyssalWassersteinDistance(void* tabulator1, void* tabulator2, double abyss_depth, double other_scale);
+//        double abyssalWassersteinDistanceGrad(void* const* envelopes, const double* scales, double* ret_gradient, size_t N, double abyss_depth_exp, double abyss_depth_the);
+
+        struct ws_match_res{
+        double res1;
+        double res2;
+        double flow;
+        };
+
+        struct ws_match_res wassersteinMatch(void* tabulator1, void* tabulator2, double flow_dist, double other_scale);
+
+        void* addEnvelopes(void* tabulator1, void* tabulator2);
+        void* convolveEnvelopes(void* tabulator1, void* tabulator2);
+
+        double getTotalProbOfEnvelope(void* envelope);
+        void scaleEnvelope(void* envelope, double factor);
+        void normalizeEnvelope(void* envelope);
+        void shiftMassEnvelope(void* envelope, double d_mass);
+        void resampleEnvelope(void* envelope, size_t ionic_current, double beta_bias);
+        void* binnedEnvelope(void* envelope, double width, double middle);
+        void* linearCombination(void* const * const envelopes, const double* intensities, size_t count);
+
+        void sortEnvelopeByMass(void* envelope);
+        void sortEnvelopeByProb(void* envelope);
+
+        void freeReleasedArray(void* array);
+        void array_add(double* array, size_t N, double what);
+        void array_mul(double* array, size_t N, double what);
+        void array_fma(double* array, size_t N, double mul, double add);
+
+        void parse_fasta_c(const char* fasta, int atomCounts[6]);
+
+        #define NUMBER_OF_ISOTOPIC_ENTRIES 292
+        extern const size_t isospec_number_of_isotopic_entries;
+        extern const int elem_table_atomicNo[NUMBER_OF_ISOTOPIC_ENTRIES];
+        extern const double elem_table_probability[NUMBER_OF_ISOTOPIC_ENTRIES];
+        extern const double elem_table_mass[NUMBER_OF_ISOTOPIC_ENTRIES];
+        extern const double elem_table_massNo[NUMBER_OF_ISOTOPIC_ENTRIES];
+        extern const int elem_table_extraNeutrons[NUMBER_OF_ISOTOPIC_ENTRIES];
+        extern const char* elem_table_element[NUMBER_OF_ISOTOPIC_ENTRIES];
+        extern const char* elem_table_symbol[NUMBER_OF_ISOTOPIC_ENTRIES];
+        extern const bool elem_table_Radioactive[NUMBER_OF_ISOTOPIC_ENTRIES];
+                        ''');
+
+        mod_dir = Path(__file__).resolve().parent
+
+        if (mod_dir.parent / 'setup.py').exists():
+            raise ImportError('''Attempted to load IsoSpecPy module from its build directory. This usually
+won't work and is generally a Bad Idea. Please cd somewhere else, or, if you're really
+sure you want to do that, edit the source and disable this check.''')
+
+        libnames  = ['IsoSpecCppPy*', 'IsoSpec++*']
+        libprefix = ['', 'lib', 'Lib']
+        extension = ['.so', '.dylib', '.dll']
+        try:
+            if platform.system() == 'Linux':
+                extension = ['.so', 'pyd']
+            elif platform.system() == 'Windows':
+                extension = ['.dll', '.pyd']
+        except:
+            pass
+
+        prebuilt =  ['', 'prebuilt-']
+
+        def cprod(ll1, ll2):
+            res = []
+            for l1 in ll1:
+                for l2 in ll2:
+                    res.append(l1+l2)
+            return res
+
+        paths_to_check = cprod(prebuilt, cprod(libprefix, cprod(libnames, extension)))
+        dpc = []
+
+        for dirpath in [mod_dir, mod_dir.parent, mod_dir.parent / 'bin', mod_dir.parent / 'lib']:
+            dpc.extend([dirpath / p for p in paths_to_check])
+
+        paths_to_check = dpc
+        # expand glob patterns using pathlib (keep only actual matches, like glob.glob did)
+        expanded = []
+        for p in paths_to_check:
+            expanded.extend(p.parent.glob(p.name))
+        paths_to_check = expanded
+        try:
+            import importlib
+            paths_to_check.insert(0, Path(importlib.util.find_spec("IsoSpecCppPy").origin))
+        except (ImportError, AttributeError):
+            pass
+
+        errors = []
+
+        self.clib = None
+        for libpath in set(paths_to_check):
+            try:
+                self.clib = self.ffi.dlopen(str(libpath))
+                self.libpath = libpath
+                break
+            except (IndexError, OSError) as e:
+                errmsg = "Load libIsoSpec++.so, tried: " + libpath + '\n' + "Got error: " + str(type(e)) + ": " + str(e)
+                errors.append(errmsg)
+
+        if self.clib == None:
+            raise ImportError("Cannot find or load the C++ part of the library\n" + '\n'.join(errors))
+
+
+isoFFI = IsoFFI()  # This is done while including the module

isospecpy-2.3.0.dev11.dist-info/METADATA

@@ -0,0 +1,43 @@
+Metadata-Version: 2.4
+Name: IsoSpecPy
+Version: 2.3.0.dev11
+Summary: IsoSpecPy is a Python library for computing isotopic distributions of molecules.
+Keywords: isotopic distribution,mass spectrometry,chemistry,isotopic envelope,isotopologues
+Author: Michał Startek, Mateusz Łącki
+License-Expression: BSD-2-Clause
+License-File: LICENCE
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Operating System :: OS Independent
+Project-URL: Homepage, https://github.com/MatteoLacki/IsoSpec
+Project-URL: Repository, https://github.com/MatteoLacki/IsoSpec
+Requires-Python: >=3.6
+Requires-Dist: cffi
+Provides-Extra: testing
+Requires-Dist: pytest; extra == "testing"
+Requires-Dist: OldIsoSpecPy; extra == "testing"
+Description-Content-Type: text/markdown
+
+IsoSpec, the isotopic fine structure calculator
+===============================================
+
+The main purpose of this software package is to be used as a library, 
+mostly in mass spectrometry software. We do not provide any standalone
+programs, except for those in Examples directory which are intended to
+showcase the usage of the library.
+
+Please see the code in Examples directory for example usage.
+
+The software is publically available under a 2-clause BSD licence. If 
+you require other licensing terms, please contact the authors. See 
+LICENCE file for more details.
+
+More details about the program may be found in the following Analytical
+Chemistry publications:
+
+https://pubs.acs.org/doi/10.1021/acs.analchem.0c00959
+https://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b01459
+
+See especially the Supporting Information for details about the algorithm.

isospecpy-2.3.0.dev11.dist-info/RECORD

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+isospecpy-2.3.0.dev11.dist-info/licenses/LICENCE,sha256=gfZw5llAwrHH4rkp5FJuq9VAuamp1x7x8MDmDjj8dpw,1705
+isospecpy-2.3.0.dev11.dist-info/RECORD,,

isospecpy-2.3.0.dev11.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: scikit-build-core 0.11.6
+Root-Is-Purelib: false
+Tag: cp313-cp313-win_arm64
+

isospecpy-2.3.0.dev11.dist-info/licenses/LICENCE

@@ -0,0 +1,35 @@
+IsoSpec is provided under the terms of 2-clause BSD licence.
+If you require other licensing terms, please contact the authors. 
+
+We would appreciate if you let us know if you use this library in 
+your own software, but you are under no legal obligation to do so.
+
+
+-------------------------------------------------------------------------
+
+
+Copyright (c) 2015-2025, Michał Startek and Mateusz Łącki
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+