Mercurial > repos > bgruening > sucos_docking_scoring
annotate sucos_cluster.py @ 1:2e67eea82ff7 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6fa2a0294d615c9f267b766337dca0b2d3637219"
author | bgruening |
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date | Fri, 11 Oct 2019 18:26:43 -0400 |
parents | f8f53668d5a2 |
children | 4f1896782f7c |
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f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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1 #!/usr/bin/env python |
f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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2 """ |
f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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3 Cluster a set of molecules based on their 3D overlays as determined by the SuCOS score. |
f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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4 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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5 This will generate a set of SD files, one for each cluster of molecules (presumably corresponding to a |
f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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6 binding pocket in the protein target). |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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7 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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8 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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9 SuCOS is the work of Susan Leung. |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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10 GitHub: https://github.com/susanhleung/SuCOS |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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11 Publication: https://doi.org/10.26434/chemrxiv.8100203.v1 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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12 """ |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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13 |
f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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14 import sucos, utils |
f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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15 import argparse, gzip |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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16 from rdkit import Chem |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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17 import numpy as np |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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18 import pandas as pd |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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19 from scipy.cluster.hierarchy import linkage, fcluster |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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20 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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21 ### start main execution ######################################### |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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22 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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23 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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24 def calc_distance_matrix(mols): |
f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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25 """ |
f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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26 Calculate a full distance matrix for the given molecules. Identical molecules get a score of 0.0 with the maximum |
f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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27 distance possible being 1.0. |
f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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28 :param mols: A list of molecules. It must be possible to iterate through this list multiple times |
f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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29 :return: A NxN 2D array of distance scores, with N being the number of molecules in the input |
f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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30 """ |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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31 |
f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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32 # TODO - do we need to calculate both sides of the matrix? Tanimoto is supposed to be a symmetric distance measure, |
f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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33 # but the matrix that is generated does not seem to be symmetric. |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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34 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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35 mol_fm_tuples = [] |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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36 for mol in mols: |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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37 features = sucos.getRawFeatures(mol) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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38 mol_fm_tuples.append((mol, features)) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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39 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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40 matrix = [] |
f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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41 for tuple1 in mol_fm_tuples: |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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42 tmp = [] |
f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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43 for tuple2 in mol_fm_tuples: |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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44 if tuple1[0] == tuple2[0]: |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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45 tmp.append(0.0) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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46 else: |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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47 #utils.log("Calculating SuCOS between", mol1, mol2) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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48 sucos_score, fm_score, tani_score = sucos.get_SucosScore(tuple1[0], tuple2[0], |
f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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49 tani=True, ref_features=tuple1[1], query_features=tuple2[1]) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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50 tmp.append(1.0 - sucos_score) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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51 matrix.append(tmp) |
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52 |
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53 |
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54 return matrix |
f8f53668d5a2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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55 |
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56 |
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57 def cluster(matrix, threshold=0.8): |
f8f53668d5a2
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58 """ |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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59 Cluster the supplied distance matrix returning an array of clusters. |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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60 :param matrix: the distance matrix, as calculated with the calc_distance_matrix function. |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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61 :param threshold: The clustering cuttoff. The default of 0.8 is a reasonable value to use. |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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62 :return: An array of clusters, each cluster being an array of the indices from the matrix. |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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63 """ |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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64 |
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65 indexes = [x for x in range(0, len(matrix))] |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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66 cols = [x for x in range(0, len(matrix[0]))] |
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67 #utils.log("indexes", indexes) |
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68 #utils.log("cols", cols) |
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69 df = pd.DataFrame(matrix, columns=cols, index=indexes) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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70 utils.log("DataFrame:", df.shape) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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71 #utils.log(df) |
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72 indices = np.triu_indices(df.shape[0], k=1) |
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73 #utils.log("Indices:", indices) |
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74 t = np.array(df)[indices] |
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75 Z = linkage(t, 'average') |
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76 lig_clusters = [] |
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77 cluster_arr = fcluster(Z, t=threshold, criterion='distance') |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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78 for i in range(np.amax(cluster_arr)): |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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79 clus = df.columns[np.argwhere(cluster_arr==i+1)] |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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80 lig_clusters.append([x[0] for x in clus.tolist()]) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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81 |
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82 utils.log("Clusters", lig_clusters) |
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83 return lig_clusters |
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84 |
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85 def write_clusters_to_sdfs(mols, clusters, basename, gzip=False): |
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86 """ |
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87 Write the molecules to SDF files, 1 file for each cluster. |
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88 :param mols The molecules to write: |
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89 :param clusters The clusters, as returned by the cluster function: |
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90 :param basename The basename for the file name. e.g. if basename is 'output' then files like |
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91 output1.sdf, output2.sdf will be written: |
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92 :param gzip Whether to gzip the output |
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93 :return: |
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94 """ |
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95 |
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96 i = 0 |
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97 for cluster in clusters: |
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98 i += 1 |
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99 filename = basename + str(i) + ".sdf" |
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100 if gzip: |
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101 filename += ".gz" |
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102 utils.log("Writing ", len(cluster), "molecules in cluster", i, "to file", filename) |
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103 output_file = utils.open_file_for_writing(filename) |
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104 writer = Chem.SDWriter(output_file) |
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105 for index in cluster: |
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106 mol = mols[index] |
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107 writer.write(mol) |
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108 writer.flush() |
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109 writer.close() |
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110 output_file.close() |
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111 |
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112 |
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113 |
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114 def main(): |
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115 parser = argparse.ArgumentParser(description='Clustering with SuCOS and RDKit') |
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116 parser.add_argument('-i', '--input', help='Input file in SDF format. Can be gzipped (*.gz).') |
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117 parser.add_argument('-o', '--output', default="cluster", help="Base name for output files in SDF format. " + |
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118 "e.g. if value is 'output' then files like output1.sdf, output2.sdf will be created") |
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119 parser.add_argument('--gzip', action='store_true', help='Gzip the outputs generating files like output1.sdf.gz, output2.sdf.gz') |
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120 parser.add_argument('-t', '--threshold', type=float, default=0.8, help='Clustering threshold') |
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121 |
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122 args = parser.parse_args() |
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123 utils.log("SuCOS Cluster Args: ", args) |
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124 |
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125 input_file = utils.open_file_for_reading(args.input) |
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126 suppl = Chem.ForwardSDMolSupplier(input_file) |
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127 mols = list(suppl) |
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128 matrix = calc_distance_matrix(mols) |
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129 clusters = cluster(matrix, threshold=args.threshold) |
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130 write_clusters_to_sdfs(mols, clusters, args.output, gzip=args.gzip) |
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131 |
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132 |
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133 if __name__ == "__main__": |
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134 main() |