Add rule-based fragmentation

.coveragerc

@@ -1,2 +1,2 @@
 [run]
-omit = tests/*,setup.py,metaboblend/__main__.py
+omit = tests/*,setup.py,metaboblend/__main__.py,notebooks/

.github/workflows/build-test.yml

@@ -8,8 +8,8 @@ jobs:
 
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.6, 3.7, 3.8]
+        os: [ ubuntu-latest, windows-latest, macos-latest ]
+        python-version: [ 3.7, 3.8, 3.9 ]
 
     env:
       OS: ${{ matrix.os }}
@@ -19,21 +19,29 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: Setup conda - Python ${{ matrix.python-version }}
-        uses: s-weigand/setup-conda@v1
+        uses: conda-incubator/setup-miniconda@v2
         with:
-          update-conda: true
+          auto-update-conda: true
+          activate-environment: metaboblend
           python-version: ${{ matrix.python-version }}
-          conda-channels: anaconda, conda-forge
+          environment-file: environment.yml
+          channels: anaconda, conda-forge
 
-      - name: Install dependencies
+      - name: Build MetaboBlend
+        shell: bash -l {0}
         run: |
+          python setup.py install
+          metaboblend --help
 
-          python --version
-          conda env update --file environment.yml --name base
+      - name: Test with pytest-cov
+        shell: bash -l {0}
+        run: |
+          conda install pytest codecov pytest-cov -c conda-forge
+          pytest --cov ./ --cov-config=.coveragerc --cov-report=xml
 
       - name: Lint with flake8
+        shell: bash -l {0}
         run: |
-
           conda install flake8
 
           # stop build if there are Python syntax errors or undefined names
@@ -42,15 +50,6 @@ jobs:
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
 
-      - name: Test with pytest-cov
-        run: |
-
-          python setup.py install
-          metaboblend --help
-
-          conda install pytest codecov pytest-cov -c conda-forge
-          pytest --cov ./ --cov-config=.coveragerc --cov-report=xml
-
       - name: Upload code coverage to codecov
         uses: codecov/codecov-action@v1
         with:

.gitignore

@@ -70,6 +70,8 @@ target/
 
 # Jupyter Notebook
 .ipynb_checkpoints
+notebooks/notebook_data
+notebooks/notebook_data/*
 
 # pyenv
 .python-version
@@ -105,4 +107,4 @@ ENV/
 # ignore test files
 */libgcc_s_dw2-1.dll
 */libstdc++-6.dll
-tests/test*
+tests/tmp*

README.rst

@@ -1,6 +1,9 @@
 MetaboBlend
 ===========
-|Version| |Py versions| |Git| |Bioconda| |Build Status| |License| |RTD doc| |codecov| |binder|
+..
+    |Version| |Py versions| |Bioconda|  |RTD doc| |License|  |binder|
+
+|Git| |Build Status| |codecov|
 
 Python package for *de novo* structural elucidation of small molecules in mass spectrometry-based Metabolomics
 
@@ -32,12 +35,11 @@ will help you to make the PR if you are new to `git`.
 Developers & Contributors
 -------------------------
  - Ralf J. M. Weber ([email protected]) - `University of Birmingham (UK) <https://www.birmingham.ac.uk/staff/profiles/biosciences/weber-ralf.aspx>`_
- - Jack Gisby ([email protected]) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_
-
+ - Jack Gisby ([email protected]) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_, `Imperial College London (UK) <https://www.imperial.ac.uk/>`_
 
 Licenses
 --------
-MetaboBlend is licensed under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/metaboblend/blob/master/LICENSE>`_ for licensing information). Copyright © 2019 - 2020 Ralf Weber
+MetaboBlend is licensed under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/metaboblend/blob/master/LICENSE>`_ for licensing information). Copyright © 2019 - 2020 Jack Gisby, Ralf Weber
 
 
 .. |Build Status| image:: https://github.com/computational-metabolomics/metaboblend/workflows/metaboblend/badge.svg

binder/environment.yml

@@ -0,0 +1,17 @@
+name: metaboblend
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python=3.7
+  - numpy
+  - scipy
+  - pandas
+  - networkx
+  - rdkit
+  - biopython
+  - matplotlib
+  - nauty
+  - pip
+  - pip:
+    - -e ../

docs/source/conf.py

@@ -20,7 +20,7 @@
 # -- Project information -----------------------------------------------------
 
 project = 'MetaboBlend'
-copyright = '2020, Ralf Weber'
+copyright = '2020, Jack Gisby, Ralf Weber'
 author = 'Jack Gisby, Ralf Weber'
 
 # -- General configuration ---------------------------------------------------

docs/source/license.rst

@@ -1,4 +1,4 @@
 License
 -------
 TODO: change package name
-*MetaboBlend* is licensed under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/metaboblend/blob/master/LICENSE>`_ for licensing information). Copyright © 2019 - 2020 Ralf Weber
+*MetaboBlend* is licensed under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/metaboblend/blob/master/LICENSE>`_ for licensing information). Copyright © 2019 - 2020 Jack Gisby, Ralf Weber

environment.yml

@@ -1,14 +1,12 @@
 name: metaboblend
 channels:
   - conda-forge
-  - bioconda
 dependencies:
- - python>=3.6
+ - python>=3.7
+ - pillow!=9.2.0
+ - pyqt
+ - matplotlib
  - numpy
- - scipy
- - pandas
  - networkx
  - rdkit
- - biopython
- - matplotlib
  - nauty

metaboblend/__init__.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2019-2020 Ralf Weber
+# Copyright © 2019-2020 Jack Gisby, Ralf Weber
 #
 # This file is part of MetaboBlend.
 #
@@ -19,7 +19,7 @@
 # along with MetaboBlend.  If not, see <https://www.gnu.org/licenses/>.
 #
 
-__author__ = 'Ralf Weber ([email protected])'
-__credits__ = 'Ralf Weber ([email protected])'
+__authors__ = ['Ralf Weber ([email protected])', 'Jack Gisby ([email protected])']
+__credits__ = ['Ralf Weber ([email protected])', 'Jack Gisby ([email protected])']
 __version__ = '0.1.0'
 __license__ = 'GPLv3'

metaboblend/__main__.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2019-2020 Ralf Weber
+# Copyright © 2019-2020 Jack Gisby, Ralf Weber
 #
 # This file is part of MetaboBlend.
 #

metaboblend/algorithms.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2019-2020 Ralf Weber
+# Copyright © 2019-2020 Jack Gisby, Ralf Weber
 #
 # This file is part of MetaboBlend.
 #
@@ -20,9 +20,10 @@
 #
 
 import numpy
+from math import sqrt
 
 
-def find_path(mass_list, sum_matrix, n, mass, max_subset_length, path=[]):
+def find_path(mass_list, sum_matrix, n, mass, max_subset_length, path=None):
     """
     Recursive solution for backtracking through the dynamic programming boolean matrix. All possible subsets are found
 
@@ -42,6 +43,9 @@ def find_path(mass_list, sum_matrix, n, mass, max_subset_length, path=[]):
     :return: Generates of lists containing the masses of valid subsets.
     """
 
+    if path is None:
+        path = []
+
     # base case - the path has generated a correct solution
     if mass == 0:
         yield sorted(path)
@@ -103,3 +107,29 @@ def subset_sum(mass_list, mass, max_subset_length=3):
 
     # backtrack through the matrix recursively to obtain all solutions
     return find_path(mass_list, sum_matrix, n, mass, max_subset_length)
+
+
+def cosine_spectrum_similarity(real_mzs, candidate_mzs):
+    """
+    Database fragmentation scoring based on the cosine similarity method. Adapted for the lack of intensities
+    available for the candidate compound.
+
+    :param real_mzs: The mz values for the original MSn spectrum.
+
+    :param candidate_mzs: The theoretical mz values for a candidate compound. Should have the same order as `real_mzs`
+        and should have a value of `0` when there is no match for the candidate for a peak in the original spectrum.
+
+    :return: Similarity metric for the two spectra.
+    """
+
+    # get weighted peaks
+    real_weighted = [(mz ** 2) for mz in real_mzs]
+    candidate_weighted = [(mz ** 2) for mz in candidate_mzs]
+
+    def dot(E, D):
+        return sum(e * d for e, d in zip(E, D))
+
+    def cosine_similarity(E, D):
+        return dot(E, D) / (sqrt(dot(E, E)) * sqrt(dot(D, D)))
+
+    return cosine_similarity(real_weighted, candidate_weighted)