modifinder 1.4b0__tar.gz

modifinder-1.4b0/LICENSE.md

@@ -0,0 +1,10 @@
+::
+
+    Academic Software License: © 2024 UCR (“Institution”). Academic or nonprofit researchers are permitted to use this Software (as defined below) subject to Paragraphs 1-4:
+
+    1. Institution hereby grants to you free of charge, so long as you are an academic or nonprofit researcher, a nonexclusive license under Institution’s copyright ownership interest in this software and any derivative works made by you thereof (collectively, the “Software”) to use, copy, and make derivative works of the Software solely for educational or academic research purposes, and to distribute such Software free of charge to other academic or nonprofit researchers for their educational or academic research purposes, in all cases subject to the terms of this Academic Software License. Except as granted herein, all rights are reserved by Institution, including the right to pursue patent protection of the Software.
+    2. Any distribution of copies of this Software -- including any derivative works made by you thereof -- must include a copy (including the copyright notice above), and be made subject to the terms, of this Academic Software License; failure by you to adhere to the requirements in Paragraphs 1 and 2 will result in immediate termination of the license granted to you pursuant to this Academic Software License effective as of the date you first used the Software.
+    3. IN NO EVENT WILL INSTITUTION BE LIABLE TO ANY ENTITY OR PERSON FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF INSTITUTION HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. INSTITUTION SPECIFICALLY DISCLAIMS ANY AND ALL WARRANTIES, EXPRESS AND IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE IS PROVIDED “AS IS.” INSTITUTION HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS OF THIS SOFTWARE.
+    4. Any academic or scholarly publication arising from the use of this Software or any derivative works thereof will include the following acknowledgment:  The Software used in this research was created by [INSERT AUTHOR NAMES] of UC Riverside. © 2024 UCR.
+
+    Commercial entities: please contact mingxun.wang@cs.ucr.edu or tp@ucr.edu for licensing opportunities.

modifinder-1.4b0/PKG-INFO

@@ -0,0 +1,77 @@
+Metadata-Version: 2.2
+Name: modifinder
+Version: 1.4b0
+Summary: ModiFinder package
+Author-email: Reza Shahneh <mzare008@ucr.edu>
+License: ::
+        
+            Academic Software License: © 2024 UCR (“Institution”). Academic or nonprofit researchers are permitted to use this Software (as defined below) subject to Paragraphs 1-4:
+        
+            1. Institution hereby grants to you free of charge, so long as you are an academic or nonprofit researcher, a nonexclusive license under Institution’s copyright ownership interest in this software and any derivative works made by you thereof (collectively, the “Software”) to use, copy, and make derivative works of the Software solely for educational or academic research purposes, and to distribute such Software free of charge to other academic or nonprofit researchers for their educational or academic research purposes, in all cases subject to the terms of this Academic Software License. Except as granted herein, all rights are reserved by Institution, including the right to pursue patent protection of the Software.
+            2. Any distribution of copies of this Software -- including any derivative works made by you thereof -- must include a copy (including the copyright notice above), and be made subject to the terms, of this Academic Software License; failure by you to adhere to the requirements in Paragraphs 1 and 2 will result in immediate termination of the license granted to you pursuant to this Academic Software License effective as of the date you first used the Software.
+            3. IN NO EVENT WILL INSTITUTION BE LIABLE TO ANY ENTITY OR PERSON FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF INSTITUTION HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. INSTITUTION SPECIFICALLY DISCLAIMS ANY AND ALL WARRANTIES, EXPRESS AND IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE IS PROVIDED “AS IS.” INSTITUTION HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS OF THIS SOFTWARE.
+            4. Any academic or scholarly publication arising from the use of this Software or any derivative works thereof will include the following acknowledgment:  The Software used in this research was created by [INSERT AUTHOR NAMES] of UC Riverside. © 2024 UCR.
+        
+            Commercial entities: please contact mingxun.wang@cs.ucr.edu or tp@ucr.edu for licensing opportunities.
+        
+Project-URL: Documentation, https://wang-bioinformatics-lab.github.io/ModiFinder_base/
+Project-URL: Repository, https://github.com/Wang-Bioinformatics-Lab/ModiFinder_base
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: cairosvg
+Requires-Dist: rdkit
+Requires-Dist: requests
+Requires-Dist: xlsxwriter
+Requires-Dist: prettytable
+Requires-Dist: dash
+Requires-Dist: numpy
+Requires-Dist: tqdm
+Requires-Dist: IPython
+Requires-Dist: furl
+Requires-Dist: pandas
+Requires-Dist: dash-bootstrap-components
+Requires-Dist: pillow
+Requires-Dist: openpyxl
+Requires-Dist: openpyxl-image-loader
+Requires-Dist: msbuddy==0.2.3
+Requires-Dist: seaborn
+Requires-Dist: pyteomics
+Requires-Dist: matplotlib
+Requires-Dist: networkx
+Provides-Extra: extras
+
+Welcome to ModiFinder's documentation!
+======================================
+
+**ModiFinder** is a tool for site localization of structural modifications using MS/MS data.
+
+
+_This project is under active development._
+
+The documentation is available at: [https://wang-bioinformatics-lab.github.io/ModiFinder_base/](https://wang-bioinformatics-lab.github.io/ModiFinder_base/)
+
+
+Citing
+------
+
+    ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization
+
+    Mohammad Reza Zare Shahneh, Michael Strobel, Giovanni Andrea Vitale, Christian Geibel, Yasin El Abiead, Neha Garg, Berenike Wagner, Karl Forchhammer, Allegra Aron, Vanessa V Phelan, Daniel Petras, and Mingxun Wang
+
+    Journal of the American Society for Mass Spectrometry 2024 35 (11), 2564-2578
+
+    DOI: 10.1021/jasms.4c00061
+
+
+License
+-------
+   
+    Academic Software License: © 2024 UCR (“Institution”). Academic or nonprofit researchers are permitted to use this Software (as defined below) subject to Paragraphs 1-4:
+
+    1. Institution hereby grants to you free of charge, so long as you are an academic or nonprofit researcher, a nonexclusive license under Institution’s copyright ownership interest in this software and any derivative works made by you thereof (collectively, the “Software”) to use, copy, and make derivative works of the Software solely for educational or academic research purposes, and to distribute such Software free of charge to other academic or nonprofit researchers for their educational or academic research purposes, in all cases subject to the terms of this Academic Software License. Except as granted herein, all rights are reserved by Institution, including the right to pursue patent protection of the Software.
+    2. Any distribution of copies of this Software -- including any derivative works made by you thereof -- must include a copy (including the copyright notice above), and be made subject to the terms, of this Academic Software License; failure by you to adhere to the requirements in Paragraphs 1 and 2 will result in immediate termination of the license granted to you pursuant to this Academic Software License effective as of the date you first used the Software.
+    3. IN NO EVENT WILL INSTITUTION BE LIABLE TO ANY ENTITY OR PERSON FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF INSTITUTION HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. INSTITUTION SPECIFICALLY DISCLAIMS ANY AND ALL WARRANTIES, EXPRESS AND IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE IS PROVIDED “AS IS.” INSTITUTION HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS OF THIS SOFTWARE.
+    4. Any academic or scholarly publication arising from the use of this Software or any derivative works thereof will include the following acknowledgment:  The Software used in this research was created by [INSERT AUTHOR NAMES] of UC Riverside. © 2024 UCR.
+
+    Commercial entities: please contact mingxun.wang@cs.ucr.edu or tp@ucr.edu for licensing opportunities.

modifinder-1.4b0/Readme.md

@@ -0,0 +1,34 @@
+Welcome to ModiFinder's documentation!
+======================================
+
+**ModiFinder** is a tool for site localization of structural modifications using MS/MS data.
+
+
+_This project is under active development._
+
+The documentation is available at: [https://wang-bioinformatics-lab.github.io/ModiFinder_base/](https://wang-bioinformatics-lab.github.io/ModiFinder_base/)
+
+
+Citing
+------
+
+    ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization
+
+    Mohammad Reza Zare Shahneh, Michael Strobel, Giovanni Andrea Vitale, Christian Geibel, Yasin El Abiead, Neha Garg, Berenike Wagner, Karl Forchhammer, Allegra Aron, Vanessa V Phelan, Daniel Petras, and Mingxun Wang
+
+    Journal of the American Society for Mass Spectrometry 2024 35 (11), 2564-2578
+
+    DOI: 10.1021/jasms.4c00061
+
+
+License
+-------
+   
+    Academic Software License: © 2024 UCR (“Institution”). Academic or nonprofit researchers are permitted to use this Software (as defined below) subject to Paragraphs 1-4:
+
+    1. Institution hereby grants to you free of charge, so long as you are an academic or nonprofit researcher, a nonexclusive license under Institution’s copyright ownership interest in this software and any derivative works made by you thereof (collectively, the “Software”) to use, copy, and make derivative works of the Software solely for educational or academic research purposes, and to distribute such Software free of charge to other academic or nonprofit researchers for their educational or academic research purposes, in all cases subject to the terms of this Academic Software License. Except as granted herein, all rights are reserved by Institution, including the right to pursue patent protection of the Software.
+    2. Any distribution of copies of this Software -- including any derivative works made by you thereof -- must include a copy (including the copyright notice above), and be made subject to the terms, of this Academic Software License; failure by you to adhere to the requirements in Paragraphs 1 and 2 will result in immediate termination of the license granted to you pursuant to this Academic Software License effective as of the date you first used the Software.
+    3. IN NO EVENT WILL INSTITUTION BE LIABLE TO ANY ENTITY OR PERSON FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF INSTITUTION HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. INSTITUTION SPECIFICALLY DISCLAIMS ANY AND ALL WARRANTIES, EXPRESS AND IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE IS PROVIDED “AS IS.” INSTITUTION HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS OF THIS SOFTWARE.
+    4. Any academic or scholarly publication arising from the use of this Software or any derivative works thereof will include the following acknowledgment:  The Software used in this research was created by [INSERT AUTHOR NAMES] of UC Riverside. © 2024 UCR.
+
+    Commercial entities: please contact mingxun.wang@cs.ucr.edu or tp@ucr.edu for licensing opportunities.

modifinder-1.4b0/modifinder/__init__.py

@@ -0,0 +1,9 @@
+"""
+ModiFinder
+==========
+
+ModiFinder is a Python package for the identification of modifications in mass spectrometry data.
+"""
+
+from modifinder.exceptions import *
+from modifinder.classes import *

modifinder-1.4b0/modifinder/arguments.py

@@ -0,0 +1,16 @@
+args = {
+    'adduct': {"name": "adduct", "short":'add', "defult":"M+H"},
+    'USI1': {"name": "USI1", "short":'USI1', "defult":""},
+    'USI2': {"name": "USI2", "short":'USI2', "defult":""},
+    'SMILES1': {"name": "SMILES1", "short":'SMILES1', "defult":""}, 
+    'SMILES2': {"name": "SMILES2", "short":'SMILES2', "defult":""},
+    'mz_tolerance': {"name": "mz_tolerance", "short":'mz', "defult":0.05},
+    'ppm': {"name": "ppm", "short":'ppm', "defult":40},
+    'filter_peaks_method': {"name": "filter_peaks_method", "short":'filter', "defult":"intensity"},
+    'filter_peaks_variable': {"name": "filter_peaks_variable", "short":'filter_var', "defult":0.01},
+    'presence_only': {"name": "presence_only", "short":'presence', "defult":False},
+    'consider_intensity': {"name": "consider_intensity", "short":'intensity', "defult":True},
+    'shifted_only': {"name": "shifted_only", "short":'shifted', "defult":False},
+    'USIhelp': {"name": "USIhelp", "short":'USIhelp', "defult":None},
+    'SMILEShelp': {"name": "SMILEShelp", "short":'SMILEShelp', "defult":None},
+}

modifinder-1.4b0/modifinder/calculate_scores.py

@@ -0,0 +1,274 @@
+
+import numpy as np
+from typing import List, Tuple
+import copy
+from . import utils as utils
+
+def is_max(G, probabilities, true_index):
+    if probabilities[true_index] == max(probabilities):
+        # find how many times the max value appears
+        count = 0
+        for i in range(len(probabilities)):
+            if probabilities[i] == max(probabilities):
+                count += 1
+
+        return 1/count
+    else:
+        return 0
+
+def dist_from_max(G, probabilities, true_index):
+    min_dist = 100000
+    eps = 0.000001
+    max_val = max(probabilities)
+    graph_diameter = np.amax(G)
+    for i in range(len(probabilities)):
+        if probabilities[i] == max_val:
+            min_dist = min(min_dist, G[true_index, i])
+    return float(min_dist/(graph_diameter))
+
+def proximity(G, probabilities, true_index):
+    min_dist = 100000
+    eps = 0.000001
+    max_val = max(probabilities)
+    graph_diameter = np.amax(G)
+    for i in range(len(probabilities)):
+        if probabilities[i] == max_val:
+            min_dist = min(min_dist, G[true_index, i])
+    return (graph_diameter - min_dist)/graph_diameter
+
+def average_dist_from_max(G, probabilities, true_index):
+    eps = 0.000001
+    max_val = max(probabilities)
+    graph_diameter = np.amax(G)
+    dists = 0
+    count = 0
+    for i in range(len(probabilities)):
+        if probabilities[i] == max_val:
+            value = G[true_index,i]/(graph_diameter)
+            dists += value * probabilities[i]
+            count += probabilities[i]
+    return float(dists/count)
+
+def average_dist(G, probabilities, true_index):
+    eps = 0.000001
+    dists = 0
+    count = 0
+    for i in range(len(probabilities)):
+        value = np.exp(-G[true_index, i])
+        # value = 1/(G[true_index, i]+ 1)
+        dists += value * probabilities[i]
+        count += probabilities[i]
+    return float(dists/count)
+
+def average_dist_normalized(G, probabilities, true_index):
+    eps = 0.000001
+    graph_diameter = np.amax(G)
+    dists = 0
+    count = 0
+    for i in range(len(probabilities)):
+        value = np.exp(-G[true_index, i]/(graph_diameter-G[true_index, i]+eps))
+        # value  = (graph_diameter - G[true_index, i])/graph_diameter
+        dists += value * probabilities[i]
+        count += probabilities[i]
+    return float(dists/count)
+
+def regulated_exp(G, probabilities, modificationSiteIdx):
+    maxScore = max(probabilities)
+    if maxScore == 0:
+        return 0
+
+
+    for i in range(len(probabilities)):
+        if probabilities[i] < 0.5 * maxScore:
+            probabilities[i] = 0
+    probabilities /= np.sum(probabilities)
+    maxScore = max(probabilities)
+    graphDiameter = np.amax(G)
+    count = 0
+    localDistances = 0
+    closestMaxAtomIndx = 0
+    # print("DUAAAM", graphDiameter, self.molMol.GetNumAtoms())
+    for i in range(len(probabilities)):
+        if probabilities[i] == maxScore:
+            # print("in if")
+            count += probabilities[i]/maxScore
+
+            # print("ASD", self.distances[modificationSiteIdx][i])
+            localDistances += (G[modificationSiteIdx, i]/graphDiameter) * probabilities[i]/maxScore
+            if probabilities[i] == maxScore and G[modificationSiteIdx, i] < G[modificationSiteIdx, closestMaxAtomIndx]:
+                closestMaxAtomIndx = i
+    
+    # score = np.exp(-self.distances[modificationSiteIdx][closestMaxAtomIndx]/3) * 0.5 + np.exp(-(localDistances/count)) * 0.5
+    # score = np.exp(-self.distances[modificationSiteIdx][closestMaxAtomIndx])
+    if count == 0:
+        return 0
+    score = np.exp(-(localDistances/count))
+    # print("the score is!", score, localDistances, count, graphDiameter, maxScore, modificationSiteIdx, closestMaxAtomIndx)
+    return score
+
+def ranking_loss(G, probabilities, modificationSiteIdx):
+    # find how far the index of the true modification site is from the max probability
+    # sort the probabilities and keep the indices
+    sorted_indices = np.argsort(probabilities)
+
+    # reverse the indices
+    sorted_indices = sorted_indices[::-1]
+
+    # find the index of the true modification site
+    true_index = np.where(sorted_indices == modificationSiteIdx)[0][0]
+
+    # return the ranking loss
+    return 1 - true_index/len(probabilities)
+
+
+def sorted_rank(G, probabilities, modificationSiteIdx):
+    # find how far the index of the true modification site is from the max probability
+    # sort the probabilities and keep the indices
+    sorted_indices = np.argsort(probabilities)
+
+    # find the index of the true modification site
+    true_index = np.where(sorted_indices == modificationSiteIdx)[0][0]
+
+    # return the ranking loss
+    return true_index/(len(probabilities)-1)
+
+
+
+
+def entropy_distance(G, probabilities, modificationSiteIdx, alpha = 0.5, gamma=1.0):
+    # penalize the entropy of the probabilities
+    H = utils.entropy(probabilities)    
+    # print("H", H, 1-H, alpha)
+    S = 1 - H
+    if S > 1e-8:
+        S = np.power(S, alpha)
+    else:
+        S = 0
+    
+    # penalize the distances between the modification site and the other sites normalized by the graph diameter and gamma regularization
+    graphDiameter = np.amax(G)
+    D = 0
+    for i in range(len(probabilities)):
+        D += G[modificationSiteIdx, i] / graphDiameter * probabilities[i]
+    D = 1 - D
+    D = np.power(D, gamma)
+
+    # print(S, D)
+    return np.sqrt(S * D)
+
+
+# def calculate_spanning_graph(G, probabilities):
+#     max_val = max(probabilities)
+#     graph = []
+#     for i in range(len(probabilities)):
+#         for j in range(len(probabilities)):
+#             if probabilities[i] == max_val and probabilities[j] == max_val:
+#                 graph.append((i, j, G[i][j]))
+#     return graph
+
+# def kruskal(graph: List[Tuple[int, int, int]]) -> List[Tuple[int, int, int]]:
+#     sorted_edges = sorted(graph, key=lambda x: x[2])
+#     components = {v: k for k, v in enumerate(set([u for u, _, _ in graph] + [v for _, v, _ in graph]))}
+#     min_spanning_tree = []
+#     for edge in sorted_edges:
+#         u, v, w = edge
+#         # If the endpoints of the edge belong to different connected components, add the edge to the minimum spanning tree
+#         if components[u] != components[v]:
+#             min_spanning_tree.append(edge)
+            
+#             # Merge the connected components
+#             old_component = components[v]
+#             new_component = components[u]
+#             for vertex, component in components.items():
+#                 if component == old_component:
+#                     components[vertex] = new_component
+    
+#     return min_spanning_tree
+
+# def calculate_minimum_spanning_graph(G, probabilities):
+#     spanning_graph = calculate_spanning_graph(G, probabilities)
+
+#     # floyd-warshall algorithm
+#     for k in range(len(spanning_graph)):
+#         for i in range(len(spanning_graph)):
+#             for j in range(len(spanning_graph)):
+#                 spanning_graph[i][j] = min(spanning_graph[i][j], spanning_graph[i][k] + spanning_graph[k][j])
+
+
+def softmax(probabilities):
+    if min(probabilities) < 0:
+        probabilities = probabilities - min(probabilities)
+    if max(probabilities) == 0:
+        return probabilities
+    smallest_non_zero = min([x for x in probabilities if x > 0])
+    probabilities /= smallest_non_zero
+    exp_x = np.exp(probabilities - np.max(probabilities))  # Subtracting the max value for numerical stability
+    # print(exp_x)
+    probabilities = exp_x / exp_x.sum()
+    return probabilities
+
+def linear(x):
+    if np.min(x) < 0:
+        x = x - np.min(x)
+    if np.sum(x) != 0:
+        x = x / np.sum(x)
+    return x
+
+def power_prob(probabilities):
+    # copy the probabilities to avoid changing the original
+    probabilities2 = copy.deepcopy(probabilities)
+    if min(probabilities2) < 0:
+        probabilities2 = probabilities2 - min(probabilities2)
+    if max(probabilities2) == 0:
+        return probabilities2
+    # make anythin less than half of the max value zero
+    probabilities2[probabilities2 < max(probabilities2) / 2] = 0
+
+    probabilities2 = np.power(probabilities2, 4)
+    if sum(probabilities2) == 0:
+        return probabilities2
+    probabilities2 = probabilities2 / probabilities2.sum()
+    return probabilities2
+
+
+def calculate(G, input_probabilities, true_modification_site, method, normalization_method = "linear"):
+    # if input_probabilities is list of lists, calculate the average
+    if isinstance(input_probabilities[0], list):
+        average = 0
+        for i in range(len(input_probabilities)):
+            average += calculate(G, input_probabilities[i], true_modification_site, method, normalization_method)
+        return average / len(input_probabilities)
+    
+    # if input_probabilities is a 2d array, calculate the average
+    if isinstance(input_probabilities[0], np.ndarray):
+        average = 0
+        for i in range(len(input_probabilities)):
+            average += calculate(G, input_probabilities[i], true_modification_site, method, normalization_method)
+        return average / len(input_probabilities)
+    
+    probabilities = linear(input_probabilities)
+    if max(probabilities) == 0:
+        return 0
+    # call the score function based on the method
+    if method == "is_max":
+        return is_max(G, probabilities, true_modification_site)
+    elif method == "dist_from_max":
+        return dist_from_max(G, probabilities, true_modification_site)
+    elif method == "average_dist_from_max":
+        return average_dist_from_max(G, probabilities, true_modification_site)
+    elif method == "average_dist":
+        return average_dist(G, probabilities, true_modification_site)
+    elif method == "average_dist_normalized":
+        return average_dist_normalized(G, probabilities, true_modification_site)
+    elif method == "regulated_exp":
+        return regulated_exp(G, probabilities, true_modification_site)
+    elif method == "ranking_loss":
+        return ranking_loss(G, probabilities, true_modification_site)
+    elif method == "entropy_distance":
+        return entropy_distance(G, probabilities, true_modification_site)
+    elif method == "sorted_rank":
+        return sorted_rank(G, probabilities, true_modification_site)
+    elif method == "proximity":
+        return proximity(G, probabilities, true_modification_site)
+    else:
+        raise Exception("Method not found")